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Fuenzalida G, Yarimizu K, Norambuena L, Fujiyoshi S, Perera IU, Rilling JI, Campos M, Ruiz-Gil T, Vilugrón J, Sandoval-Sanhueza A, Ortiz M, Espinoza-González O, Guzmán L, Acuña JJ, Jorquera MA, Maruyama F. Environmental evaluation of the Reloncaví estuary in southern Chile based on lipophilic shellfish toxins as related to harmful algal blooms. Sci Total Environ 2024; 928:172374. [PMID: 38615760 DOI: 10.1016/j.scitotenv.2024.172374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 04/08/2024] [Accepted: 04/08/2024] [Indexed: 04/16/2024]
Abstract
The Reloncaví estuary in southern Chile is famous for its aquaculture. However, recurring harmful algal blooms have adversely affected mussel production. Therefore, regular monitoring of algal toxins is urgently needed to better understand the contamination status of the estuary. In this study, we quantified 15 types of lipophilic shellfish toxins in Metri Bay in the Reloncaví estuary on a biweekly basis for 4 years. We identified algal species using microscopy and metabarcoding analysis. We also measured water temperature, salinity, chlorophyll-a, and dissolved oxygen to determine the potential relationships of these parameters with algal toxin production. Our results revealed the presence of a trace amount of pectenotoxin and the causal phytoplankton Dinophysis, as well as yessotoxin and the causal phytoplankton Protoceratium. Statistical analysis indicated that fluctuations in water temperature affected the detection of these toxins. Additionally, metabarcoding analysis detected the highly toxic phytoplankton Alexandrium spp. in some samples. Although our results suggest that the level of lipophilic shellfish toxins in Metri Bay during the study period was insignificantly low using our current LC-MS method, the confirmed presence of highly toxic algae in Metri Bay raises concerns, given that favorable environmental conditions could cause blooms.
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Affiliation(s)
- Gonzalo Fuenzalida
- Centro de Estudios de Algas Nocivas (CREAN), Instituto de Fomento Pesquero (IFOP), Padre Harter 547, Puerto Montt 5480000, Chile; Departamento de Ciencias Basicas, Facultad de Ciencias, Universidad Santo Tomas, Buena Vecindad #91, Puerto Montt 5480000, Chile.
| | - Kyoko Yarimizu
- Microbial Genomics and Ecology, The IDEC Institute, Hiroshima University, 1-3-2 Kagamiyama, Higashi-Hiroshima City, Hiroshima 739-8511, Japan.
| | - Luis Norambuena
- Centro de Estudios de Algas Nocivas (CREAN), Instituto de Fomento Pesquero (IFOP), Padre Harter 547, Puerto Montt 5480000, Chile.
| | - So Fujiyoshi
- Microbial Genomics and Ecology, The IDEC Institute, Hiroshima University, 1-3-2 Kagamiyama, Higashi-Hiroshima City, Hiroshima 739-8511, Japan.
| | - Ishara Uhanie Perera
- Microbial Genomics and Ecology, The IDEC Institute, Hiroshima University, 1-3-2 Kagamiyama, Higashi-Hiroshima City, Hiroshima 739-8511, Japan.
| | - Joaquin-Ignacio Rilling
- Laboratorio de Ecología Microbiana Aplicada (EMALAB), Departamento de Ciencias Quimicas y Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar 01145, Temuco 4780000, Chile.
| | - Marco Campos
- Laboratorio de Ecología Microbiana Aplicada (EMALAB), Departamento de Ciencias Quimicas y Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar 01145, Temuco 4780000, Chile; Laboratorio de Investigación en Salud de Precisión, Departamento de Procesos Diagnósticos y Evaluación, Facultad de Ciencias de la Salud, Universidad Católica de Temuco, Manuel Montt 056, Temuco 4780000, Chile
| | - Tay Ruiz-Gil
- Laboratorio de Ecología Microbiana Aplicada (EMALAB), Departamento de Ciencias Quimicas y Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar 01145, Temuco 4780000, Chile
| | - Jonnathan Vilugrón
- Centro de Estudios de Algas Nocivas (CREAN), Instituto de Fomento Pesquero (IFOP), Padre Harter 547, Puerto Montt 5480000, Chile.
| | - Alondra Sandoval-Sanhueza
- Centro de Estudios de Algas Nocivas (CREAN), Instituto de Fomento Pesquero (IFOP), Padre Harter 547, Puerto Montt 5480000, Chile
| | - Mario Ortiz
- Centro de Estudios de Algas Nocivas (CREAN), Instituto de Fomento Pesquero (IFOP), Padre Harter 547, Puerto Montt 5480000, Chile
| | - Oscar Espinoza-González
- Centro de Estudios de Algas Nocivas (CREAN), Instituto de Fomento Pesquero (IFOP), Padre Harter 547, Puerto Montt 5480000, Chile.
| | - Leonardo Guzmán
- Centro de Estudios de Algas Nocivas (CREAN), Instituto de Fomento Pesquero (IFOP), Padre Harter 547, Puerto Montt 5480000, Chile.
| | - Jacqueline J Acuña
- Laboratorio de Ecología Microbiana Aplicada (EMALAB), Departamento de Ciencias Quimicas y Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar 01145, Temuco 4780000, Chile.
| | - Milko A Jorquera
- Laboratorio de Ecología Microbiana Aplicada (EMALAB), Departamento de Ciencias Quimicas y Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar 01145, Temuco 4780000, Chile.
| | - Fumito Maruyama
- Microbial Genomics and Ecology, The IDEC Institute, Hiroshima University, 1-3-2 Kagamiyama, Higashi-Hiroshima City, Hiroshima 739-8511, Japan.
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Kanatani JI, Fujiyoshi S, Isobe J, Kimata K, Watahiki M, Maenishi E, Izumiyama S, Amemura-Maekawa J, Maruyama F, Oishi K. Correlation between bacterial microbiome and Legionella species in water from public bath facilities by 16S rRNA gene amplicon sequencing. Microbiol Spectr 2024; 12:e0345923. [PMID: 38363136 PMCID: PMC10986325 DOI: 10.1128/spectrum.03459-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 01/24/2024] [Indexed: 02/17/2024] Open
Abstract
Public bath facilities are a major source of Legionella infections in Japan. In this study, we performed 16S rRNA gene amplicon sequencing to characterize the bacterial community in bath and shower water from public bath facilities, along with chemical parameters, and investigated the effect of the bacterial microbiome on the presence of Legionella species. Although no significant difference in bacterial community richness was observed between bath and shower water samples, there was a remarkable difference in the bacterial community structure between them. Distance-based redundancy analysis revealed that several factors (free residual chlorine, pH, and conductivity) were correlated with the bacterial community in bath water. The most abundant bacterial genera in the samples were Pseudomonas (13.7%) in bath water and Phreatobacter (13.6%) in shower water, as indicated by the taxonomic composition, and the dominant bacteria differed between these environmental samples. Legionella pneumophila was the most frequently detected Legionella species, with additional 15 other Legionella species detected in water samples. In Legionella-positive water samples, several unassigned and uncultured bacteria were enriched together. In addition, the co-occurrence network showed that Legionella was strongly interconnected with two uncultured bacteria. Corynebacterium and Sphingomonas negatively correlated with Legionella species. The present study reveals the ecology of Legionella species, especially their interactions with other bacteria that are poorly understood to date. IMPORTANCE Public bath facilities are major sources of sporadic cases and outbreaks of Legionella infections. Recently, 16S rRNA gene amplicon sequencing has been used to analyze bacterial characteristics in various water samples from both artificial and natural environments, with a particular focus on Legionella bacterial species. However, the relationship between the bacterial community and Legionella species in the water from public bath facilities remains unclear. In terms of hygiene management, it is important to reduce the growth of Legionella species by disinfecting the water in public bath facilities. Our findings contribute to the establishment of appropriate hygiene management practices and provide a basis for understanding the potential health effects of using bath and shower water available in public bath facilities.
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Affiliation(s)
- Jun-ichi Kanatani
- Department of Bacteriology, Toyama Institute of Health, Imizu, Toyama, Japan
| | - So Fujiyoshi
- Section of Microbial Genomics and Ecology, Hiroshima University, Hiroshima, Japan
| | - Junko Isobe
- Department of Bacteriology, Toyama Institute of Health, Imizu, Toyama, Japan
| | - Keiko Kimata
- Department of Bacteriology, Toyama Institute of Health, Imizu, Toyama, Japan
| | - Masanori Watahiki
- Department of Bacteriology, Toyama Institute of Health, Imizu, Toyama, Japan
| | - Emi Maenishi
- Department of Bacteriology, Toyama Institute of Health, Imizu, Toyama, Japan
| | - Shinji Izumiyama
- Department of Parasitology, National Institute of Infectious Diseases, Toyama, Japan
| | - Junko Amemura-Maekawa
- Department of Bacteriology, National Institute of Infectious Diseases, Toyama, Japan
| | - Fumito Maruyama
- Section of Microbial Genomics and Ecology, Hiroshima University, Hiroshima, Japan
| | - Kazunori Oishi
- Department of Bacteriology, Toyama Institute of Health, Imizu, Toyama, Japan
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Tanaka D, Maruyama F. Editorial for Special Issue: "Airborne Microbes and Their Potential Influence". Microorganisms 2024; 12:361. [PMID: 38399765 PMCID: PMC10893233 DOI: 10.3390/microorganisms12020361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 02/07/2024] [Indexed: 02/25/2024] Open
Abstract
Airborne microbes, comprising a diverse range of bacteria and fungi, are a pervasive component of the atmosphere, with concentrations typically ranging from 102 to 107 cells per cubic meter [...].
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Affiliation(s)
- Daisuke Tanaka
- School of Science, Academic Assembly, University of Toyama, 3190 Gofuku, Toyama City 930-8555, Toyama, Japan
| | - Fumito Maruyama
- Center for the Planetary Health and Innovation Science (PHIS), The IDEC Institute, Hiroshima University, 1-3-2 Kagamiyama, Higashi-Hiroshima City 739-8511, Hiroshima, Japan
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Saibu S, Uhanie Perera I, Suzuki S, Rodó X, Fujiyoshi S, Maruyama F. Resistomes in freshwater bioaerosols and their impact on drinking and recreational water safety: A perspective. Environ Int 2024; 183:108377. [PMID: 38103344 DOI: 10.1016/j.envint.2023.108377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 12/07/2023] [Accepted: 12/07/2023] [Indexed: 12/19/2023]
Abstract
Antibiotic resistance genes (ARGs) are widespread environmental pollutants of biological origin that pose a significant threat to human, animal, and plant health, as well as to ecosystems. ARGs are found in soil, water, air, and waste, and several pathways for global dissemination in the environment have been described. However, studies on airborne ARG transport through atmospheric particles are limited. The ARGs in microorganisms inhabiting an environment are referred to as the "resistome". A global search was conducted of air-resistome studies by retrieving bioaerosol ARG-related papers published in the last 30 years from PubMed. We found that there is no dedicated methodology for isolating ARGs in bioaerosols; instead, conventional methods for microbial culture and metagenomic analysis are used in combination with standard aerosol sampling techniques. There is a dearth of information on the bioaerosol resistomes of freshwater environments and their impact on freshwater sources used for drinking and recreational activities. More studies of aerobiome freshwater environments are needed to ensure the safe use of water and sanitation. In this review we outline and synthesize the few studies that address the freshwater air microbiome (from tap water, bathroom showers, rivers, lakes, and swimming pools) and their resistomes, as well as the likely impacts on drinking and recreational waters. We also discuss current knowledge gaps for the freshwater airborne resistome. This review will stimulate new investigations of the atmospheric microbiome, particularly in areas where both air and water quality are of public health concern.
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Affiliation(s)
- Salametu Saibu
- Department of Microbiology, Lagos State University of Ojo, Lagos, Nigeria
| | - Ishara Uhanie Perera
- Section of Microbial Genomics and Ecology, Planetary Health and Innovation Science Center (PHIS), The IDEC Institute, Hiroshima University, Japan
| | - Satoru Suzuki
- Graduate School of Science and Engineering, Center for Marine Environmental Studies, Ehime University, Japan
| | - Xavier Rodó
- ICREA and CLIMA Program, Barcelona Institute for Global Health (-ISGlobal), Barcelona, Spain
| | - So Fujiyoshi
- Section of Microbial Genomics and Ecology, Planetary Health and Innovation Science Center (PHIS), The IDEC Institute, Hiroshima University, Japan
| | - Fumito Maruyama
- Section of Microbial Genomics and Ecology, Planetary Health and Innovation Science Center (PHIS), The IDEC Institute, Hiroshima University, Japan.
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Carrazana E, Ruiz-Gil T, Fujiyoshi S, Tanaka D, Noda J, Maruyama F, Jorquera MA. Potential airborne human pathogens: A relevant inhabitant in built environments but not considered in indoor air quality standards. Sci Total Environ 2023; 901:165879. [PMID: 37517716 DOI: 10.1016/j.scitotenv.2023.165879] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 07/13/2023] [Accepted: 07/27/2023] [Indexed: 08/01/2023]
Abstract
Potential airborne human pathogens (PAHPs) may be a relevant component of the air microbiome in built environments. Despite that PAHPs can cause infections, particularly in immunosuppressed patients at medical centers, they are scarcely considered in standards of indoor air quality (IAQ) worldwide. Here, we reviewed the current information on microbial aerosols (bacteria, fungal and viruses) and PAHPs in different types of built environments (e.g., medical center, industrial and non-industrial), including the main factors involved in their dispersion, the methodologies used in their study and their associated biological risks. Our analysis identified the human occupancy and ventilation systems as the primary sources of dispersal of microbial aerosols indoors. We also observed temperature and relative humidity as relevant physicochemical factors regulating the dispersion and viability of some PAHPs. Our analysis revealed that some PAHPs can survive and coexist in different environments while other PAHPs are limited or specific for an environment. In relation to the methodologies (conventional or molecular) the nature of PAHPs and sampling type are pivotal. In this context, indoors air-borne viruses are the less studies because their small size, environmental lability, and absence of efficient sampling techniques and universal molecular markers for their study. Finally, it is noteworthy that PAHPs are not commonly considered and included in IAQ standards worldwide, and when they are included, the total abundance is the single parameter considered and biological risks is excluded. Therefore, we propose a revision, design and establishment of public health policies, regulations and IAQ standards, considering the interactions of diverse factors, such as nature of PAHPs, human occupancy and type of built environments where they develop.
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Affiliation(s)
- Elizabeth Carrazana
- Programa de Doctorado en Ciencias Mención Biología Celular y Molecular Aplicada, Universidad de La Frontera, Temuco, Chile; Laboratorio de Ecología Microbiana Aplicada, Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Temuco, Chile
| | - Tay Ruiz-Gil
- Laboratorio de Ecología Microbiana Aplicada, Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Temuco, Chile; Programa de Doctorado en Ciencias de Recursos Naturales, Universidad de La Frontera, Temuco, Chile
| | - So Fujiyoshi
- Center for Holobiome and Built Environment (CHOBE), Hiroshima University, Japan; Microbial Genomics and Ecology, PHIS, The IDEC institute, Hiroshima University, Hiroshima, Japan
| | - Daisuke Tanaka
- School of Science Academic Assembly, University of Toyama, Toyama, Japan
| | - Jun Noda
- Graduate School of Veterinary Medicine, Rakuno Gakuen University, Hokkaido, Japan
| | - Fumito Maruyama
- Center for Holobiome and Built Environment (CHOBE), Hiroshima University, Japan; Microbial Genomics and Ecology, PHIS, The IDEC institute, Hiroshima University, Hiroshima, Japan
| | - Milko A Jorquera
- Laboratorio de Ecología Microbiana Aplicada, Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Temuco, Chile; Center for Holobiome and Built Environment (CHOBE), Hiroshima University, Japan; Network for Extreme Environment Research (NEXER), Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Temuco, Chile.
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Komatsu T, Ohya K, Ota A, Nishiuchi Y, Yano H, Matsuo K, Odoi JO, Suganuma S, Sawai K, Hasebe A, Asai T, Yanai T, Fukushi H, Wada T, Yoshida S, Ito T, Arikawa K, Kawai M, Ato M, Baughn AD, Iwamoto T, Maruyama F. Unique genomic sequences in a novel Mycobacterium avium subsp. hominissuis lineage enable fine scale transmission route tracing during pig movement. One Health 2023; 16:100559. [PMID: 37363238 PMCID: PMC10288077 DOI: 10.1016/j.onehlt.2023.100559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 04/30/2023] [Accepted: 05/04/2023] [Indexed: 06/28/2023] Open
Abstract
Mycobacterium avium subsp. hominissuis (MAH) is one of the most prevalent mycobacteria causing non-tuberculous mycobacterial disease in humans and animals. Of note, MAH is a major cause of mycobacterial granulomatous mesenteric lymphadenitis outbreaks in pig populations. To determine the precise source of infection of MAH in a pig farm and to clarify the epidemiological relationship among pig, human and environmental MAH lineages, we collected 50 MAH isolates from pigs reared in Japan and determined draft genome sequences of 30 isolates. A variable number of tandem repeat analysis revealed that most pig MAH isolates in Japan were closely related to North American, European and Russian human isolates but not to those from East Asian human and their residential environments. Historical recombination analysis revealed that most pig isolates could be classified into SC2/4 and SC3, which contain MAH isolated from pig, European human and environmental isolates. Half of the isolates in SC2/4 had many recombination events with MAH lineages isolated from humans in East Asia. To our surprise, four isolates belonged to a new lineage (SC5) in the global MAH population. Members of SC5 had few footprints of inter-lineage recombination in the genome, and carried 80 unique genes, most of which were located on lineage specific-genomic islands. Using unique genetic features, we were able to trace the putative transmission route via their host pigs. Together, we clarify the possibility of species-specificity of MAH in addition to local adaptation. Our results highlight two transmission routes of MAH, one exposure on pig farms from the environment and the other via pig movement. Moreover, our study also warns that the evolution of MAH in pigs is influenced by MAH from patients and their residential environments, even if the MAH are genetically distinct.
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Affiliation(s)
- Tetsuya Komatsu
- Aichi Prefectural Tobu Livestock Hygiene Service Center, Toyohashi, Aichi, Japan
| | - Kenji Ohya
- Faculty of Applied Biological Sciences, Gifu University, Gifu, Japan
- United Graduate School of Veterinary Sciences, Gifu University, Gifu, Japan
- Education and Research Center for Food Animal Health, Gifu University (GeFAH), Gifu, Japan
| | - Atsushi Ota
- Data Science Center, Division of Biological Science, Nara Institute of Science and Technology, Ikoma, Nara, Japan
| | - Yukiko Nishiuchi
- Office of Academic Research and Industry-Government Collaboration, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
| | - Hirokazu Yano
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, Japan
| | - Kayoko Matsuo
- Faculty of Applied Biological Sciences, Gifu University, Gifu, Japan
- Kumamoto Prefectural Aso Public Health Center, Aso, Kumamoto, Japan
| | - Justice Opare Odoi
- United Graduate School of Veterinary Sciences, Gifu University, Gifu, Japan
| | - Shota Suganuma
- Faculty of Applied Biological Sciences, Gifu University, Gifu, Japan
| | - Kotaro Sawai
- Faculty of Applied Biological Sciences, Gifu University, Gifu, Japan
- Division of Transboundary Animal Disease Research, National Institute of Animal Health, National Agriculture Research Organization, Tsukuba, Ibaraki, Japan
| | - Akemi Hasebe
- Toyama Prefectural Meat Inspection Center, Imizu, Toyama, Japan
| | - Tetsuo Asai
- United Graduate School of Veterinary Sciences, Gifu University, Gifu, Japan
- Education and Research Center for Food Animal Health, Gifu University (GeFAH), Gifu, Japan
| | - Tokuma Yanai
- Faculty of Applied Biological Sciences, Gifu University, Gifu, Japan
- United Graduate School of Veterinary Sciences, Gifu University, Gifu, Japan
- Hiwa Natural History Museum, Shobara, Hiroshima, Japan
| | - Hideto Fukushi
- Faculty of Applied Biological Sciences, Gifu University, Gifu, Japan
- United Graduate School of Veterinary Sciences, Gifu University, Gifu, Japan
| | - Takayuki Wada
- Graduate School of Human Life and Ecology, Osaka Metropolitan University, Osaka, Japan
| | - Shiomi Yoshida
- Clinical Research Center, National Hospital Organization Kinki-Chuo Chest Medical Center, Sakai, Osaka, Japan
| | - Toshihiro Ito
- Laboratory of Proteome Research, Proteome Research Center, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka, Japan
| | - Kentaro Arikawa
- Department of Infectious Diseases, Kobe Institute of Health, Kobe, Hyogo, Japan
| | - Mikihiko Kawai
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan
| | - Manabu Ato
- Department of Mycobacteriology, Leprosy Research Center, National Institute of Infectious Diseases, Higashimurayama, Tokyo, Japan
| | - Anthony D. Baughn
- Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Tomotada Iwamoto
- Department of Infectious Diseases, Kobe Institute of Health, Kobe, Hyogo, Japan
| | - Fumito Maruyama
- Office of Academic Research and Industry-Government Collaboration, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
- Project Research Center for Holobiome and Built Environment (CHOBE), Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
- Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco, Chile
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Dutta K, Shityakov S, Maruyama F. DSF inactivator RpfB homologous FadD upregulated in Bradyrhizobium japonicum under iron limiting conditions. Sci Rep 2023; 13:8701. [PMID: 37248242 DOI: 10.1038/s41598-023-35487-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 05/18/2023] [Indexed: 05/31/2023] Open
Abstract
Phytopathogenic bacteria Xanthomonas campestris pv. campestris (Xcc) causes black rot and other plant diseases. Xcc senses diffusible signal factor (DSF) as a quorum-sensing (QS) signal that mediates mainly iron uptake and virulence. RpfB deactivates DSF in this DSF-QS circuit. We examined differential gene expression profiles of Bradyrhizobium japonicum under low versus high iron conditions and found that fadD and irr were upregulated under low iron (log2 fold change 0.825 and 1.716, respectively). In addition to having similar protein folding patterns and functional domain similarities, FadD shared 58% sequence similarity with RpfB of Xcc. The RpfB-DSF and FadD-DSF complexes had SWISSDock molecular docking scores of - 8.88 kcal/mol and - 9.85 kcal/mol, respectively, and the 100 ns molecular dynamics simulation results were in accord with the docking results. However, significant differences were found between the binding energies of FadD-DSF and RpfB-DSF, indicating possible FadD-dependent DSF turnover. The protein-protein interaction network showed that FadD connected indirectly with ABC transporter permease (ABCtp), which was also upregulated (log2 fold change 5.485). We speculate that the low iron condition may be a mimetic environmental stimulus for fadD upregulation in B. japonicum to deactivate DSF, inhibit iron uptake and virulence of DSF-producing neighbors. This finding provides a new option of using B. japonicum or a genetically improved B. japonicum as a potential biocontrol agent against Xcc, with the added benefit of plant growth-promoting properties.
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Affiliation(s)
- Kunal Dutta
- Laboratory of Chemoinformatics, Infochemistry Scientific Center, ITMO University, Saint Petersburg, Russian Federation.
| | - Sergey Shityakov
- Laboratory of Chemoinformatics, Infochemistry Scientific Center, ITMO University, Saint Petersburg, Russian Federation.
| | - Fumito Maruyama
- Microbial Genomics and Ecology, The IDEC Institute, Hiroshima University, Higashihiroshima, Japan.
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Fujiyoshi S, Yarimizu K, Fuenzalida G, Campos M, Rilling JI, Acuña JJ, Miranda PC, Cascales EK, Perera I, Espinoza-González O, Guzmán L, Jorquera MA, Maruyama F. Monitoring bacterial composition and assemblage in the Gulf of Corcovado, southern Chile: Bacteria associated with harmful algae. Curr Res Microb Sci 2023; 4:100194. [PMID: 37346179 PMCID: PMC10279789 DOI: 10.1016/j.crmicr.2023.100194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/23/2023] Open
Abstract
Harmful Algal Blooms (HABs) have caused damage to the marine environment in Isla San Pedro in the Gulf of Corcovado, Chile. While rising water temperature and artificial eutrophication are the most discussed topics as a cause, marine bacteria is a recent attractive parameter as an algal bloom driver. This study monitored algal and bacterial compositions in the water of Isla San Pedro for one year using microscopy and 16S rRNA metabarcoding analysis, along with physicochemical parameters. The collected data were analyzed with various statistical tools to understand how the particle-associated bacteria (PA) and the free-living (FL) bacteria were possibly involved in algal blooms. Both FL and PA fractions maintained a stable bacterial composition: the FL fraction was dominated by Proteobacteria (α-Proteobacteria and γ-Proteobacteria), and Cyanobacteria dominated the PA fraction. The two fractions contained equivalent bacterial taxonomic richness (c.a. 8,000 Operational Taxonomic Units) and shared more than 50% of OTU; however, roughly 20% was exclusive to each fraction. The four most abundant algal genera in the Isla San Pedro water were Thalassiosira, Skeletonema, Chaetoceros, and Pseudo-nitzchia. Statistical analysis identified that the bacterial species Polycyclovorans algicola was correlated with Pseudo-nitzschia spp., and our monitoring data recorded a sudden increase of particle-associated Polycyclovorans algicola shortly after the increase of Pseudo-nitzschia, suggesting that P. algicola may have regression effect on Pseudo-nitzschia spp. The study also investigated the physicochemical parameter effect on algal-bacterial interactions. Oxygen concentration and chlorophyll-a showed a strong correlation with both FL and PA bacteria despite their assemblage differences, suggesting that the two groups had different mechanisms for interacting with algal species.
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Affiliation(s)
- So Fujiyoshi
- Microbial Genomics and Ecology, The IDEC Institute, Hiroshima University, 1-3-2 Kagamiyama, Higashi-Hiroshima City, Hiroshima 739-8511, Japan
| | - Kyoko Yarimizu
- Microbial Genomics and Ecology, The IDEC Institute, Hiroshima University, 1-3-2 Kagamiyama, Higashi-Hiroshima City, Hiroshima 739-8511, Japan
| | - Gonzalo Fuenzalida
- Centro de Estudios de Algas Nocivas (CREAN), Instituto de Fomento Pesquero (IFOP), Padre Harter 574, Puerto Montt 5480000, Chile
- Departamento de Ciencias Básicas, Facultad de Ciencias, Universidad Santo Tomás, Buena Vecindad #91, Puerto Montt, Chile
| | - Marco Campos
- Laboratorio de Ecología Microbiana Aplicada (EMAlab), Departamento de Ciencias Quimicas y Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar 01145, Temuco 4811230, Chile
| | - Joaquin-Ignacio Rilling
- Laboratorio de Ecología Microbiana Aplicada (EMAlab), Departamento de Ciencias Quimicas y Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar 01145, Temuco 4811230, Chile
| | - Jacquelinne J. Acuña
- Laboratorio de Ecología Microbiana Aplicada (EMAlab), Departamento de Ciencias Quimicas y Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar 01145, Temuco 4811230, Chile
| | - Pedro Calabrano Miranda
- Centro de Estudios de Algas Nocivas (CREAN), Instituto de Fomento Pesquero (IFOP), Padre Harter 574, Puerto Montt 5480000, Chile
| | - Emma-Karin Cascales
- Centro de Estudios de Algas Nocivas (CREAN), Instituto de Fomento Pesquero (IFOP), Padre Harter 574, Puerto Montt 5480000, Chile
| | - Ishara Perera
- Microbial Genomics and Ecology, The IDEC Institute, Hiroshima University, 1-3-2 Kagamiyama, Higashi-Hiroshima City, Hiroshima 739-8511, Japan
| | - Oscar Espinoza-González
- Centro de Estudios de Algas Nocivas (CREAN), Instituto de Fomento Pesquero (IFOP), Padre Harter 574, Puerto Montt 5480000, Chile
| | - Leonardo Guzmán
- Centro de Estudios de Algas Nocivas (CREAN), Instituto de Fomento Pesquero (IFOP), Padre Harter 574, Puerto Montt 5480000, Chile
| | - Milko A. Jorquera
- Laboratorio de Ecología Microbiana Aplicada (EMAlab), Departamento de Ciencias Quimicas y Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar 01145, Temuco 4811230, Chile
| | - Fumito Maruyama
- Microbial Genomics and Ecology, The IDEC Institute, Hiroshima University, 1-3-2 Kagamiyama, Higashi-Hiroshima City, Hiroshima 739-8511, Japan
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9
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Koizumi Y, Maruyama F. Editorial: Ecology, environment, and human microbiome interaction with infection. Front Public Health 2023; 11:1217927. [PMID: 37287813 PMCID: PMC10242724 DOI: 10.3389/fpubh.2023.1217927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 05/12/2023] [Indexed: 06/09/2023] Open
Affiliation(s)
- Yukiko Koizumi
- Applied Research, American Dental Association Science and Research Institute, Chicago, IL, United States
| | - Fumito Maruyama
- Microbial Genomics and Ecology, Center for the Planetary Health and Innovation Science, The IDEC Institute, Hiroshima University, Higashihiroshima, Japan
- Project Research Center for Holobiome and Built Environment (CHOBE), Hiroshima University, Higashihiroshima, Japan
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10
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Hou J, Fujiyoshi S, Perera IU, Nishiuchi Y, Nakajima M, Ogura D, Yarimizu K, Maruyama F. Perspectives on Sampling and New Generation Sequencing Methods for Low-Biomass Bioaerosols in Atmospheric Environments. J Indian Inst Sci 2023; 103:1-11. [PMID: 37362849 PMCID: PMC10176311 DOI: 10.1007/s41745-023-00380-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 03/13/2023] [Indexed: 06/28/2023]
Abstract
Bioaerosols play essential roles in the atmospheric environment and can affect human health. With a few exceptions (e.g., farm or rainforest environments), bioaerosol samples from wide-ranging environments typically have a low biomass, including bioaerosols from indoor environments (e.g., residential homes, offices, or hospitals), outdoor environments (e.g., urban or rural air). Some specialized environments (e.g., clean rooms, the Earth's upper atmosphere, or the international space station) have an ultra-low-biomass. This review discusses the primary sources of bioaerosols and influencing factors, the recent advances in air sampling techniques and the new generation sequencing (NGS) methods used for the characterization of low-biomass bioaerosol communities, and challenges in terms of the bias introduced by different air samplers when samples are subjected to NGS analysis with a focus on ultra-low biomass. High-volume filter-based or liquid-based air samplers compatible with NGS analysis are required to improve the bioaerosol detection limits for microorganisms. A thorough understanding of the performance and outcomes of bioaerosol sampling using NGS methods and a robust protocol for aerosol sample treatment for NGS analysis are needed. Advances in NGS techniques and bioinformatic tools will contribute toward the precise high-throughput identification of the taxonomic profiles of bioaerosol communities and the determination of their functional and ecological attributes in the atmospheric environment. In particular, long-read amplicon sequencing, viability PCR, and meta-transcriptomics are promising techniques for discriminating and detecting pathogenic microorganisms that may be active and infectious in bioaerosols and, therefore, pose a threat to human health. Supplementary Information The online version contains supplementary material available at 10.1007/s41745-023-00380-x.
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Affiliation(s)
- Jianjian Hou
- Microbial Genomics and Ecology, Center for the Planetary Health and Innovation Science (PHIS), The IDEC Institute, Hiroshima University, Hiroshima, 739-0046 Japan
| | - So Fujiyoshi
- Microbial Genomics and Ecology, Center for the Planetary Health and Innovation Science (PHIS), The IDEC Institute, Hiroshima University, Hiroshima, 739-0046 Japan
- Center for Holobiome and Built Environment (CHOBE), Hiroshima University, Hiroshima, 739-0046 Japan
| | - Ishara Uhanie Perera
- Microbial Genomics and Ecology, Center for the Planetary Health and Innovation Science (PHIS), The IDEC Institute, Hiroshima University, Hiroshima, 739-0046 Japan
| | - Yukiko Nishiuchi
- Microbial Genomics and Ecology, Center for the Planetary Health and Innovation Science (PHIS), The IDEC Institute, Hiroshima University, Hiroshima, 739-0046 Japan
| | - Makiko Nakajima
- Center for Holobiome and Built Environment (CHOBE), Hiroshima University, Hiroshima, 739-0046 Japan
- Department of Architectural Engineering, Faculty of Engineering, Hiroshima Institute of Technology, Hiroshima, 731-5193 Japan
| | - Daisuke Ogura
- Center for Holobiome and Built Environment (CHOBE), Hiroshima University, Hiroshima, 739-0046 Japan
- Department of Architecture and Architectural Engineering, Graduate School of Engineering, Kyoto University, Kyoto, 615-8540 Japan
| | - Kyoko Yarimizu
- Microbial Genomics and Ecology, Center for the Planetary Health and Innovation Science (PHIS), The IDEC Institute, Hiroshima University, Hiroshima, 739-0046 Japan
| | - Fumito Maruyama
- Microbial Genomics and Ecology, Center for the Planetary Health and Innovation Science (PHIS), The IDEC Institute, Hiroshima University, Hiroshima, 739-0046 Japan
- Center for Holobiome and Built Environment (CHOBE), Hiroshima University, Hiroshima, 739-0046 Japan
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11
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Fujiyoshi S, Yarimizu K, Perera I, Abanto M, Jorquera M, Maruyama F. Learning from mistakes: challenges in finding holobiont factors from environmental samples and the importance of methodological consistency. Curr Opin Biotechnol 2023; 80:102897. [PMID: 36736005 DOI: 10.1016/j.copbio.2023.102897] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 12/22/2022] [Accepted: 01/02/2023] [Indexed: 02/05/2023]
Abstract
The cause of harmful algal blooms has been a mystery, but research to elucidate its mechanism has progressed over the years thanks to genetic technologies. We have monitored toxic algae and its associated bacteria as a community, the so-called 'holobiont' in Chilean coastal waters for years from the perspective of bacteria as an algal bloom driver. This review describes the challenges of holobiont monitoring, specifically with respect to standardizing and compliance with the monitoring protocols to collect reliable and sustainable data. Further, we suggest adopting the high-throughput sequencing (HTS) standard operating procedure (SOP) by the International Human Microbiome to improve the quality and consistency of holobiont monitoring in the harmful algal world.
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Affiliation(s)
- So Fujiyoshi
- Microbial Genomics and Ecology, Center for the Planetary Health and Innovation Science (PHIS), The IDEC Institute, Hiroshima University, 1-3-2 Kagamiyama, Higashi-Hiroshima City, Hiroshima 739-8511, Japan
| | - Kyoko Yarimizu
- Microbial Genomics and Ecology, Center for the Planetary Health and Innovation Science (PHIS), The IDEC Institute, Hiroshima University, 1-3-2 Kagamiyama, Higashi-Hiroshima City, Hiroshima 739-8511, Japan.
| | - Ishara Perera
- Microbial Genomics and Ecology, Center for the Planetary Health and Innovation Science (PHIS), The IDEC Institute, Hiroshima University, 1-3-2 Kagamiyama, Higashi-Hiroshima City, Hiroshima 739-8511, Japan
| | - Michel Abanto
- Núcleo Científico y Tecnológico en Biorecursos (BIOREN), Universidad de La Frontera, Ave. Francisco Salazar 01145, 4811230 Temuco, Chile
| | - Milko Jorquera
- Núcleo Científico y Tecnológico en Biorecursos (BIOREN), Universidad de La Frontera, Ave. Francisco Salazar 01145, 4811230 Temuco, Chile
| | - Fumito Maruyama
- Microbial Genomics and Ecology, Center for the Planetary Health and Innovation Science (PHIS), The IDEC Institute, Hiroshima University, 1-3-2 Kagamiyama, Higashi-Hiroshima City, Hiroshima 739-8511, Japan.
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12
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Morita D, Arai H, Isobe J, Maenishi E, Kumagai T, Maruyama F, Kuroda T. Whole-Genome and Plasmid Comparative Analysis of Campylobacter jejuni from Human Patients in Toyama, Japan, from 2015 to 2019. Microbiol Spectr 2023; 11:e0265922. [PMID: 36622198 PMCID: PMC9927224 DOI: 10.1128/spectrum.02659-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Campylobacter jejuni is a major causative agent of food poisoning, and increasing antimicrobial resistance is a concern. This study investigated 116 clinical isolates of C. jejuni from Toyama, Japan, which were isolated from 2015 to 2019. Antimicrobial susceptibility testing and whole-genome sequencing were used for phenotypic and genotypic characterization to compare antimicrobial resistance (AMR) profiles and phylogenic linkage. The multilocus sequence typing approach identified 37 sequence types (STs) and 15 clonal complexes (CCs), including 7 novel STs, and the high frequency CCs were CC21 (27.7%), CC48 (10.9%), and CC354 (9.9%). The AMR profiles and related resistant factors were as follows: fluoroquinolones (51.7%), mutation in quinolone resistance-determining region (QRDRs) (GyrA T86I); tetracyclines (27.6%), acquisition of tet(O); ampicillin (7.8%), harboring blaOXA184 or a promoter mutation in blaOXA193; aminoglycosides (1.7%), acquisition of ant(6)-Ia and aph(3')-III; chloramphenicol (0.9%), acquisition of cat. The acquired resistance genes tet(O), ant(6)-Ia, aph(3')-III, and cat were located on pTet family plasmids. Furthermore, three pTet family plasmids formed larger plasmids that incorporated additional genes such as the type IV secretion system. Sequence type 4526 (ST4526; 10.9%), which is reported only in Japan, was the most predominant, suggesting continued prevalence. This study reveals the sequences of the pTet family plasmids harbored by C. jejuni in Japan, which had been unclear, and the acquisition of the insertion sequences in a part of the pTet family plasmids. Because pTet family plasmids can be horizontally transmitted and are a major factor in acquired resistance in Campylobacter, the risk of spreading pTet that has acquired further resistance should be considered. IMPORTANCE Campylobacter jejuni is among the major causes of enteritis and diarrhea in humans in many countries. Drug-resistant Campylobacter is increasing in both developing and developed countries, and in particular, fluoroquinolone-resistant Campylobacter was one of the species included on the priority list of antibiotic-resistant bacteria. Campylobacter drug resistance surveillance is important and has been conducted worldwide. In this study, we performed whole-genome analysis of Campylobacter jejuni isolated from diarrhea patients at a hospital in Toyama, Japan. This revealed the continued prevalence of Campylobacter jejuni ST4526, which has been reported to be prevalent in Japan, and the acquisition of resistance and virulence factors in the pTet family plasmids. The diversity of pTet family plasmids, the major resistance transmission factor, is expected to potentially increase the risk of Campylobacter. The usefulness of whole-genome sequencing in Campylobacter surveillance was also demonstrated.
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Affiliation(s)
- Daichi Morita
- Department of Microbiology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Hiroki Arai
- Department of Microbiology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | | | | | - Takanori Kumagai
- Department of Microbiology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Fumito Maruyama
- Section of Microbial Genomics and Ecology, The IDEC Institute, Hiroshima University, Hiroshima, Japan
| | - Teruo Kuroda
- Department of Microbiology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
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13
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Perera IU, Fujiyoshi S, Nishiuchi Y, Nakai T, Maruyama F. Zooplankton act as cruise ships promoting the survival and pathogenicity of pathogenic bacteria. Microbiol Immunol 2022; 66:564-578. [PMID: 36128640 PMCID: PMC10091822 DOI: 10.1111/1348-0421.13029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 08/12/2022] [Accepted: 09/12/2022] [Indexed: 12/13/2022]
Abstract
Bacteria in general interact with zooplankton in aquatic ecosystems. These zooplankton-bacterial interactions help to shape the bacterial community by regulating bacterial abundances. Such interactions are even more significant and crucially in need of investigation in the case of pathogenic bacteria, which cause severe diseases in humans and animals. Among the many associations between a host metazoan and pathogenic bacteria, zooplankton provide nutrition and protection from stressful conditions, promote the horizontal transfer of virulence genes, and act as a mode of pathogen transport. These interactions allow the pathogen to survive and proliferate in aquatic environments and to endure water treatment processes, thereby creating a potential risk to human health. This review highlights current knowledge on the contributions of zooplankton to the survival and pathogenicity of pathogenic bacteria. We also discuss the need to consider these interactions as a risk factor in water treatment processes.
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Affiliation(s)
- Ishara U Perera
- Center for the Planetary Health and Innovation Science (PHIS), The IDEC Institute, Hiroshima University, Higashi-Hiroshima City, Hiroshima, Japan.,Center for Holobiome and Built Environment (CHOBE), Hiroshima University, Higashi-Hiroshima City, Hiroshima, Japan
| | - So Fujiyoshi
- Center for the Planetary Health and Innovation Science (PHIS), The IDEC Institute, Hiroshima University, Higashi-Hiroshima City, Hiroshima, Japan.,Center for Holobiome and Built Environment (CHOBE), Hiroshima University, Higashi-Hiroshima City, Hiroshima, Japan
| | - Yukiko Nishiuchi
- Center for the Planetary Health and Innovation Science (PHIS), The IDEC Institute, Hiroshima University, Higashi-Hiroshima City, Hiroshima, Japan
| | - Toshihiro Nakai
- Takehara Marine Science Station, Graduate School of Integrated Science for Life, Hiroshima University, Takehara City, Hiroshima, Japan
| | - Fumito Maruyama
- Center for the Planetary Health and Innovation Science (PHIS), The IDEC Institute, Hiroshima University, Higashi-Hiroshima City, Hiroshima, Japan.,Center for Holobiome and Built Environment (CHOBE), Hiroshima University, Higashi-Hiroshima City, Hiroshima, Japan
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14
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Koba K, Yarimizu K, Fujiyoshi S, Oshiro K, Wakizaka Y, Takano M, Maruyama F. Protocol of living cell separation using the microfluidic dielectrophoresis integrated chip. STAR Protoc 2022; 3:101527. [PMID: 35779257 PMCID: PMC9256945 DOI: 10.1016/j.xpro.2022.101527] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 05/23/2022] [Accepted: 06/13/2022] [Indexed: 11/24/2022] Open
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15
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Nishiuchi Y, Tateishi Y, Hirano H, Ozeki Y, Yamaguchi T, Miki M, Kitada S, Maruyama F, Matsumoto S. Direct Attachment with Erythrocytes Augments Extracellular Growth of Pathogenic Mycobacteria. Microbiol Spectr 2022; 10:e0245421. [PMID: 35293805 PMCID: PMC9045221 DOI: 10.1128/spectrum.02454-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 02/14/2022] [Indexed: 11/20/2022] Open
Abstract
Pathogenic intracellular mycobacteria, such as Mycobacterium tuberculosis and Mycobacterium avium, which cause lung diseases, can grow in macrophages. Extracellular mycobacteria have been reported in the lungs, blood, and sputum of patients, indicating the involvement of these pathogens in disease progression. Erythrocytes are involved in the symptoms associated with pulmonary mycobacterial diseases, such as bloody sputum and hemoptysis; however, little attention has been paid to the role of erythrocytes in mycobacterial diseases. Herein, we found that Mycobacterium avium subsp. hominissuis (MAH) and Mycobacterium intracellulare colocalized with erythrocytes at the sites of lung infection, inside capillaries and necrotic areas of granulomas, using histopathological examinations. Electron microscopy showed that MAH adhered and entered human erythrocytes when they were cocultured in vitro. MAH adhered to erythrocytes through complement receptor 1 and cell-surface sialo-glycoproteins. Importantly, MAH grew vigorously without causing any pronounced damage to erythrocytes. This erythrocyte-mediated enhancement of MAH growth occurred extracellularly depending on its direct attachment to erythrocytes. In contrast, MAH failed to multiply inside erythrocytes. Similarly, erythrocytes augmented the growth of other pathogenic mycobacteria, such as M. intracellulare and M. tuberculosis. THP-1 cell-derived human macrophages preferentially phagocytosed erythrocytes that were attached to mycobacteria (compared to bacteria alone), suggesting that erythrocyte-attached mycobacteria are an efficient infectious source for macrophages. Our findings provide new insights into the pathogenesis of mycobacterial diseases and offer an alternative and useful strategy for treating mycobacterial disease. IMPORTANCE Pathogenic mycobacteria, such as Mycobacterium tuberculosis, Mycobacterium avium subsp. hominissuis (MAH), and Mycobacterium intracellulare, cause pulmonary infections as intracellular parasites of lung macrophages and epithelial cells. Here, using histopathological examinations we found that MAH and M. intracellulare colocalized with erythrocytes in lung infection sites. Subsequent studies demonstrated that direct interaction with erythrocytes enhances the extracellular proliferation of mycobacteria based on the following results: 1. MAH adhered and invaded human erythrocytes upon coculture in vitro; 2. MAH adhered to erythrocytes through complement receptor 1 and cell-surface sialo-glycoproteins; 3. MAH rapidly proliferated when directly attached to erythrocytes but not within them; 4. other mycobacteria, such as M. intracellulare and M. tuberculosis, also proliferated in the same way as MAH. The finding that pathogenic mycobacteria grow extracellularly in an erythrocyte-dependent manner is of considerable clinical importance for understanding disease progression and latent infection.
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Affiliation(s)
- Yukiko Nishiuchi
- Toneyama Institute for Tuberculosis Research, Osaka City University Graduate School of Medicine, Toyonaka, Japan
- Office of Industry-Academia-Government and Community Collaboration, Hiroshima University, Higashi-Hiroshima, Japan
| | - Yoshitaka Tateishi
- Department of Bacteriology, Niigata University Graduate School of Medicine, Niigata, Japan
| | - Hiroshi Hirano
- Department of Diagnostic Pathology, Tokyo Medical University Hachioji Medical Center, Tokyo, Japan
| | - Yuriko Ozeki
- Department of Bacteriology, Niigata University Graduate School of Medicine, Niigata, Japan
| | - Takehiro Yamaguchi
- Department of Pharmacology, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - Mari Miki
- National Hospital Organization, Osaka Toneyama Medical Center, Toyonaka, Japan
| | - Seigo Kitada
- National Hospital Organization, Osaka Toneyama Medical Center, Toyonaka, Japan
| | - Fumito Maruyama
- Office of Industry-Academia-Government and Community Collaboration, Hiroshima University, Higashi-Hiroshima, Japan
| | - Sohkichi Matsumoto
- Department of Bacteriology, Niigata University Graduate School of Medicine, Niigata, Japan
- Laboratory of Tuberculosis, Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia
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16
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Komatsu T, Ohya K, Ota A, Nishiuchi Y, Yano H, Matsuo K, Odoi JO, Suganuma S, Sawai K, Hasebe A, Asai T, Yanai T, Fukushi H, Wada T, Yoshida S, Ito T, Arikawa K, Kawai M, Ato M, Baughn AD, Iwamoto T, Maruyama F. Genomic features of Mycobacterium avium subsp. hominissuis isolated from pigs in Japan. GigaByte 2021; 2021:gigabyte33. [PMID: 36824340 PMCID: PMC9650289 DOI: 10.46471/gigabyte.33] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 11/05/2021] [Indexed: 11/09/2022] Open
Abstract
Mycobacterium avium subsp. hominissuis (MAH) is one of the most important agents causing non-tuberculosis mycobacterial infection in humans and pigs. There have been advances in genome analysis of MAH from human isolates, but studies of isolates from pigs are limited despite its potential source of infection to human. Here, we obtained 30 draft genome sequences of MAH from pigs reared in Japan. The 30 draft genomes were 4,848,678-5,620,788 bp in length, comprising 4652-5388 coding genes and 46-75 (median: 47) tRNAs. All isolates had restriction modification-associated genes and 185-222 predicted virulence genes. Two isolates had tRNA arrays and one isolate had a clustered regularly interspaced short palindromic repeat (CRISPR) region. Our results will be useful for evaluation of the ecology of MAH by providing a foundation for genome-based epidemiological studies.
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Affiliation(s)
- Tetsuya Komatsu
- Aichi Prefectural Chuo Livestock Hygiene Service Center, Okazaki, Aichi, Japan
| | - Kenji Ohya
- Faculty of Applied Biological Sciences, Gifu University, Gifu, Gifu, Japan,United Graduate School of Veterinary Sciences, Gifu University, Gifu, Gifu, Japan
| | - Atsushi Ota
- Data Science Center, Division of Biological Science, Nara Institute of Science and Technology, Ikoma, Nara, Japan
| | - Yukiko Nishiuchi
- Office of Academic Research and Industry-Government Collaboration, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
| | - Hirokazu Yano
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, Japan
| | - Kayoko Matsuo
- Kumamoto Prefectural Aso Public Health Center, Aso, Kumamoto, Japan
| | - Justice Opare Odoi
- United Graduate School of Veterinary Sciences, Gifu University, Gifu, Gifu, Japan
| | - Shota Suganuma
- Faculty of Applied Biological Sciences, Gifu University, Gifu, Gifu, Japan
| | - Kotaro Sawai
- Faculty of Applied Biological Sciences, Gifu University, Gifu, Gifu, Japan,Viral Disease and Epidemiology Research Division, National Institute of Animal Health, National Agriculture Research Organization, Tsukuba, Ibaraki, Japan
| | - Akemi Hasebe
- Toyama Prefectural Meat Inspection Center, Imizu, Toyama, Japan
| | - Tetsuo Asai
- United Graduate School of Veterinary Sciences, Gifu University, Gifu, Gifu, Japan
| | - Tokuma Yanai
- Faculty of Applied Biological Sciences, Gifu University, Gifu, Gifu, Japan,United Graduate School of Veterinary Sciences, Gifu University, Gifu, Gifu, Japan,Hiwa Natural History Museum, Shobara, Hiroshima, Japan
| | - Hideto Fukushi
- Faculty of Applied Biological Sciences, Gifu University, Gifu, Gifu, Japan,United Graduate School of Veterinary Sciences, Gifu University, Gifu, Gifu, Japan
| | - Takayuki Wada
- Graduate School of Human Life Science, Osaka City University, Osaka, Osaka, Japan
| | - Shiomi Yoshida
- Clinical Research Center, National Hospital Organization Kinki-Chuo Chest Medical Center, Sakai, Osaka, Japan
| | - Toshihiro Ito
- Laboratory of Proteome Research, Proteome Research Center, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka, Japan
| | - Kentaro Arikawa
- Department of Infectious Diseases, Kobe Institute of Health, Kobe, Hyogo, Japan
| | - Mikihiko Kawai
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Kyoto, Japan
| | - Manabu Ato
- Department of Mycobacteriology, Leprosy Research Center, National Institute of Infectious Diseases, Higashimurayama, Tokyo, Japan
| | - Anthony D Baughn
- Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, Minnesota, USA
| | - Tomotada Iwamoto
- Department of Infectious Diseases, Kobe Institute of Health, Kobe, Hyogo, Japan
| | - Fumito Maruyama
- Office of Academic Research and Industry-Government Collaboration, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan,Project Research Center for Holobiome and Built Environment (CHOBE), Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan,Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco, Chile, Corresponding author. E-mail:
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17
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Yarimizu K, Mardones JI, Paredes-Mella J, Norambuena-Subiabre L, Carrano CJ, Maruyama F. The effect of iron on Chilean Alexandrium catenella growth and paralytic shellfish toxin production as related to algal blooms. Biometals 2021; 35:39-51. [PMID: 34716889 PMCID: PMC8803708 DOI: 10.1007/s10534-021-00349-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Accepted: 10/22/2021] [Indexed: 11/30/2022]
Abstract
The dinoflagellate Alexandrium catenella is a well-known paralytic shellfish toxin producer that forms harmful algal blooms (HABs) worldwide. Blooms of this species have repeatedly brought severe ecological and economic impacts to Chile, especially in the southern region, where the shellfish and salmon industries are world-famous. The mechanisms of such HABs have been intensively studied but are still unclear. Nutrient overloading is one of the often-discussed drivers for HABs. The present study used the A. catenella strain isolated from southern Chile to investigate how iron conditions could affect their growth and toxin production as related to HAB. Our results showed that an optimum concentration of iron was pivotal for proper A. catenella growth. Thus, while excess iron exerted a toxic effect, low iron media led to iron insufficiency and growth inhibition. In addition, the study shows that the degree of paralytic shellfish toxin production by A. catenella varied depending on the iron concentration in the culture media. The A. catenella strain from southern Chile produced GTX1-4 exclusively in the fmol cell−1 scale. Based on these findings, we suggest that including iron and paralytic shellfish toxin measurements in the fields can improve the current HAB monitoring and contribute to an understanding of A. catenella bloom dynamics in Chile.
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Affiliation(s)
- Kyoko Yarimizu
- Microbial Genomics and Ecology, Office of Academic Research and Industry-Government Collaboration, Hiroshima University, 1-3-2 Kagamiyama, Higashi-Hiroshima City, Hiroshima 739-8511 Japan
| | - Jorge I. Mardones
- Centro de Estudios de Algas Nocivas (CREAN), Instituto de Fomento Pesquero (IFOP), Padre Harter 547, 5480000 Puerto Montt, Chile
- Centro FONDAP de Investigación en Dinámica de Ecosistemas Marinos de Altas Latitudes (IDEAL), Valdivia, Chile
| | - Javier Paredes-Mella
- Centro de Estudios de Algas Nocivas (CREAN), Instituto de Fomento Pesquero (IFOP), Padre Harter 547, 5480000 Puerto Montt, Chile
| | - Luis Norambuena-Subiabre
- Centro de Estudios de Algas Nocivas (CREAN), Instituto de Fomento Pesquero (IFOP), Padre Harter 547, 5480000 Puerto Montt, Chile
| | - Carl J. Carrano
- Department of Chemistry and Biochemistry, San Diego State University, 5500 Campanile Dr., San Diego, CA 92182-1030 USA
| | - Fumito Maruyama
- Microbial Genomics and Ecology, Office of Academic Research and Industry-Government Collaboration, Hiroshima University, 1-3-2 Kagamiyama, Higashi-Hiroshima City, Hiroshima 739-8511 Japan
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18
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Yarimizu K, Fujiyoshi S, Kawai M, Acuña JJ, Rilling JI, Campos M, Vilugrón J, Cameron H, Vergara K, Gajardo G, Espinoza-González O, Guzmán L, Nagai S, Riquelme C, Jorquera MA, Maruyama F. A Standardized Procedure for Monitoring Harmful Algal Blooms in Chile by Metabarcoding Analysis. J Vis Exp 2021. [PMID: 34515692 DOI: 10.3791/62967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Harmful algae blooms (HABs) monitoring has been implemented worldwide, and Chile, a country famous for its fisheries and aquaculture, has intensively used microscopic and toxin analyses for decades for this purpose. Molecular biological methods, such as high-throughput DNA sequencing and bacterial assemblage-based approaches, are just beginning to be introduced in Chilean HAB monitoring, and the procedures have not yet been standardized. Here, 16S rRNA and 18S rRNA metabarcoding analyses for monitoring Chilean HABs are introduced stepwise. According to a recent hypothesis, algal-bacterial mutualistic association plays a critical synergetic or antagonistic relationship accounting for bloom initiation, maintenance, and regression. Thus, monitoring HAB from algal-bacterial perspectives may provide a broader understanding of HAB mechanisms and the basis for early warning. Metabarcoding analysis is one of the best suited molecular-based tools for this purpose because it can detect massive algal-bacterial taxonomic information in a sample. The visual procedures of sampling to metabarcoding analysis herein provide specific instructions, aiming to reduce errors and collection of reliable data.
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Affiliation(s)
- Kyoko Yarimizu
- Office of Research and Academia-Government-Community Collaboration, Hiroshima University;
| | - So Fujiyoshi
- Office of Research and Academia-Government-Community Collaboration, Hiroshima University
| | - Mikihiko Kawai
- Graduate School of Human and Environmental Studies, Kyoto University
| | - Jacquelinne J Acuña
- Scientific and Biotechnological Bioresource Nucleus, Universidad de La Frontera
| | | | - Marco Campos
- Scientific and Biotechnological Bioresource Nucleus, Universidad de La Frontera
| | | | - Henry Cameron
- Ciencias del Mar y Recursos Biologicos, Universidad de Antofagasta
| | - Karen Vergara
- Departamento de Ciencias Biológicas y Biodiversidad, Universidad de Los Lagos
| | - Gonzalo Gajardo
- Departamento de Ciencias Biológicas y Biodiversidad, Universidad de Los Lagos
| | | | - Leonardo Guzmán
- Centro de Estudios de Algas Nocivas, Instituto de Fomento Pesquero
| | - Satoshi Nagai
- Japan Fisheries Research and Education Agency, Fisheries Resources Institute
| | - Carlos Riquelme
- Ciencias del Mar y Recursos Biologicos, Universidad de Antofagasta
| | - Milko A Jorquera
- Scientific and Biotechnological Bioresource Nucleus, Universidad de La Frontera
| | - Fumito Maruyama
- Office of Research and Academia-Government-Community Collaboration, Hiroshima University;
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19
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Rilling JI, Maruyama F, Sadowsky MJ, Acuña JJ, Jorquera MA. CRISPR loci-PCR as Tool for Tracking Azospirillum sp. Strain B510. Microorganisms 2021; 9:1351. [PMID: 34206618 PMCID: PMC8307223 DOI: 10.3390/microorganisms9071351] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 06/16/2021] [Accepted: 06/17/2021] [Indexed: 11/16/2022] Open
Abstract
Azospirillum-based plant and soil inoculants are widely used in agriculture. The inoculated Azospirillum strains are commonly tracked by both culture-dependent and culture-independent methods, which are time-consuming or expensive. In this context, clustered regularly interspaced short palindromic repeats (CRISPR) loci structure is unique in the bacterial genome, including some Azospirillum species. Here, we investigated the use of CRISPR loci to track specific Azospirillum strains in soils systems by PCR. Primer sets for Azospirillum sp. strain B510 were designed and evaluated by colony and endpoint PCR. The CRISPRloci-PCR approach was standardized for Azospirillum sp. strain B510, and its specificity was observed by testing against 9 different Azospirillum strains, and 38 strains of diverse bacterial genera isolated from wheat plants. The CRISPRloci-PCR approach was validated in assays with substrate and wheat seedlings. Azospirillum sp. strain B510 was detected after of two weeks of inoculation in both sterile and nonsterile substrates as well as rhizosphere grown in sterile substrate. The CRISPRloci-PCR approach was found to be a useful molecular tool for specific tracking of Azospirillum at the strain level. This technique can be easily adapted to other microbial inoculants carrying CRISPR loci and can be used to complement other microbiological techniques.
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Affiliation(s)
- Joaquin I. Rilling
- Applied Microbial Ecology Laboratory (EMAlab), Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Temuco 4780000, Chile;
- Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Temuco 4780000, Chile
| | - Fumito Maruyama
- Office of Industry-Academia-Government and Community Collaboration, Hiroshima University, Hiroshima 739-8511, Japan;
| | - Michael J. Sadowsky
- Department of Soil, Water, and Climate, Department of Plant and Microbial Biology, and BioTechnology Institute, University of Minnesota, St. Paul, MN 55812, USA;
| | - Jacquelinne J. Acuña
- Applied Microbial Ecology Laboratory (EMAlab), Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Temuco 4780000, Chile;
- Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Temuco 4780000, Chile
| | - Milko A. Jorquera
- Applied Microbial Ecology Laboratory (EMAlab), Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Temuco 4780000, Chile;
- Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Temuco 4780000, Chile
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20
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Fujiyoshi S, Yarimizu K, Miyashita Y, Rilling J, Acuña JJ, Ueki S, Gajardo G, Espinoza-González O, Guzmán L, Jorquera MA, Nagai S, Maruyama F. Suitcase Lab: new, portable, and deployable equipment for rapid detection of specific harmful algae in Chilean coastal waters. Environ Sci Pollut Res Int 2021; 28:14144-14155. [PMID: 33206296 PMCID: PMC7673245 DOI: 10.1007/s11356-020-11567-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 11/05/2020] [Indexed: 05/15/2023]
Abstract
Phytoplankton blooms, including harmful algal blooms (HABs), have serious impacts on ecosystems, public health, and productivity activities. Rapid detection and monitoring of marine microalgae are important in predicting and managing HABs. We developed a toolkit, the Suitcase Lab, to detect harmful algae species in the field. We demonstrated the Suitcase Lab's capabilities for sampling, filtration, DNA extraction, and loop-mediated isothermal amplification (LAMP) detection in cultured Alexandrium catenella cells as well as Chilean coastal waters from four sites: Repollal, Isla García, Puerto Montt, and Metri. A LAMP assay using the Suitcase Lab in the field confirmed microscopic observations of A. catenella in samples from Repollal and Isla García. The Suitcase Lab allowed the rapid detection of A. catenella, within 2 h from the time of sampling, even at a single cell per milliliter concentrations, demonstrating its usefulness for quick and qualitative on-site diagnosis of target toxic algae species. This method is applicable not only to detecting harmful algae but also to other field studies that seek a rapid molecular diagnostic test.
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Affiliation(s)
- So Fujiyoshi
- Office of Industry-Academia-Government and Community Collaboration, Hiroshima University, 1-3-2 Kagamiyama, Higashi-Hiroshima City, Hiroshima, 739-8511, Japan.
- Center for holobiome and built Environment (CHOBE), Hiroshima University, 1-3-2 Kagamiyama, Higashi-Hiroshima City, Hiroshima, 739-8511, Japan.
- Laboratorio de Ecología Microbiana Aplicada, Departamento de Ciencias Químicas y Recursos Naturales, Scientific and Biotechnological Bioresource Nucleus (BIOREN-UFRO), Universidad de La Frontera, Ave. Francisco Salazar 01145, Temuco, Chile.
| | - Kyoko Yarimizu
- Office of Industry-Academia-Government and Community Collaboration, Hiroshima University, 1-3-2 Kagamiyama, Higashi-Hiroshima City, Hiroshima, 739-8511, Japan
| | - Yohei Miyashita
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama, 710-0046, Japan
| | - Joaquín Rilling
- Laboratorio de Ecología Microbiana Aplicada, Departamento de Ciencias Químicas y Recursos Naturales, Scientific and Biotechnological Bioresource Nucleus (BIOREN-UFRO), Universidad de La Frontera, Ave. Francisco Salazar 01145, Temuco, Chile
| | - Jacquelinne J Acuña
- Center for holobiome and built Environment (CHOBE), Hiroshima University, 1-3-2 Kagamiyama, Higashi-Hiroshima City, Hiroshima, 739-8511, Japan
- Laboratorio de Ecología Microbiana Aplicada, Departamento de Ciencias Químicas y Recursos Naturales, Scientific and Biotechnological Bioresource Nucleus (BIOREN-UFRO), Universidad de La Frontera, Ave. Francisco Salazar 01145, Temuco, Chile
| | - Shoko Ueki
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama, 710-0046, Japan
| | - Gonzalo Gajardo
- Laboratorio de Genética, Acuicultura & Biodiversidad. Departamento de Ciencias Biológicas y Biodiversidad, Universidad de Los Lagos, Osorno, Chile
| | - Oscar Espinoza-González
- Centro de Estudios de Algas Nocivas (CREAN), Instituto de Fomento Pesquero (IFOP), Padre Harter 547, 5480000, Puerto Montt, Chile
| | - Leonardo Guzmán
- Instituto de Fomento Pesquero, IFOP, Balmaceda 252, 5480000, Puerto Montt, Chile
| | - Milko A Jorquera
- Center for holobiome and built Environment (CHOBE), Hiroshima University, 1-3-2 Kagamiyama, Higashi-Hiroshima City, Hiroshima, 739-8511, Japan
- Laboratorio de Ecología Microbiana Aplicada, Departamento de Ciencias Químicas y Recursos Naturales, Scientific and Biotechnological Bioresource Nucleus (BIOREN-UFRO), Universidad de La Frontera, Ave. Francisco Salazar 01145, Temuco, Chile
| | - Satoshi Nagai
- Japan Fisheries Research and Education Agency, Fisheries Stock Assessment Center, Bioinformatics and Biosciences Division, Genome Structure Analysis Group, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-8648, Japan
| | - Fumito Maruyama
- Office of Industry-Academia-Government and Community Collaboration, Hiroshima University, 1-3-2 Kagamiyama, Higashi-Hiroshima City, Hiroshima, 739-8511, Japan.
- Center for holobiome and built Environment (CHOBE), Hiroshima University, 1-3-2 Kagamiyama, Higashi-Hiroshima City, Hiroshima, 739-8511, Japan.
- Laboratorio de Ecología Microbiana Aplicada, Departamento de Ciencias Químicas y Recursos Naturales, Scientific and Biotechnological Bioresource Nucleus (BIOREN-UFRO), Universidad de La Frontera, Ave. Francisco Salazar 01145, Temuco, Chile.
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21
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Yévenes M, Quiroz M, Maruyama F, Jorquera M, Gajardo G. Vibrio sp. ArtGut-C1, a polyhydroxybutyrate producer isolated from the gut of the aquaculture live diet Artemia (Crustacea). ELECTRON J BIOTECHN 2021. [DOI: 10.1016/j.ejbt.2020.10.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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22
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Ruiz-Gil T, Acuña JJ, Fujiyoshi S, Tanaka D, Noda J, Maruyama F, Jorquera MA. Airborne bacterial communities of outdoor environments and their associated influencing factors. Environ Int 2020; 145:106156. [PMID: 33039877 DOI: 10.1016/j.envint.2020.106156] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 09/20/2020] [Accepted: 09/21/2020] [Indexed: 05/16/2023]
Abstract
Microbial entities (such bacteria, fungi, archaea and viruses) within outdoor aerosols have been scarcely studied compared with indoor aerosols and nonbiological components, and only during the last few decades have their studies increased. Bacteria represent an important part of the microbial abundance and diversity in a wide variety of rural and urban outdoor bioaerosols. Currently, airborne bacterial communities are mainly sampled in two aerosol size fractions (2.5 and 10 µm) and characterized by culture-dependent (plate-counting) and culture-independent (DNA sequencing) approaches. Studies have revealed a large diversity of bacteria in bioaerosols, highlighting Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes as ubiquitous phyla. Seasonal variations in and dispersion of bacterial communities have also been observed between geographical locations as has their correlation with specific atmospheric factors. Several investigations have also suggested the relevance of airborne bacteria in the public health and agriculture sectors as well as remediation and atmospheric processes. However, although factors influencing airborne bacterial communities and standardized procedures for their assessment have recently been proposed, the use of bacterial taxa as microbial indicators of specific bioaerosol sources and seasonality have not been broadly explored. Thus, in this review, we summarize and discuss recent advances in the study of airborne bacterial communities in outdoor environments and the possible factors influencing their abundance, diversity, and seasonal variation. Furthermore, airborne bacterial activity and bioprospecting in different fields (e.g., the textile industry, the food industry, medicine, and bioremediation) are discussed. We expect that this review will reveal the relevance and influencing factors of airborne bacteria in outdoor environments as well as stimulate new investigations on the atmospheric microbiome, particularly in areas where air quality is a public concern.
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Affiliation(s)
- Tay Ruiz-Gil
- Doctorado en Ciencias de Recursos Naturales, Facultad de Ingeniería y Ciencias, Universidad de La Frontera, Temuco, Chile; Laboratorio de Ecología Microbiana Aplicada (EMALAB), Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Temuco, Chile
| | - Jacquelinne J Acuña
- Laboratorio de Ecología Microbiana Aplicada (EMALAB), Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Temuco, Chile; Network for Extreme Environment Research (NEXER), Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Temuco, Chile; Center for Holobiome and Built Environment (CHOBE), Hiroshima University, Japan
| | - So Fujiyoshi
- Laboratorio de Ecología Microbiana Aplicada (EMALAB), Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Temuco, Chile; Network for Extreme Environment Research (NEXER), Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Temuco, Chile; Microbial Genomics and Ecology, Office of Industry-Academia-Government and Community Collaboration, Hiroshima University, Hiroshima, Japan; Center for Holobiome and Built Environment (CHOBE), Hiroshima University, Japan
| | - Daisuke Tanaka
- Graduate School of Science and Engineering, University of Toyama, Toyama, Japan
| | - Jun Noda
- Center for Holobiome and Built Environment (CHOBE), Hiroshima University, Japan; Graduate School of Veterinary Science, Rakuno Gakuen University, Hokkaido, Japan
| | - Fumito Maruyama
- Laboratorio de Ecología Microbiana Aplicada (EMALAB), Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Temuco, Chile; Network for Extreme Environment Research (NEXER), Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Temuco, Chile; Microbial Genomics and Ecology, Office of Industry-Academia-Government and Community Collaboration, Hiroshima University, Hiroshima, Japan; Center for Holobiome and Built Environment (CHOBE), Hiroshima University, Japan
| | - Milko A Jorquera
- Laboratorio de Ecología Microbiana Aplicada (EMALAB), Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Temuco, Chile; Network for Extreme Environment Research (NEXER), Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Temuco, Chile; Center for Holobiome and Built Environment (CHOBE), Hiroshima University, Japan.
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23
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Yarimizu K, Fujiyoshi S, Kawai M, Norambuena-Subiabre L, Cascales EK, Rilling JI, Vilugrón J, Cameron H, Vergara K, Morón-López J, Acuña JJ, Gajardo G, Espinoza-González O, Guzmán L, Jorquera MA, Nagai S, Pizarro G, Riquelme C, Ueki S, Maruyama F. Protocols for Monitoring Harmful Algal Blooms for Sustainable Aquaculture and Coastal Fisheries in Chile. Int J Environ Res Public Health 2020; 17:ijerph17207642. [PMID: 33092111 PMCID: PMC7589761 DOI: 10.3390/ijerph17207642] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Revised: 10/14/2020] [Accepted: 10/18/2020] [Indexed: 11/16/2022]
Abstract
Harmful algae blooms (HABs) cause acute effects on marine ecosystems due to their production of endogenous toxins or their enormous biomass, leading to significant impacts on local economies and public health. Although HAB monitoring has been intensively performed at spatiotemporal scales in coastal areas of the world over the last decades, procedures have not yet been standardized. HAB monitoring procedures are complicated and consist of many methodologies, including physical, chemical, and biological water sample measurements. Each monitoring program currently uses different combinations of methodologies depending on site specific purposes, and many prior programs refer to the procedures in quotations. HAB monitoring programs in Chile have adopted the traditional microscopic and toxin analyses but not molecular biology and bacterial assemblage approaches. Here we select and optimize the HAB monitoring methodologies suitable for Chilean geography, emphasizing on metabarcoding analyses accompanied by the classical tools with considerations including cost, materials and instrument availability, and easiness and efficiency of performance. We present results from a pilot study using the standardized stepwise protocols, demonstrating feasibility and plausibility for sampling and analysis for the HAB monitoring. Such specific instructions in the standardized protocol are critical obtaining quality data under various research environments involving multiple stations, different analysts, various time-points, and long HAB monitoring duration.
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Affiliation(s)
- Kyoko Yarimizu
- Office of Industry-Academia-Government and Community Collaboration, Hiroshima University, 1-3-2 Kagamiyama, Higashi-Hiroshima City, Hiroshima 739-8511, Japan;
- Correspondence: (K.Y.); (F.M.); Tel.: +81-082-424-7048 (K.Y. & F.M.)
| | - So Fujiyoshi
- Office of Industry-Academia-Government and Community Collaboration, Hiroshima University, 1-3-2 Kagamiyama, Higashi-Hiroshima City, Hiroshima 739-8511, Japan;
| | - Mikihiko Kawai
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshidanihonmatsu-cho, Kyoto 606-8501, Japan;
| | - Luis Norambuena-Subiabre
- Centro de Estudios de Algas Nocivas (CREAN), Instituto de Fomento Pesquero (IFOP), Padre Harter 547, Puerto Montt 5480000, Chile; (L.N.-S.); (E.-K.C.); (J.V.); (O.E.-G.); (L.G.)
| | - Emma-Karin Cascales
- Centro de Estudios de Algas Nocivas (CREAN), Instituto de Fomento Pesquero (IFOP), Padre Harter 547, Puerto Montt 5480000, Chile; (L.N.-S.); (E.-K.C.); (J.V.); (O.E.-G.); (L.G.)
| | - Joaquin-Ignacio Rilling
- Scientific and Biotechnological Bioresource Nucleus (BIOREN-UFRO), Universidad de La Frontera, Ave. Francisco Salazar 01145, Temuco 4811230, Chile; (J.-I.R.); (J.J.A.); (M.A.J.)
| | - Jonnathan Vilugrón
- Centro de Estudios de Algas Nocivas (CREAN), Instituto de Fomento Pesquero (IFOP), Padre Harter 547, Puerto Montt 5480000, Chile; (L.N.-S.); (E.-K.C.); (J.V.); (O.E.-G.); (L.G.)
| | - Henry Cameron
- Centro de Bioinnovacion, Facultad de Ciencias del Mar y Recursos Biologicos, Universidad de Antofagasta, Av. Angamos 601, Antofagasta 1270300, Chile; (H.C.); (C.R.)
| | - Karen Vergara
- Laboratorio de Genética, Acuicultura & Biodiversidad, Departamento de Ciencias Biológicas y Biodiversidad, Universidad de Los Lagos, Osorno 5290000, Chile; (K.V.); (G.G.)
| | - Jesus Morón-López
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama 710-0046, Japan; (J.M.-L.); (S.U.)
| | - Jacquelinne J. Acuña
- Scientific and Biotechnological Bioresource Nucleus (BIOREN-UFRO), Universidad de La Frontera, Ave. Francisco Salazar 01145, Temuco 4811230, Chile; (J.-I.R.); (J.J.A.); (M.A.J.)
| | - Gonzalo Gajardo
- Laboratorio de Genética, Acuicultura & Biodiversidad, Departamento de Ciencias Biológicas y Biodiversidad, Universidad de Los Lagos, Osorno 5290000, Chile; (K.V.); (G.G.)
| | - Oscar Espinoza-González
- Centro de Estudios de Algas Nocivas (CREAN), Instituto de Fomento Pesquero (IFOP), Padre Harter 547, Puerto Montt 5480000, Chile; (L.N.-S.); (E.-K.C.); (J.V.); (O.E.-G.); (L.G.)
| | - Leonardo Guzmán
- Centro de Estudios de Algas Nocivas (CREAN), Instituto de Fomento Pesquero (IFOP), Padre Harter 547, Puerto Montt 5480000, Chile; (L.N.-S.); (E.-K.C.); (J.V.); (O.E.-G.); (L.G.)
| | - Milko A. Jorquera
- Scientific and Biotechnological Bioresource Nucleus (BIOREN-UFRO), Universidad de La Frontera, Ave. Francisco Salazar 01145, Temuco 4811230, Chile; (J.-I.R.); (J.J.A.); (M.A.J.)
| | - Satoshi Nagai
- Japan Fisheries Research and Education Agency, Fisheries Resources Institute, Fisheries Stock Assessment Center, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 236-8648, Japan;
| | - Gemita Pizarro
- Laboratorio de toxinas y fitoplancton, IFOP, Enrique Abello 0552, Punta Arenas 6200000, Chile;
| | - Carlos Riquelme
- Centro de Bioinnovacion, Facultad de Ciencias del Mar y Recursos Biologicos, Universidad de Antofagasta, Av. Angamos 601, Antofagasta 1270300, Chile; (H.C.); (C.R.)
| | - Shoko Ueki
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama 710-0046, Japan; (J.M.-L.); (S.U.)
| | - Fumito Maruyama
- Office of Industry-Academia-Government and Community Collaboration, Hiroshima University, 1-3-2 Kagamiyama, Higashi-Hiroshima City, Hiroshima 739-8511, Japan;
- Correspondence: (K.Y.); (F.M.); Tel.: +81-082-424-7048 (K.Y. & F.M.)
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Kawai M, Ota A, Takemura T, Nakai T, Maruyama F. Continuation and replacement of Vibrio cholerae non-O1 clonal genomic groups isolated from Plecoglossus altivelis fish in freshwaters. Environ Microbiol 2020; 22:4473-4484. [PMID: 33448654 DOI: 10.1111/1462-2920.15199] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 08/11/2020] [Accepted: 08/13/2020] [Indexed: 01/14/2023]
Abstract
The dissemination and abundances of Vibrio species in aquatic environments are of interest, as some species cause emerging diseases in humans and in aquatic organisms like fish. It is suggested that Vibrio cholerae non-O1 infections of Plecoglossus altivelis ('ayu') were spread to various parts of Japan through the annual transplantation of juvenile fish. To investigate this, we used genome-aided tracing of 17 V. cholerae strains isolated from ayu between the 1970s and 1990s in different Japanese freshwater systems. The strains formed a genomic clade distinct from all known clades, which we designate as the Ayu clade. Two clonal genomic groups identified within the clade, Ayu-1 and Ayu-2, persisted for a few years (between 1977 to 1979 and 1987 to 1990, respectively), and clonal replacement of Ayu-1 by Ayu-2 took place over an 8-year period. Despite the high similarity between Ayu-1 and Ayu-2 (> 99.9% identity and > 97% fraction of genomes shared), differences in their gene repertoires were found, raising the possibility that they are phenotypically distinct. These results highlight the importance of genome-based studies for understanding the long-term dynamics of populations over the timescale of years.
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Affiliation(s)
- Mikihiko Kawai
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan
| | - Atsushi Ota
- Office of Industry-Academia-Government and Community Collaboration, Hiroshima University, Higashihiroshima, Japan
| | - Taichiro Takemura
- Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Toshihiro Nakai
- Graduate School of Biosphere Science, Hiroshima University, Higashihiroshima, Japan
| | - Fumito Maruyama
- Office of Industry-Academia-Government and Community Collaboration, Hiroshima University, Higashihiroshima, Japan
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25
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Walter JM, Coutinho FH, Leomil L, Hargreaves PI, Campeão ME, Vieira VV, Silva BS, Fistarol GO, Salomon PS, Sawabe T, Mino S, Hosokawa M, Miyashita H, Maruyama F, van Verk MC, Dutilh BE, Thompson CC, Thompson FL. Ecogenomics of the Marine Benthic Filamentous Cyanobacterium Adonisia. Microb Ecol 2020; 80:249-265. [PMID: 32060621 DOI: 10.1007/s00248-019-01480-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 12/22/2019] [Indexed: 06/10/2023]
Abstract
Turfs are among the major benthic components of reef systems worldwide. The nearly complete genome sequences, basic physiological characteristics, and phylogenomic reconstruction of two phycobiliprotein-rich filamentous cyanobacteria strains isolated from turf assemblages from the Abrolhos Bank (Brazil) are investigated. Both Adonisia turfae CCMR0081T (= CBAS 745T) and CCMR0082 contain approximately 8 Mbp in genome size and experiments identified that both strains exhibit chromatic acclimation. Whereas CCMR0081T exhibits chromatic acclimation type 3 (CA3) regulating both phycocyanin (PC) and phycoerythrin (PE), CCMR0082 strain exhibits chromatic acclimation type 2 (CA2), in correspondence with genes encoding specific photosensors and regulators for PC and PE. Furthermore, a high number and diversity of secondary metabolite synthesis gene clusters were identified in both genomes, and they were able to grow at high temperatures (28 °C, with scant growth at 30 °C). These characteristics provide insights into their widespread distribution in reef systems.
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Affiliation(s)
- Juline M Walter
- Laboratory of Microbiology, Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
- Radboud Institute for Molecular Life Sciences, Centre for Molecular and Biomolecular Informatics (CMBI), Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Felipe H Coutinho
- Laboratory of Microbiology, Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
- Radboud Institute for Molecular Life Sciences, Centre for Molecular and Biomolecular Informatics (CMBI), Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Luciana Leomil
- Laboratory of Microbiology, Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Paulo I Hargreaves
- Laboratory of Microbiology, Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Mariana E Campeão
- Laboratory of Microbiology, Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | | | - Beatriz S Silva
- Marine Phytoplankton Laboratory, Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Giovana O Fistarol
- Marine Phytoplankton Laboratory, Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Paulo S Salomon
- Marine Phytoplankton Laboratory, Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Tomoo Sawabe
- Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
| | - Sayaka Mino
- Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
| | - Masashi Hosokawa
- Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
| | - Hideaki Miyashita
- Office of Academic Research and Industry-Government Collaboration, Hiroshima University, 739-8530, Hiroshima, Japan
| | - Fumito Maruyama
- Office of Academic Research and Industry-Government Collaboration, Hiroshima University, 739-8530, Hiroshima, Japan
| | - Marcel C van Verk
- Plant-Microbe Interactions, Bioinformatics, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Bas E Dutilh
- Radboud Institute for Molecular Life Sciences, Centre for Molecular and Biomolecular Informatics (CMBI), Radboud University Medical Centre, Nijmegen, The Netherlands
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands
| | - Cristiane C Thompson
- Laboratory of Microbiology, Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Fabiano L Thompson
- Laboratory of Microbiology, Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
- Center of Technology-CT2, SAGE-COPPE, Federal University of Rio de Janeiro (UFRJ), Av. Carlos Chagas Filho, 373, CCS-IB-Biomar, Lab. de Microbiologia, Bloco A3, (Anexo), sl. 102, Cidade Universitária, Rio de Janeiro, RJ, CEP 21941-599, Brazil.
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26
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Okubo T, Yossapol M, Ikushima S, Kakooza S, Wampande EM, Asai T, Tsuchida S, Ohya K, Maruyama F, Kabasa JD, Ushida K. Isolation and Characterization of Antimicrobial-Resistant Escherichia coli from Retail Meats from Roadside Butcheries in Uganda. Foodborne Pathog Dis 2020; 17:666-671. [PMID: 32551973 DOI: 10.1089/fpd.2020.2796] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Retail meats are one of the main routes for spreading antimicrobial-resistant bacteria (ARB) from livestock to humans through the food chain. In African countries, retail meats are often sold at roadside butcheries without chilling or refrigeration. Retail meats in those butcheries are suspected to be contaminated by ARB, but it was not clear. In this study, we tested for the presence of antimicrobial-resistant Escherichia coli from retail meats (n = 64) from roadside butcheries in Kampala, Uganda. The meat surfaces were swabbed and inoculated on PetriFilm SEC agar to isolate E. coli. We successfully isolated E. coli from 90.6% of these retail meat samples. We identified the phylogenetic type, antimicrobial susceptibility, and antimicrobial resistance genes prevalence between retail meat isolates (n = 89). Phylogenetic type B1 was identified from 70.8% of the retail meat isolates, suggesting that the isolates originated primarily from fecal contamination during meat processing. Tetracycline (TET)-resistant isolates with tetA and/or tetB gene(s) were the most frequently detected (28.1%), followed by ampicillin (AMP) resistance genes with blaTEM (15.7%,) and sulfamethoxazole-trimethoprim (SXT) resistance genes with sul2 (15.7%). No extended-spectrum beta-lactamase-producing isolates were detected. A conjugation assay showed that resistance to AMP, TET, and SXT could be simultaneously transferred to recipients. These findings suggest that antimicrobial-resistant E. coli can easily be transferred from farms to tables from retail meats obtained from roadside butcheries.
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Affiliation(s)
- Torahiko Okubo
- Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University Graduate School of Health Sciences, Sapporo, Japan
| | - Montira Yossapol
- Department of Applied Veterinary Sciences, United Graduate School of Veterinary Sciences, Gifu University, Gifu, Japan.,Office of Academic Affairs, Faculty of Veterinary Sciences, Mahasarakham University, Maha Sarakham, Thailand
| | - Shiori Ikushima
- Department of Applied Veterinary Sciences, United Graduate School of Veterinary Sciences, Gifu University, Gifu, Japan
| | - Steven Kakooza
- Department of Veterinary Pharmacy, Clinics and Comparative Medicine, School of Veterinary Medicine and Animal Resources, College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Eddie M Wampande
- Department of Veterinary Pharmacy, Clinics and Comparative Medicine, School of Veterinary Medicine and Animal Resources, College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda.,Central Diagnostic Laboratory, College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Tetsuo Asai
- Department of Applied Veterinary Sciences, United Graduate School of Veterinary Sciences, Gifu University, Gifu, Japan.,Education and Research Center for Food Animal Health, Gifu University (GeFAH), Gifu, Japan
| | - Sayaka Tsuchida
- Chubu University Academy of Emerging Sciences, Kasugai, Japan.,Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto, Japan
| | - Kenji Ohya
- Department of Applied Veterinary Sciences, United Graduate School of Veterinary Sciences, Gifu University, Gifu, Japan.,Education and Research Center for Food Animal Health, Gifu University (GeFAH), Gifu, Japan
| | - Fumito Maruyama
- Microbial Genomics and Ecology, Office of Academic Research and Industry-Government Collaboration, Academy of Hiroshima University, Hiroshima, Japan
| | - John D Kabasa
- Department of Pharmacy, Clinical and Comparative Medicine, School of Veterinary Medicine and Animal Resources, Makerere University, Kampala, Uganda
| | - Kazunari Ushida
- Chubu University Academy of Emerging Sciences, Kasugai, Japan.,Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto, Japan
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27
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Soliman AM, Maruyama F, Zarad HO, Ota A, Nariya H, Shimamoto T, Shimamoto T. Emergence of a Multidrug-Resistant Enterobacter hormaechei Clinical Isolate from Egypt Co-Harboring mcr-9 and blaVIM-4. Microorganisms 2020; 8:microorganisms8040595. [PMID: 32325973 PMCID: PMC7232449 DOI: 10.3390/microorganisms8040595] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 04/17/2020] [Accepted: 04/17/2020] [Indexed: 11/17/2022] Open
Abstract
This study describes the first full genomic sequence of an mcr-9 and blaVIM-4-carrying multidrug-resistant Enterobacter hormaechei clinical isolate from Egypt. The strain was isolated in April 2015 from the sputum of a patient in Cairo, Egypt. The mcr-9 and blaVIM-4 genes were identified by PCR screening and DNA sequencing; the isolate was subjected to antimicrobial susceptibility testing, conjugation experiments, and whole genomic sequencing. mcr-9 and blaVIM-4 were carried by an IncHI2 plasmid, pAMS-38a (281,121 bp in size); the plasmid also carried genes conferring resistance against sulfonamides (sul1), quinolones (qnrA1), trimethoprim (dfrA1), β-lactams (blaTEM-1B), aminoglycosides (aac (6’)-II, aadA23, aadA2b, and ant(2’’)-Ia). The strain was susceptible to colistin (MIC, <0.25 μg/mL); this could be due to the absence of the qseC/qseB regulatory system located downstream of mcr-9 in Enterobacterales, which is involved in the induction of colistin-resistance. The genetic context of mcr-9 and blaVIM-4 was identified as IS1-mcr-9-IS903-pcoS-∆pcoE-rcnA and intI1-blaVIM-4—aac (6’)-II-dfrA1-∆aadA23-smr-ISPa21-qacE∆1, respectively. This is the first report of an mcr-9 and blaVIM-4 /IncHI2-carrying multidrug-resistant E. hormaechei clinical isolate from Africa and the Middle East. Plasmids of the IncHI2 group and the two insertion sequences (IS1, and IS903) might be the main vehicles for dissemination of mcr-9. Further screening for mcr-9 is essential for identifying its incidence and to prevent its dissemination.
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Affiliation(s)
- Ahmed M. Soliman
- Laboratory of Food Microbiology and Hygiene, Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima 739-8528, Japan; (A.M.S.); (H.O.Z.)
- Department of Microbiology and Immunology, Faculty of Pharmacy, Kafrelsheikh University, Kafr El-Sheikh 33516, Egypt
| | - Fumito Maruyama
- Microbial Genomics and Ecology, Office of Academic Research and Industry-Government Collaboration, Hiroshima University, Higashi-Hiroshima 739-8530, Japan; (F.M.); (A.O.)
| | - Hoda O. Zarad
- Laboratory of Food Microbiology and Hygiene, Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima 739-8528, Japan; (A.M.S.); (H.O.Z.)
| | - Atsushi Ota
- Microbial Genomics and Ecology, Office of Academic Research and Industry-Government Collaboration, Hiroshima University, Higashi-Hiroshima 739-8530, Japan; (F.M.); (A.O.)
| | - Hirofumi Nariya
- Laboratory of Food Microbiology and Hygiene, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima 739-8528, Japan; (H.N.); (T.S.)
| | - Toshi Shimamoto
- Laboratory of Food Microbiology and Hygiene, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima 739-8528, Japan; (H.N.); (T.S.)
| | - Tadashi Shimamoto
- Laboratory of Food Microbiology and Hygiene, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima 739-8528, Japan; (H.N.); (T.S.)
- Correspondence: ; Tel.: +81-82-424-7897; Fax: +81-82-424-7916
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28
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Takahashi I, Hosomi K, Nagatake T, Toubou H, Yamamoto D, Hayashi I, Kurashima Y, Sato S, Shibata N, Goto Y, Maruyama F, Nakagawa I, Kuwae A, Abe A, Kunisawa J, Kiyono H. Persistent colonization of non-lymphoid tissue-resident macrophages by Stenotrophomonas maltophilia. Int Immunol 2020; 32:133-141. [PMID: 31630178 PMCID: PMC10689348 DOI: 10.1093/intimm/dxz071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 10/17/2019] [Indexed: 11/14/2022] Open
Abstract
Accumulating evidence has revealed that lymphoid tissue-resident commensal bacteria (e.g. Alcaligenes spp.) survive within dendritic cells. We extended our previous study by investigating microbes that persistently colonize colonic macrophages. 16S rRNA-based metagenome analysis using DNA purified from murine colonic macrophages revealed the presence of Stenotrophomonas maltophilia. The in situ intracellular colonization by S. maltophilia was recapitulated in vitro by using bone marrow-derived macrophages (BMDMs). Co-culture of BMDMs with clinically isolated S. maltophilia led to increased mitochondrial respiration and robust IL-10 production. We further identified a 25-kDa protein encoded by the gene assigned as smlt2713 (recently renamed as SMLT_RS12935) and secreted by S. maltophilia as the factor responsible for enhanced IL-10 production by BMDMs. IL-10 production is critical for maintenance of the symbiotic condition, because intracellular colonization by S. maltophilia was impaired in IL-10-deficient BMDMs, and smlt2713-deficient S. maltophilia failed to persistently colonize IL-10-competent BMDMs. These findings indicate a novel commensal network between colonic macrophages and S. maltophilia that is mediated by IL-10 and smlt2713.
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Affiliation(s)
- Ichiro Takahashi
- Department of Mucosal Immunology, Graduate School of Biomedical and Health Science, Hiroshima University, Hiroshima, Japan
- Laboratory of Vaccine Materials, Center for Vaccine and Adjuvant Research and Laboratory of Gut Environmental System, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki-Osaka, Japan
| | - Koji Hosomi
- Laboratory of Vaccine Materials, Center for Vaccine and Adjuvant Research and Laboratory of Gut Environmental System, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki-Osaka, Japan
| | - Takahiro Nagatake
- Laboratory of Vaccine Materials, Center for Vaccine and Adjuvant Research and Laboratory of Gut Environmental System, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki-Osaka, Japan
| | - Hirokazu Toubou
- Department of Mucosal Immunology, Graduate School of Biomedical and Health Science, Hiroshima University, Hiroshima, Japan
| | - Daiki Yamamoto
- Department of Mucosal Immunology, Graduate School of Biomedical and Health Science, Hiroshima University, Hiroshima, Japan
| | - Ikue Hayashi
- Department of Mucosal Immunology, Graduate School of Biomedical and Health Science, Hiroshima University, Hiroshima, Japan
| | - Yosuke Kurashima
- International Research and Development Center for Mucosal Vaccines, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Shintaro Sato
- International Research and Development Center for Mucosal Vaccines, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Naoko Shibata
- International Research and Development Center for Mucosal Vaccines, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yoshiyuki Goto
- International Research and Development Center for Mucosal Vaccines, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Fumito Maruyama
- Department of Microbiology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Ichiro Nakagawa
- Department of Microbiology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Asaomi Kuwae
- Laboratory of Bacterial Infection, Kitasato Institute for Life Sciences, Kitasato University, Tokyo, Japan
| | - Akio Abe
- Laboratory of Bacterial Infection, Kitasato Institute for Life Sciences, Kitasato University, Tokyo, Japan
| | - Jun Kunisawa
- Laboratory of Vaccine Materials, Center for Vaccine and Adjuvant Research and Laboratory of Gut Environmental System, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki-Osaka, Japan
- International Research and Development Center for Mucosal Vaccines, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Graduate School of Medicine, Graduate School of Pharmaceutical Sciences, and Graduate School of Dentistry, Osaka University, Suita-Osaka, Japan
- Graduate School of Medicine, Kobe University, Kobe-Hyogo, Japan
| | - Hiroshi Kiyono
- International Research and Development Center for Mucosal Vaccines, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
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29
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Okura M, Maruyama F, Ota A, Tanaka T, Matoba Y, Osawa A, Sadaat SM, Osaki M, Toyoda A, Ogura Y, Hayashi T, Takamatsu D. Genotypic diversity of Streptococcus suis and the S. suis-like bacterium Streptococcus ruminantium in ruminants. Vet Res 2019; 50:94. [PMID: 31727180 PMCID: PMC6854688 DOI: 10.1186/s13567-019-0708-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 09/25/2019] [Indexed: 11/13/2022] Open
Abstract
Although Streptococcus suis has attracted public attention as a major swine and human pathogen, this bacterium has also been isolated from other animals, including ruminants. However, recent taxonomic studies revealed the existence of other species that were previously identified as S. suis, and some of these isolates were reclassified as the novel species Streptococcus ruminantium. In Japan, biochemically identified S. suis is frequently isolated from diseased ruminants; however, such isolates have not yet been identified accurately, and their aetiological importance in ruminants is unclear. Therefore, to understand the importance of S. suis and S. suis-like bacteria in ruminants, we reclassified S. suis isolates from ruminants according to the updated classification and investigated their genetic diversity. Although both S. suis and S. ruminantium were isolated from healthy and diseased ruminants, most of the isolates from diseased animals were S. ruminantium, implying that S. ruminantium is more likely to be associated with ruminant disease than S. suis. However, the ruminant S. suis and S. ruminantium isolates from diseased animals were classified into diverse genotypes rather than belonging to certain clonal groups. Genome sequence analysis of 20 S. ruminantium isolates provided information about the antibiotic resistance, potential virulence, and serological diversity of this species. We further developed an S. ruminantium-specific PCR assay to aid in the identification of this bacterium. The information obtained and the method established in this study will contribute to the accurate diagnosis of ruminant streptococcal infections.
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Affiliation(s)
- Masatoshi Okura
- Division of Bacterial and Parasitic Diseases, National Institute of Animal Health, National Agriculture and Food Research Organization, Tsukuba, Japan.
| | - Fumito Maruyama
- Department of Microbiology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco, Chile
| | - Atsushi Ota
- Department of Microbiology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Takeshi Tanaka
- Nairiku Meat Inspection Center, Yamagata Prefectural Government, Yamagata, Japan
| | - Yohei Matoba
- Murayama Public Health Center, Yamagata Prefectural Government, Yamagata, Japan
| | - Aya Osawa
- Matsumoto Livestock Hygiene Service Center, Nagano Prefectural Government, Matsumoto, Japan
| | - Sayed Mushtaq Sadaat
- Ministry of Agriculture, Irrigation and Livestock, Animal Health Directorate, Central Veterinary Diagnostic and Research Laboratory, Kabul, Afghanistan
| | - Makoto Osaki
- Division of Bacterial and Parasitic Diseases, National Institute of Animal Health, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Atsushi Toyoda
- Department of Genomics and Evolutionary Biology, National Institute of Genetics, Shizuoka, Japan.,Advanced Genomics Center, National Institute of Genetics, Shizuoka, Japan
| | - Yoshitoshi Ogura
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Daisuke Takamatsu
- Division of Bacterial and Parasitic Diseases, National Institute of Animal Health, National Agriculture and Food Research Organization, Tsukuba, Japan.,United Graduate School of Veterinary Sciences, Gifu University, Gifu, Japan
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30
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Yano H, Suzuki H, Maruyama F, Iwamoto T. The recombination-cold region as an epidemiological marker of recombinogenic opportunistic pathogen Mycobacterium avium. BMC Genomics 2019; 20:752. [PMID: 31623552 PMCID: PMC6798384 DOI: 10.1186/s12864-019-6078-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Accepted: 09/04/2019] [Indexed: 11/10/2022] Open
Abstract
Background The rapid identification of lineage remains a challenge in the genotyping of clinical isolates of recombinogenic pathogens. The chromosome of Mycobacterium avium subsp. hominissuis (MAH), an agent of Mycobacterium avium complex (MAC) lung disease, is often mosaic and is composed of chromosomal segments originating from different lineages. This makes it difficult to infer the MAH lineage in a simple experimental set-up. To overcome this difficulty, we sought to identify chromosomal marker genes containing lineage-specific alleles by genome data mining. Results We conducted genetic population structure analysis, phylogenetic analysis, and a survey of historical recombination using data from 125 global MAH isolates. Six MAH lineages (EA1, EA2, SC1, SC2, SC3, and SC4) were identified in the current dataset. One P-450 gene (locus_tag MAH_0788/MAV_0940) in the recombination-cold region was found to have multiple alleles that could discriminate five lineages. By combining the information about allele type from one additional gene, the six MAH lineages as well as other M. avium subspecies were distinguishable. A recombination-cold region of 116 kb contains an insertion hotspot and is flanked by a mammalian cell-entry protein operon where allelic variants have previously been reported to occur. Hence, we speculate that the acquisition of lineage- or strain-specific insertions has introduced homology breaks in the chromosome, thereby reducing the chance of interlineage recombination. Conclusions The allele types of the newly identified marker genes can be used to predict major lineages of M. avium. The single nucleotide polymorphism typing approach targeting multiallelic loci in recombination-cold regions will facilitate the epidemiological study of MAC, and may also be useful for equivalent studies of other nontuberculous mycobacteria potentially carrying mosaic genomes.
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Affiliation(s)
- Hirokazu Yano
- Graduate School of Life Sciences, Tohoku University, Katahira, Aoba-ku, Sendai, Japan.
| | - Haruo Suzuki
- Faculty of Environment and Information Studies, Keio University, Fujisawa, Japan
| | - Fumito Maruyama
- Office of Industry-Academia-Government and Community Collaboration, Hiroshima University, Hiroshima, Japan
| | - Tomotada Iwamoto
- Department of Infectious Diseases, Kobe Institute of Health, Kobe, Japan.
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31
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Jorquera MA, Graether SP, Maruyama F. Editorial: Bioprospecting and Biotechnology of Extremophiles. Front Bioeng Biotechnol 2019; 7:204. [PMID: 31552232 PMCID: PMC6736590 DOI: 10.3389/fbioe.2019.00204] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 08/09/2019] [Indexed: 11/21/2022] Open
Affiliation(s)
- Milko A Jorquera
- Laboratorio de Ecología Microbiana Aplicada, Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Temuco, Chile.,Network for Extreme Environment Research, Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco, Chile
| | - Steffen P Graether
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - Fumito Maruyama
- Laboratorio de Ecología Microbiana Aplicada, Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Temuco, Chile.,Office of Industry-Academia-Government and Community Collaboration, Hiroshima University, Hiroshima, Japan
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32
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Minato Y, Gohl DM, Thiede JM, Chacón JM, Harcombe WR, Maruyama F, Baughn AD. Genomewide Assessment of Mycobacterium tuberculosis Conditionally Essential Metabolic Pathways. mSystems 2019; 4:e00070-19. [PMID: 31239393 PMCID: PMC6593218 DOI: 10.1128/msystems.00070-19] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 06/07/2019] [Indexed: 11/30/2022] Open
Abstract
A better understanding of essential cellular functions in pathogenic bacteria is important for the development of more effective antimicrobial agents. We performed a comprehensive identification of essential genes in Mycobacterium tuberculosis, the major causative agent of tuberculosis, using a combination of transposon insertion sequencing (Tn-seq) and comparative genomic analysis. To identify conditionally essential genes by Tn-seq, we used media with different nutrient compositions. Although many conditional gene essentialities were affected by the presence of relevant nutrient sources, we also found that the essentiality of genes in a subset of metabolic pathways was unaffected by metabolite availability. Comparative genomic analysis revealed that not all essential genes identified by Tn-seq were fully conserved within the M. tuberculosis complex, including some existing antitubercular drug target genes. In addition, we utilized an available M. tuberculosis genome-scale metabolic model, iSM810, to predict M. tuberculosis gene essentiality in silico Comparing the sets of essential genes experimentally identified by Tn-seq to those predicted in silico reveals the capabilities and limitations of gene essentiality predictions, highlighting the complexity of M. tuberculosis essential metabolic functions. This study provides a promising platform to study essential cellular functions in M. tuberculosis IMPORTANCE Mycobacterium tuberculosis causes 10 million cases of tuberculosis (TB), resulting in over 1 million deaths each year. TB therapy is challenging because it requires a minimum of 6 months of treatment with multiple drugs. Protracted treatment times and the emergent spread of drug-resistant M. tuberculosis necessitate the identification of novel targets for drug discovery to curb this global health threat. Essential functions, defined as those indispensable for growth and/or survival, are potential targets for new antimicrobial drugs. In this study, we aimed to define gene essentialities of M. tuberculosis on a genomewide scale to comprehensively identify potential targets for drug discovery. We utilized a combination of experimental (functional genomics) and in silico approaches (comparative genomics and flux balance analysis). Our functional genomics approach identified sets of genes whose essentiality was affected by nutrient availability. Comparative genomics revealed that not all essential genes were fully conserved within the M. tuberculosis complex. Comparing sets of essential genes identified by functional genomics to those predicted by flux balance analysis highlighted gaps in current knowledge regarding M. tuberculosis metabolic capabilities. Thus, our study identifies numerous potential antitubercular drug targets and provides a comprehensive picture of the complexity of M. tuberculosis essential cellular functions.
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Affiliation(s)
- Yusuke Minato
- Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, Minnesota, USA
| | - Daryl M Gohl
- University of Minnesota Genomics Center, Minneapolis, Minnesota, USA
| | - Joshua M Thiede
- Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, Minnesota, USA
| | - Jeremy M Chacón
- Biotechnology Institute and Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota, USA
| | - William R Harcombe
- Biotechnology Institute and Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota, USA
| | - Fumito Maruyama
- Department of Microbiology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- The Japan Science and Technology Agency/Japan International Cooperation Agency, Science and Technology Research Partnership for Sustainable Development (JST/JICA, SATREPS), Tokyo, Japan
- Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco, Chile
| | - Anthony D Baughn
- Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, Minnesota, USA
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Komatsu T, Ohya K, Sawai K, Odoi JO, Otsu K, Ota A, Ito T, Kawai M, Maruyama F. Draft genome sequences of Mycolicibacterium peregrinum isolated from a pig with lymphadenitis and from soil on the same Japanese pig farm. BMC Res Notes 2019; 12:341. [PMID: 31208450 PMCID: PMC6580614 DOI: 10.1186/s13104-019-4380-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 06/11/2019] [Indexed: 01/31/2023] Open
Abstract
Objectives Mycolicibacterium peregrinum, a rapidly growing mycobacterial species, can opportunistically infect humans and other animals. Although M. peregrinum infections in animals have been reported, the infection sources are unknown, as is information on its virulence and drug resistant genes, which limits our current understanding of this bacterium. To address this knowledge gap, we obtained draft genome sequences for two M. peregrinum isolates; one from a case of pig lymphadenitis and one from the pig farm’s soil. Data description We report here the draft genome sequences of M. peregrinum isolates 131_1 and 138 (6,451,733-bp and 6,479,047-bp). They were isolated from a pig with mesenteric lymph node lymphadenitis and from soil on the Japanese farm where the pig was reared. A sequence alignment identity score of 100% was obtained by in silico DNA–DNA hybridization of the two isolates, while 98.28% (isolate 131_1) and 98.27% (isolate 138) scores were recorded for hybridization with a human isolate. Both isolates carry arr-1, AAC(2′)-Ib, RbpA, mtrA and tap drug-resistance genes. Isolates 131_1 and 138 carry 234 and 236 putative virulence genes, respectively. Therefore, environment M. peregrinum is potentially drug resistant and can cause swine lymphadenitis. Our data provides valuable new information for future studies on nontuberculous mycobacteria.
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Affiliation(s)
- Tetsuya Komatsu
- Aichi Prefectural Chuo Livestock Hygiene Service Center, 1-306 Jizouno, Miaicho, Okazaki, 4440805, Japan
| | - Kenji Ohya
- Laboratory of Veterinary Microbiology, Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu, 5011193, Japan.,United Graduate School of Veterinary Sciences, Gifu University, 1-1 Yanagido, Gifu, 5011193, Japan.,Education and Research Center for Food Animal Health, Gifu University (GeFAH), 1-1 Yanagido, Gifu, 5011193, Japan.,Division of Microbiology, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki, 210-9501, Japan
| | - Kotaro Sawai
- Laboratory of Veterinary Microbiology, Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu, 5011193, Japan.,Viral Disease and Epidemiology Research Division, National Institute of Animal Health, National Agriculture Research Organization, 3-1-5 Kannondai, Tsukuba, Ibaraki, 3050856, Japan
| | - Justice Opare Odoi
- United Graduate School of Veterinary Sciences, Gifu University, 1-1 Yanagido, Gifu, 5011193, Japan
| | - Keiko Otsu
- Gifu Prefectural Chuo Livestock Hygiene Service Center, 1-1 Yanagido, Gifu, 5011112, Japan
| | - Atsushi Ota
- Data Science Center, Division of Biological Science, Nara Institute of Science and Technology, Ikoma, Nara, 6300192, Japan
| | - Toshihiro Ito
- Department of Microbiology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 6068501, Japan.,Laboratory of Proteome Research, Proteome Research Center, National Institute of Biomedical Innovation, Ibaraki, Osaka, 567-0085, Japan
| | - Mikihiko Kawai
- Department of Microbiology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 6068501, Japan
| | - Fumito Maruyama
- Department of Microbiology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 6068501, Japan. .,Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Av. Francisco Salazar 01145, Temuco, 4811230, Chile.
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Arikawa K, Ichijo T, Nakajima S, Nishiuchi Y, Yano H, Tamaru A, Yoshida S, Maruyama F, Ota A, Nasu M, Starkova DA, Mokrousov I, Narvskaya OV, Iwamoto T. Genetic relatedness of Mycobacterium avium subsp. hominissuis isolates from bathrooms of healthy volunteers, rivers, and soils in Japan with human clinical isolates from different geographical areas. Infect Genet Evol 2019; 74:103923. [PMID: 31207401 DOI: 10.1016/j.meegid.2019.103923] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Revised: 06/05/2019] [Accepted: 06/13/2019] [Indexed: 12/20/2022]
Abstract
Japan reportedly has high incidence rate of nontuberculous mycobacterial lung disease (14.7 cases per 100,000 person in 2014). In Japan, the most common etiology is Mycobacterium avium subsp. hominissuis (MAH). MAH is a typical inhabitant of the environment, especially bathrooms, which are considered as a potential source of infection. To corroborate this hypothesis, we determined the detection rate of MAH in bathrooms of healthy volunteers by an ordinary culture method and we analyzed the genetic relatedness of these isolates with those from patients and other sources. We collected swabs of bathtub inlets, showerheads, bathroom drains, and shower water from 180 residences throughout Japan. The overall MAH detection rate was 16.1%, but the rate varied among regions: it was high in Kanto (9/34, 26.5%) and Kinki (9/33, 27.3%), but low in Kyushu (0/11, 0%), Tohoku (1/23, 4.3%), and Hokkaido (2/23, 8.7%). MAH was detected primarily in bathtub inlet samples (25 out of 170 residences). Variable numbers of tandem repeats (VNTR) analysis was used to examine the genetic relatedness of 57 MAH isolates from bathrooms of the healthy volunteers with human clinical isolates. A minimum spanning tree generated on the basis of the VNTR data indicated that isolates from the bathrooms of the healthy volunteers had a high degree of genetic relatedness with those from Japanese patients, bathrooms of patients, and river water, but not with those from Russian patients and Japanese pigs. These results showed that bathtub inlets in Japan provide an environmental niche for MAH and suggest that bathrooms are one of the important infection sources of MAH in Japan. Understanding country-specific lifestyle habits, such as bathing in Japan, as well as the genetic diversity of MAH, will help in elucidating the sources of this pathogen.
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Affiliation(s)
- Kentaro Arikawa
- Department of Infectious Diseases, Kobe Institute of Health, Kobe, Japan
| | - Tomoaki Ichijo
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, Japan
| | - Satomi Nakajima
- Department of Infectious Diseases, Kobe Institute of Health, Kobe, Japan
| | - Yukiko Nishiuchi
- Toneyama Institute for Tuberculosis Research, Osaka City University Medical School, Osaka, Japan
| | - Hirokazu Yano
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Aki Tamaru
- Bacteriology Section, Division of Microbiology, Osaka Institute of Public Health, Osaka, Japan
| | - Shiomi Yoshida
- Clinical Research Center, National Hospital Organization, Kinki-Chuo Chest Medical Center, Osaka, Japan
| | - Fumito Maruyama
- Department of Microbiology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Atsushi Ota
- Toneyama Institute for Tuberculosis Research, Osaka City University Medical School, Osaka, Japan; Department of Microbiology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Masao Nasu
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, Japan; Graduate School of Pharmaceutical Sciences, Osaka Ohtani University, Osaka, Japan
| | | | - Igor Mokrousov
- St. Petersburg Pasteur Institute, St. Petersburg, Russia
| | | | - Tomotada Iwamoto
- Department of Infectious Diseases, Kobe Institute of Health, Kobe, Japan.
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Sari NIP, Mertaniasih NM, Soedarsono, Maruyama F. Application of serial tests for Mycobacterium tuberculosis detection to active lung tuberculosis cases in Indonesia. BMC Res Notes 2019; 12:313. [PMID: 31159846 PMCID: PMC6547566 DOI: 10.1186/s13104-019-4350-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 05/29/2019] [Indexed: 11/13/2022] Open
Abstract
Objective Rapid detection and accurate diagnosis are very important in managing active tuberculosis because they provide an advantage in preventing further disease transmission. In accordance with the recommendation of the World Health Organization, the Indonesian Tuberculosis Control Program uses the acid fast bacilli (AFB) smear and Chest X-ray methods as the primary methods for detecting tuberculosis, especially in new cases of suspected tuberculosis. The genus Mycobacterium has many species, strains, and variants, and their natural differences may affect the clinical outcome of the diseases they induce. The purpose of this study was to assess different tuberculosis detection methods as part of serial tests and determine the best diagnostic approach for detecting active lung tuberculosis in Indonesia. Results This study used clinical samples from tuberculosis patients and assessed them using a series of tests, aiming to increase the sensitivity of active tuberculosis detection. Some samples that yielded negative results in the AFB smear test were detected as positive for Mycobacterium tuberculosis using the nucleic acid amplification test, with a sensitivity of 83.1%. Additionally, nucleic acid amplification also detected positive results among samples assessed as M. tuberculosis-negative using the culture method, this method yielded the same results as the Gene Xpert test.
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Affiliation(s)
- Nastiti Intan Permata Sari
- Doctoral Program of Medical Science, Faculty of Medicine, Universitas Airlangga, Jl. Mayjen. Prof. Dr. Moestopo No. 47, Surabaya, 60131, Indonesia. .,Laboratory of Tuberculosis, Institute of Tropical Disease, Universitas Airlangga, Kampus C, Jl. Mulyorejo, Surabaya, 60115, Indonesia.
| | - Ni Made Mertaniasih
- Department of Clinical Microbiology, Faculty of Medicine, Universitas Airlangga, Jl. Mayjen. Prof. Dr. Moestopo No. 47, Surabaya, 60131, Indonesia. .,Laboratory of Tuberculosis, Institute of Tropical Disease, Universitas Airlangga, Kampus C, Jl. Mulyorejo, Surabaya, 60115, Indonesia.
| | - Soedarsono
- Department of Pulmonology and Respiratory Medicine, Faculty of Medicine, Universitas Airlangga, Jl. Mayjen. Prof. Dr. Moestopo No. 47, Surabaya, 60131, Indonesia
| | - Fumito Maruyama
- Department of Microbiology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
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36
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Núñez-Montero K, Lamilla C, Abanto M, Maruyama F, Jorquera MA, Santos A, Martinez-Urtaza J, Barrientos L. Antarctic Streptomyces fildesensis So13.3 strain as a promising source for antimicrobials discovery. Sci Rep 2019; 9:7488. [PMID: 31097761 PMCID: PMC6522549 DOI: 10.1038/s41598-019-43960-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 05/01/2019] [Indexed: 12/29/2022] Open
Abstract
Antarctic have been suggested as an attractive source for antibiotics discovery and members of Streptomyces genus have historically been studied as natural producers of antimicrobial metabolites. Nonetheless, our knowledge on antibiotic-producing Streptomyces from Antarctic is very limited. In this study, the antimicrobial activity of organic extracts from Antarctic Streptomyces strains was evaluated by disk diffusion assays and minimum inhibitory concentration. The strain Streptomyces sp. So13.3 showed the greatest antibiotic activity (MIC = 15.6 μg/mL) against Gram-positive bacteria and growth reduction of Gram‒negative pathogens. The bioactive fraction in the crude extract was revealed by TLC‒bioautography at Rf = 0.78 with molecular weight between 148 and 624 m/z detected by LC-ESI-MS/MS. The strain So13.3 was taxonomically affiliated as Streptomyces fildesensis. Whole genome sequencing and analysis suggested a 9.47 Mb genome size with 42 predicted biosynthetic gene clusters (BGCs) and 56 putative clusters representing a 22% of total genome content. Interestingly, a large number of them (11 of 42 BGCs and 40 of 56 putative BGCs), did not show similarities with other known BGCs. Our results highlight the potential of the Antarctic Streptomyces strains as a promising source of novel antimicrobials, particularly the strain Streptomyces fildesensis So13.3, which first draft genome is reported in this work.
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Affiliation(s)
- Kattia Núñez-Montero
- Laboratorio de Biología Molecular Aplicada, Centro de Excelencia en Medicina Traslacional, Universidad de La Frontera, Temuco, Chile.,Núcleo Científico y Tecnológico en Biorecursos (BIOREN), Universidad de La Frontera, Temuco, Chile.,Centro de Investigación en Biotecnología, Escuela de Biología, Instituto Tecnológico de Costa Rica, Cartago, Costa Rica
| | - Claudio Lamilla
- Laboratorio de Biología Molecular Aplicada, Centro de Excelencia en Medicina Traslacional, Universidad de La Frontera, Temuco, Chile.,Núcleo Científico y Tecnológico en Biorecursos (BIOREN), Universidad de La Frontera, Temuco, Chile
| | - Michel Abanto
- Núcleo Científico y Tecnológico en Biorecursos (BIOREN), Universidad de La Frontera, Temuco, Chile
| | - Fumito Maruyama
- Núcleo Científico y Tecnológico en Biorecursos (BIOREN), Universidad de La Frontera, Temuco, Chile.,Department of Microbiology, Graduate School of Medicine, Kyoto University, Yoshida‒Konoe‒cho, Sakyo‒ku, Kyoto, Japan
| | - Milko A Jorquera
- Núcleo Científico y Tecnológico en Biorecursos (BIOREN), Universidad de La Frontera, Temuco, Chile.,Laboratorio de Ecología Microbiana Aplicada, Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Temuco, Chile
| | - Andrés Santos
- Laboratorio de Biología Molecular Aplicada, Centro de Excelencia en Medicina Traslacional, Universidad de La Frontera, Temuco, Chile.,Núcleo Científico y Tecnológico en Biorecursos (BIOREN), Universidad de La Frontera, Temuco, Chile.,Centre for Environment, Fisheries and Aquaculture Science (CEFAS), Barrack Road, Weymouth, Dorset, DT4 8UB, UK
| | - Jaime Martinez-Urtaza
- Centre for Environment, Fisheries and Aquaculture Science (CEFAS), Barrack Road, Weymouth, Dorset, DT4 8UB, UK
| | - Leticia Barrientos
- Laboratorio de Biología Molecular Aplicada, Centro de Excelencia en Medicina Traslacional, Universidad de La Frontera, Temuco, Chile. .,Núcleo Científico y Tecnológico en Biorecursos (BIOREN), Universidad de La Frontera, Temuco, Chile.
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37
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Tanaka D, Sato K, Goto M, Fujiyoshi S, Maruyama F, Takato S, Shimada T, Sakatoku A, Aoki K, Nakamura S. Airborne Microbial Communities at High-Altitude and Suburban Sites in Toyama, Japan Suggest a New Perspective for Bioprospecting. Front Bioeng Biotechnol 2019; 7:12. [PMID: 30805335 PMCID: PMC6370616 DOI: 10.3389/fbioe.2019.00012] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 01/17/2019] [Indexed: 01/18/2023] Open
Abstract
Airborne microorganisms, especially those at high altitude, are exposed to hostile conditions, including ultraviolet (UV) radiation, desiccation, and low temperatures. This study was conducted to compare the composition and abundance of airborne microorganisms at a high-altitude site, Mt. Jodo [2,839 m above mean sea level (AMSL)] and a suburban site (23 m AMSL) in Toyama, Japan. To our knowledge, this is the first study to investigate microbial communities in air samples collected simultaneously at two sites in relatively close proximity, from low and high altitude. Air samples were collected over a period of 3 years during 2009-2011. We then examined the bacterial and eukaryotic communities and estimated the abundance of bacteria and fungi with real-time TaqMan PCR. The airborne bacterial and eukaryotic communities differed between high-altitude and suburban sites on each sampling day. Backward trajectory analysis of air masses that arrived at high-altitude and suburban sites on each sampling day displayed almost the same paths. The bacterial communities were dominated by Actinobacteria, Firmicutes, and Proteobacteria, while the eukaryotic communities included Ascomycota, Basidiomycota, and Streptophyta. We also predicted some application of such microbial communities. The airborne bacterial and fungal abundance at the high-altitude site was about two times lower than that at the suburban site. These results showed that each airborne microbial communities have locality even if they are collected close location.
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Affiliation(s)
- Daisuke Tanaka
- Graduate School of Science and Engineering, University of Toyama, Toyama, Japan
| | - Kei Sato
- Graduate School of Science and Engineering, University of Toyama, Toyama, Japan
| | - Motoshi Goto
- Graduate School of Science and Engineering, University of Toyama, Toyama, Japan
| | - So Fujiyoshi
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan
- JST/JICA, Science and Technology Research Partnership for Sustainable Development Program, Tokyo, Japan
| | - Fumito Maruyama
- JST/JICA, Science and Technology Research Partnership for Sustainable Development Program, Tokyo, Japan
- Department of Microbiology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Shunsuke Takato
- Graduate School of Science and Engineering, University of Toyama, Toyama, Japan
| | - Takamune Shimada
- Graduate School of Science and Engineering, University of Toyama, Toyama, Japan
| | - Akihiro Sakatoku
- Graduate School of Science and Engineering, University of Toyama, Toyama, Japan
| | - Kazuma Aoki
- Graduate School of Science and Engineering, University of Toyama, Toyama, Japan
| | - Shogo Nakamura
- Graduate School of Science and Engineering, University of Toyama, Toyama, Japan
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38
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Okubo T, Yossapol M, Maruyama F, Wampande EM, Kakooza S, Ohya K, Tsuchida S, Asai T, Kabasa JD, Ushida K. Phenotypic and genotypic analyses of antimicrobial resistant bacteria in livestock in Uganda. Transbound Emerg Dis 2018; 66:317-326. [PMID: 30260584 DOI: 10.1111/tbed.13024] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 09/03/2018] [Accepted: 09/13/2018] [Indexed: 12/11/2022]
Abstract
Antimicrobial resistant bacteria (ARB) in livestock are a global public health concern, not only because they prolong infectious diseases but also they can be transferred from animals to humans via the food chain. Here, we studied ARB in livestock at commercial and subsistence farms (n = 13) in Wakiso and Mpigi districts, Uganda. We enquired from the farmers about the type and the purpose of antimicrobial agents they have used to treat their livestock. After collecting faeces, we isolated antimicrobial resistant Escherichia coli from livestock faeces (n = 134) as an indicator bacterium. These strains showed resistance to ampicillin (44.8%), tetracycline (97.0%), and sulfamethoxazole-trimethoprim (56.7%). The frequency of ampicillin-resistance was significantly correlated with the usage of penicillins to livestock in the farms (p = 0.04). The metagenomics data detected 911 antimicrobial resistant genes that were classified into 16 categories. Genes for multidrug efflux pumps were the most prevalent category in all except in one sample. Interestingly, the genes encoding third-generation cephalosporins (blaCTX-M ), carbapenems (blaACT ), and colistin (arnA) were detected by metagenomics analysis although these phenotypes were not detected in our E. coli strains. Our results suggest that the emergence and transmission of cephalosporin, carbapenem, and/or colistin-resistant bacteria among livestock can occur in future if these antimicrobial agents are used.
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Affiliation(s)
- Torahiko Okubo
- Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University Graduate School of Health Sciences, Sapporo, Hokkaido, Japan
| | - Montira Yossapol
- Department of Applied Veterinary Sciences, United Graduate School of Veterinary Sciences, Gifu University, Gifu, Japan.,Office of Academic Affairs, Faculty of Veterinary Sciences, Mahasarakham University, Maha Sarakham, Thailand
| | - Fumito Maruyama
- Department of Microbiology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Eddie M Wampande
- Department of Veterinary Pharmacy, Clinics and Comparative Medicine, School of Veterinary Medicine and Animal Resources, College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda.,Central Diagnostic Laboratory, College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Steven Kakooza
- Central Diagnostic Laboratory, College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Kenji Ohya
- Department of Applied Veterinary Sciences, United Graduate School of Veterinary Sciences, Gifu University, Gifu, Japan.,Education and Research Center for Food Animal Health, Gifu University (GeFAH), Gifu, Japan
| | - Sayaka Tsuchida
- Graduate School of Life and Environmental Science, Kyoto Prefectural University, Kyoto, Japan
| | - Tetsuo Asai
- Department of Applied Veterinary Sciences, United Graduate School of Veterinary Sciences, Gifu University, Gifu, Japan.,Education and Research Center for Food Animal Health, Gifu University (GeFAH), Gifu, Japan
| | - John D Kabasa
- Department of Pharmacy, Clinical and Comparative Medicine, School of Veterinary Medicine and Animal Resources, Makerere University, Kampala, Uganda
| | - Kazunari Ushida
- Graduate School of Life and Environmental Science, Kyoto Prefectural University, Kyoto, Japan.,Chubu University Academy of Emerging Sciences, Kasugai, Aichi, Japan
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39
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Arai S, Kim H, Watanabe T, Tohya M, Suzuki E, Ishida-Kuroki K, Maruyama F, Murase K, Nakagawa I, Sekizaki T. Assessment of pig saliva as aStreptococcus suisreservoir and potential source of infection on farms by use of a novel quantitative polymerase chain reaction assay. Am J Vet Res 2018; 79:941-948. [DOI: 10.2460/ajvr.79.9.941] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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40
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Nonaka L, Yamamoto T, Maruyama F, Hirose Y, Onishi Y, Kobayashi T, Suzuki S, Nomura N, Masuda M, Yano H. Interplay of a non-conjugative integrative element and a conjugative plasmid in the spread of antibiotic resistance via suicidal plasmid transfer from an aquaculture Vibrio isolate. PLoS One 2018; 13:e0198613. [PMID: 29879198 PMCID: PMC5991714 DOI: 10.1371/journal.pone.0198613] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 05/22/2018] [Indexed: 12/01/2022] Open
Abstract
The capture of antimicrobial resistance genes (ARGs) by mobile genetic elements (MGEs) plays a critical role in resistance acquisition for human-associated bacteria. Although aquaculture environments are recognized as important reservoirs of ARGs, intra- and intercellular mobility of MGEs discovered in marine organisms is poorly characterized. Here, we show a new pattern of interspecies ARGs transfer involving a 'non-conjugative' integrative element. To identify active MGEs in a Vibrio ponticus isolate, we conducted whole-genome sequencing of a transconjugant obtained by mating between Escherichia coli and Vibrio ponticus. This revealed integration of a plasmid (designated pSEA1) into the chromosome, consisting of a self-transmissible plasmid backbone of the MOBH group, ARGs, and a 13.8-kb integrative element Tn6283. Molecular genetics analysis suggested a two-step gene transfer model. First, Tn6283 integrates into the recipient chromosome during suicidal plasmid transfer, followed by homologous recombination between the Tn6283 copy in the chromosome and that in the newly transferred pSEA1. Tn6283 is unusual among integrative elements in that it apparently does not encode transfer function and its excision barely generates unoccupied donor sites. Thus, its movement is analogous to the transposition of insertion sequences rather than to that of canonical integrative and conjugative elements. Overall, this study reveals the presence of a previously unrecognized type of MGE in a marine organism, highlighting diversity in the mode of interspecies gene transfer.
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Affiliation(s)
- Lisa Nonaka
- Department of Microbiology, Dokkyo Medical University School of Medicine, Mibu, Tochigi, Japan
| | - Tatsuya Yamamoto
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tennodai, Tsukuba, Japan
| | | | - Yuu Hirose
- Department of Environmental and Life Sciences, Toyohashi University of Technology, Tempaku, Toyohashi, Aichi, Japan
| | - Yuki Onishi
- Center for Marine Environmental Studies, Ehime University, Matsuyama, Ehime, Japan
| | | | - Satoru Suzuki
- Center for Marine Environmental Studies, Ehime University, Matsuyama, Ehime, Japan
| | - Nobuhiko Nomura
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tennodai, Tsukuba, Japan
| | - Michiaki Masuda
- Department of Microbiology, Dokkyo Medical University School of Medicine, Mibu, Tochigi, Japan
| | - Hirokazu Yano
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tennodai, Tsukuba, Japan
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41
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Yano H, Iwamoto T, Nishiuchi Y, Nakajima C, Starkova DA, Mokrousov I, Narvskaya O, Yoshida S, Arikawa K, Nakanishi N, Osaki K, Nakagawa I, Ato M, Suzuki Y, Maruyama F. Population Structure and Local Adaptation of MAC Lung Disease Agent Mycobacterium avium subsp. hominissuis. Genome Biol Evol 2018; 9:2403-2417. [PMID: 28957464 PMCID: PMC5622343 DOI: 10.1093/gbe/evx183] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/08/2017] [Indexed: 12/11/2022] Open
Abstract
Mycobacterium avium subsp. hominissuis (MAH) is one of the most common nontuberculous mycobacterial species responsible for chronic lung disease in humans. Despite increasing worldwide incidence, little is known about the genetic mechanisms behind the population evolution of MAH. To elucidate the local adaptation mechanisms of MAH, we assessed genetic population structure, the mutual homologous recombination, and gene content for 36 global MAH isolates, including 12 Japanese isolates sequenced in the present study. We identified five major MAH lineages and found that extensive mutual homologous recombination occurs among them. Two lineages (MahEastAsia1 and MahEastAsia2) were predominant in the Japanese isolates. We identified alleles unique to these two East Asian lineages in the loci responsible for trehalose biosynthesis (treS and mak) and in one mammalian cell entry operon, which presumably originated from as yet undiscovered mycobacterial lineages. Several genes and alleles unique to East Asian strains were located in the fragments introduced via recombination between East Asian lineages, suggesting implication of recombination in local adaptation. These patterns of MAH genomes are consistent with the signature of distribution conjugative transfer, a mode of sexual reproduction reported for other mycobacterial species.
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Affiliation(s)
- Hirokazu Yano
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan.,Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Tomotada Iwamoto
- Department of Infectious Diseases, Kobe Institute of Health, Kobe, Japan
| | - Yukiko Nishiuchi
- Toneyama Institute for Tuberculosis Research, Osaka City University Medical School, Osaka, Japan
| | - Chie Nakajima
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan.,The Global Station for Zoonosis Control, Hokkaido University Global Institution for Collaborative Research and Education, Sapporo, Japan
| | | | - Igor Mokrousov
- St. Petersburg Pasteur Institute, St. Petersburg, Russia
| | - Olga Narvskaya
- St. Petersburg Pasteur Institute, St. Petersburg, Russia
| | - Shiomi Yoshida
- Clinical Research Center, National Hospital Organization, Kinki-Chuo Chest Medical Center, Osaka, Japan
| | - Kentaro Arikawa
- Department of Infectious Diseases, Kobe Institute of Health, Kobe, Japan
| | - Noriko Nakanishi
- Department of Infectious Diseases, Kobe Institute of Health, Kobe, Japan
| | - Ken Osaki
- TOMY Digital Biology Co. Ltd, Taito-Ku, Tokyo, Japan
| | - Ichiro Nakagawa
- Department of Microbiology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Manabu Ato
- Department of Immunology, National Institute of Infectious Diseases, Shinjuku-Ku, Tokyo, Japan
| | - Yasuhiko Suzuki
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan.,The Global Station for Zoonosis Control, Hokkaido University Global Institution for Collaborative Research and Education, Sapporo, Japan
| | - Fumito Maruyama
- Department of Microbiology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
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Cid FP, Maruyama F, Murase K, Graether SP, Larama G, Bravo LA, Jorquera MA. Draft genome sequences of bacteria isolated from the Deschampsia antarctica phyllosphere. Extremophiles 2018; 22:537-552. [PMID: 29492666 DOI: 10.1007/s00792-018-1015-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 02/18/2018] [Indexed: 11/28/2022]
Abstract
Genome analyses are being used to characterize plant growth-promoting (PGP) bacteria living in different plant compartiments. In this context, we have recently isolated bacteria from the phyllosphere of an Antarctic plant (Deschampsia antarctica) showing ice recrystallization inhibition (IRI), an activity related to the presence of antifreeze proteins (AFPs). In this study, the draft genomes of six phyllospheric bacteria showing IRI activity were sequenced and annotated according to their functional gene categories. Genome sizes ranged from 5.6 to 6.3 Mbp, and based on sequence analysis of the 16S rRNA genes, five strains were identified as Pseudomonas and one as Janthinobacterium. Interestingly, most strains showed genes associated with PGP traits, such as nutrient uptake (ammonia assimilation, nitrogen fixing, phosphatases, and organic acid production), bioactive metabolites (indole acetic acid and 1-aminocyclopropane-1-carboxylate deaminase), and antimicrobial compounds (hydrogen cyanide and pyoverdine). In relation with IRI activity, a search of putative AFPs using current bioinformatic tools was also carried out. Despite that genes associated with reported AFPs were not found in these genomes, genes connected to ice-nucleation proteins (InaA) were found in all Pseudomonas strains, but not in the Janthinobacterium strain.
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Affiliation(s)
- Fernanda P Cid
- Programa de Doctorado en Ciencias de Recursos Naturales, Universidad de La Frontera, Temuco, Chile
- Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco, Chile
- Applied Microbial Ecology Laboratory, Departamento de Ciencias Químicas y Recursos Naturales, Facultad de Ingeniería y Ciencias, Universidad de La Frontera, Avenida Francisco Salazar 01145, Temuco, Chile
| | - Fumito Maruyama
- Department of Microbiology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- The Japan Science and Technology Agency/Japan International Cooperation Agency, Science and Technology Research Partnership for Sustainable Development (JST/JICA, SATREPS), Tokyo, Japan
| | - Kazunori Murase
- Department of Microbiology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Steffen P Graether
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - Giovanni Larama
- Department of Mathematical Engineering, Universidad de La Frontera, Temuco, Chile
| | - Leon A Bravo
- Departamento de Ciencias Agronómicas y Recursos Naturales, Facultad de Ciencias Agropecuarias y Forestales, Universidad de la Frontera, Temuco, Chile
- Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco, Chile
| | - Milko A Jorquera
- Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco, Chile.
- Applied Microbial Ecology Laboratory, Departamento de Ciencias Químicas y Recursos Naturales, Facultad de Ingeniería y Ciencias, Universidad de La Frontera, Avenida Francisco Salazar 01145, Temuco, Chile.
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43
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Fujiyoshi S, Tanaka D, Maruyama F. Transmission of Airborne Bacteria across Built Environments and Its Measurement Standards: A Review. Front Microbiol 2017; 8:2336. [PMID: 29238327 PMCID: PMC5712571 DOI: 10.3389/fmicb.2017.02336] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 11/13/2017] [Indexed: 11/13/2022] Open
Abstract
Human health is influenced by various factors including microorganisms present in built environments where people spend most of their lives (approximately 90%). It is therefore necessary to monitor and control indoor airborne microbes for occupational safety and public health. Most studies concerning airborne microorganisms have focused on fungi, with scant data available concerning bacteria. The present review considers papers published from 2010 to 2017 approximately and factors affecting properties of indoor airborne bacteria (communities and concentration) with respect to temporal perspective and to multiscale interaction viewpoint. From a temporal perspective, bacterial concentrations in built environments change depending on numbers of human occupancy, while properties of bacterial communities tend to remain stable. Similarly, the bacteria found in social and community spaces such as offices, classrooms and hospitals are mainly associated with human occupancy. Other major sources of indoor airborne bacteria are (i) outdoor environments, and (ii) the building materials themselves. Indoor bacterial communities and concentrations are varied with varying interferences by outdoor environment. Airborne bacteria from the outdoor environment enter an indoor space through open doors and windows, while indoor bacteria are simultaneously released to the outer environment. Outdoor bacterial communities and their concentrations are also affected by geographical factors such as types of land use and their spatial distribution. The bacteria found in built environments therefore originate from any of the natural and man-made surroundings around humans. Therefore, to better understand the factors influencing bacterial concentrations and communities in built environments, we should study all the environments that humans contact as a single ecosystem. In this review, we propose the establishment of a standard procedure for assessing properties of indoor airborne bacteria using four factors: temperature, relative humidity (RH), air exchange rate, and occupant density, as a minimum requirement. We also summarize the relevant legislation by country. Choice of factors to measure remain controversial are discussed.
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Affiliation(s)
- So Fujiyoshi
- Department of Microbiology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Daisuke Tanaka
- Graduate School of Science and Engineering, University of Toyama, Toyama, Japan
| | - Fumito Maruyama
- Department of Microbiology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- JST/JICA, Science and Technology Research Partnership for Sustainable Development Program (SATREPS), Tokyo, Japan
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44
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Watanabe T, Shibasaki M, Maruyama F, Sekizaki T, Nakagawa I. Investigation of potential targets of Porphyromonas CRISPRs among the genomes of Porphyromonas species. PLoS One 2017; 12:e0183752. [PMID: 28837670 PMCID: PMC5570325 DOI: 10.1371/journal.pone.0183752] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 08/10/2017] [Indexed: 12/13/2022] Open
Abstract
The oral bacterial species Porphyromonas gingivalis, a periodontal pathogen, has plastic genomes that may be driven by homologous recombination with exogenous deoxyribonucleic acid (DNA) that is incorporated by natural transformation and conjugation. However, bacteriophages and plasmids, both of which are main resources of exogenous DNA, do not exist in the known P. gingivalis genomes. This could be associated with an adaptive immunity system conferred by clustered regularly interspaced short palindromic repeat (CRISPR) and CRISPR-associated (cas) genes in P. gingivalis as well as innate immune systems such as a restriction-modification system. In a previous study, few immune targets were predicted for P. gingivalis CRISPR/Cas. In this paper, we analyzed 51 P. gingivalis genomes, which were newly sequenced, and publicly available genomes of 13 P. gingivalis and 46 other Porphyromonas species. We detected 6 CRISPR/Cas types (classified by sequence similarity of repeat) in P. gingivalis and 12 other types in the remaining species. The Porphyromonas CRISPR spacers with potential targets in the genus Porphyromonas were approximately 23 times more abundant than those with potential targets in other genus taxa (1,720/6,896 spacers vs. 74/6,896 spacers). Porphyromonas CRISPR/Cas may be involved in genome plasticity by exhibiting selective interference against intra- and interspecies nucleic acids.
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Affiliation(s)
- Takayasu Watanabe
- Laboratory of Food-borne Pathogenic Microbiology, Research Center for Food Safety, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, Japan
- * E-mail:
| | - Masaki Shibasaki
- Department of Oral Implantology and Regenerative Dental Medicine, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, Japan
| | - Fumito Maruyama
- Department of Microbiology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, Japan
| | - Tsutomu Sekizaki
- Laboratory of Food-borne Pathogenic Microbiology, Research Center for Food Safety, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, Japan
| | - Ichiro Nakagawa
- Department of Microbiology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, Japan
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45
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Tsuchida S, Maruyama F, Ogura Y, Toyoda A, Hayashi T, Okuma M, Ushida K. Genomic Characteristics of Bifidobacterium thermacidophilum Pig Isolates and Wild Boar Isolates Reveal the Unique Presence of a Putative Mobile Genetic Element with tetW for Pig Farm Isolates. Front Microbiol 2017; 8:1540. [PMID: 28861055 PMCID: PMC5561799 DOI: 10.3389/fmicb.2017.01540] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 07/31/2017] [Indexed: 01/16/2023] Open
Abstract
Genomic analysis was performed on seven strains of Bifidobacterium thermacidophilum, a Sus-associated Bifidobacterium. Three strains from the feces of domestic pigs (Sus scrofa domesticus) and four strains from the rectal feces of free-range Japanese wild boars (S. s. scrofa) were compared. The phylogenetic position of these isolates suggested by genomic analyses were not concordant with that suggested by 16S rRNA sequence. There was biased distribution of genes for virulence, phage, metabolism of aromatic compounds, iron acquisition, cell division, and DNA metabolism. In particular four wild boar isolates harbored fiber-degrading enzymes, such as endoglucanase, while two of the pig isolates obtained from those grown under an intensive feeding practice with routine use of antimicrobials, particularly tetracycline harbored a tetracycline resistance gene, which was further proved functional by disk diffusion test. The tetW gene is associated with a serine recombinase of an apparently non-bifidobacterial origin. The insertion site of the tetW cassette was precisely defined by analyzing the corresponding genomic regions in the other tetracycline-susceptible isolates. The cassette may have been transferred from some other bacteria in the pig gut.
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Affiliation(s)
- Sayaka Tsuchida
- Laboratory of Animal Science, Graduate School of Life and Environmental Sciences, Kyoto Prefectural UniversityKyoto, Japan
| | - Fumito Maruyama
- Department of Microbiology, Graduate School of Medicine, Kyoto UniversityKyoto, Japan
| | - Yoshitoshi Ogura
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu UniversityFukuoka, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of GeneticsMishima, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu UniversityFukuoka, Japan
| | - Moriya Okuma
- Japan Collection of Microorganisms, RIKEN BioResource CenterTsukuba, Japan
| | - Kazunari Ushida
- Laboratory of Animal Science, Graduate School of Life and Environmental Sciences, Kyoto Prefectural UniversityKyoto, Japan
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46
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Takemura T, Murase K, Maruyama F, Tran TL, Ota A, Nakagawa I, Nguyen DT, Ngo TC, Nguyen TH, Tokizawa A, Morita M, Ohnishi M, Nguyen BM, Yamashiro T. Genetic diversity of environmental Vibrio cholerae O1 strains isolated in Northern Vietnam. Infect Genet Evol 2017. [PMID: 28642158 DOI: 10.1016/j.meegid.2017.06.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Cholera epidemics have been recorded periodically in Vietnam during the seventh cholera pandemic. Since cholera is a water-borne disease, systematic monitoring of environmental waters for Vibrio cholerae presence is important for predicting and preventing cholera epidemics. We conducted monitoring, isolation, and genetic characterization of V. cholerae strains in Nam Dinh province of Northern Vietnam from Jul 2013 to Feb 2015. In this study, four V. cholerae O1 strains were detected and isolated from 110 analyzed water samples (3.6%); however, none of them carried the cholera toxin gene, ctxA, in their genomes. Whole genome sequencing and phylogenetic analysis revealed that the four O1 isolates were separated into two independent clusters, and one of them diverged from a common ancestor with pandemic strains. The analysis of pathogenicity islands (CTX prophage, VPI-I, VPI-II, VSP-I, and VSP-II) indicated that one strain (VNND_2014Jun_6SS) harbored an unknown prophage-like sequence with high homology to vibriophage KSF-1 phi and VCY phi, identified from Bangladesh and the USA, respectively, while the other three strains carried tcpA gene with a distinct sequence demonstrating a separate clonal lineage. These results suggest that the aquatic environment can harbor highly divergent V. cholera strains and serve as a reservoir for multiple V. cholerae virulence-associated genes which may be exchanged via mobile genetic elements. Therefore, continuous monitoring and genetic characterization of V. cholerae strains in the environment should contribute to the early detection of the sources of infection and prevention of cholera outbreaks as well as to understanding the natural ecology and evolution of V. cholerae.
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Affiliation(s)
- Taichiro Takemura
- Vietnam Research Station, Institute of Tropical Medicine, Nagasaki University, Japan
| | - Kazunori Murase
- Section of Microbiology, Graduated School of Medicine, Kyoto University, Japan
| | - Fumito Maruyama
- Section of Microbiology, Graduated School of Medicine, Kyoto University, Japan
| | - Thi Luong Tran
- Vietnam Research Station, Institute of Tropical Medicine, Nagasaki University, Japan
| | - Atsushi Ota
- Section of Microbiology, Graduated School of Medicine, Kyoto University, Japan
| | - Ichiro Nakagawa
- Section of Microbiology, Graduated School of Medicine, Kyoto University, Japan
| | - Dong Tu Nguyen
- Department of Bacteriology, National Institute of Hygiene and Epidemiology, Vietnam
| | - Tu Cuong Ngo
- Department of Bacteriology, National Institute of Hygiene and Epidemiology, Vietnam
| | - Thi Hang Nguyen
- Vietnam Research Station, Institute of Tropical Medicine, Nagasaki University, Japan
| | - Asako Tokizawa
- Vietnam Research Station, Institute of Tropical Medicine, Nagasaki University, Japan
| | - Masatomo Morita
- Department of Bacteriology, National Institute of Infectious Diseases, Japan
| | - Makoto Ohnishi
- Department of Bacteriology, National Institute of Infectious Diseases, Japan
| | - Binh Minh Nguyen
- Department of Bacteriology, National Institute of Hygiene and Epidemiology, Vietnam
| | - Tetsu Yamashiro
- Vietnam Research Station, Institute of Tropical Medicine, Nagasaki University, Japan; Department of Bacteriology, Graduate School of Medicine, University of the Ryukyus, Japan.
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47
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Okura M, Nozawa T, Watanabe T, Murase K, Nakagawa I, Takamatsu D, Osaki M, Sekizaki T, Gottschalk M, Hamada S, Maruyama F. A Locus Encoding Variable Defense Systems against Invading DNA Identified in Streptococcus suis. Genome Biol Evol 2017; 9:1000-1012. [PMID: 28379509 PMCID: PMC5398294 DOI: 10.1093/gbe/evx062] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/03/2017] [Indexed: 12/21/2022] Open
Abstract
Streptococcus suis, an important zoonotic pathogen, is known to have an open pan-genome and to develop a competent state. In S. suis, limited genetic lineages are suggested to be associated with zoonosis. However, little is known about the evolution of diversified lineages and their respective phenotypic or ecological characteristics. In this study, we performed comparative genome analyses of S. suis, with a focus on the competence genes, mobile genetic elements, and genetic elements related to various defense systems against exogenous DNAs (defense elements) that are associated with gene gain/loss/exchange mediated by horizontal DNA movements and their restrictions. Our genome analyses revealed a conserved competence-inducing peptide type (pherotype) of the competence system and large-scale genome rearrangements in certain clusters based on the genome phylogeny of 58 S. suis strains. Moreover, the profiles of the defense elements were similar or identical to each other among the strains belonging to the same genomic clusters. Our findings suggest that these genetic characteristics of each cluster might exert specific effects on the phenotypic or ecological differences between the clusters. We also found certain loci that shift several types of defense elements in S. suis. Of note, one of these loci is a previously unrecognized variable region in bacteria, at which strains of distinct clusters code for different and various defense elements. This locus might represent a novel defense mechanism that has evolved through an arms race between bacteria and invading DNAs, mediated by mobile genetic elements and genetic competence.
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Affiliation(s)
- Masatoshi Okura
- Division of Bacterial and Parasitic Diseases, National Institute of Animal Health, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Takashi Nozawa
- Department of Microbiology, Kyoto University Graduate School of Medicine, Japan
| | - Takayasu Watanabe
- Research Center for Food Safety, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Japan
| | - Kazunori Murase
- Department of Microbiology, Kyoto University Graduate School of Medicine, Japan
| | - Ichiro Nakagawa
- Department of Microbiology, Kyoto University Graduate School of Medicine, Japan
| | - Daisuke Takamatsu
- Division of Bacterial and Parasitic Diseases, National Institute of Animal Health, National Agriculture and Food Research Organization, Tsukuba, Japan.,The United Graduate School of Veterinary Sciences, Gifu University, Japan
| | - Makoto Osaki
- Division of Bacterial and Parasitic Diseases, National Institute of Animal Health, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Tsutomu Sekizaki
- Research Center for Food Safety, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Japan
| | - Marcelo Gottschalk
- Groupe de Recherche sur les Maladies Infectieuses du Porc, Faculté de Médecine Vétérinaire, Université de Montréal, St-Hyacinthe, Quebec, Canada
| | - Shigeyuki Hamada
- Research Institute for Microbial Diseases, Thailand-Japan Collaboration Center for Emerging and Re-emerging Infections, Osaka University, Suita-Osaka, Japan
| | - Fumito Maruyama
- Department of Microbiology, Kyoto University Graduate School of Medicine, Japan
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48
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Nishiuchi Y, Iwamoto T, Maruyama F. Infection Sources of a Common Non-tuberculous Mycobacterial Pathogen, Mycobacterium avium Complex. Front Med (Lausanne) 2017; 4:27. [PMID: 28326308 PMCID: PMC5339636 DOI: 10.3389/fmed.2017.00027] [Citation(s) in RCA: 110] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 02/22/2017] [Indexed: 01/08/2023] Open
Abstract
Numerous studies have revealed a continuous increase in the worldwide incidence and prevalence of non-tuberculous mycobacteria (NTM) diseases, especially pulmonary Mycobacterium avium complex (MAC) diseases. Although it is not clear why NTM diseases have been increasing, one possibility is an increase of mycobacterial infection sources in the environment. Thus, in this review, we focused on the infection sources of pathogenic NTM, especially MAC. The environmental niches for MAC include water, soil, and dust. The formation of aerosols containing NTM arising from shower water, soil, and pool water implies that these niches can be infection sources. Furthermore, genotyping has shown that clinical isolates are identical to environmental ones from household tap water, bathrooms, potting soil, and garden soil. Therefore, to prevent and treat MAC diseases, it is essential to identify the infection sources for these organisms, because patients with these diseases often suffer from reinfections and recurrent infections with them. In the environmental sources, MAC and other NTM organisms can form biofilms, survive within amoebae, and exist in a free-living state. Mycobacterial communities are also likely to occur in these infection sources in households. Water distribution systems are a transmission route from natural water reservoirs to household tap water. Other infection sources include areas with frequent human contact, such as soil and bathrooms, indicating that individuals may carry NTM organisms that concomitantly attach to their household belongings. To explore the mechanisms associated with the global spread of infection and MAC transmission routes, an epidemiological population-wide genotyping survey would be very useful. A good example of the power of genotyping comes from M. avium subsp. hominissuis, where close genetic relatedness was found between isolates of it from European patients and pigs in Japan and Europe, implying global transmission of this bacterium. It is anticipated that whole genome sequencing technologies will improve NTM surveys so that the mechanisms for the global spread of MAC disease will become clearer in the near future. Better understanding of the niches exploited by MAC and its ecology is essential for preventing MAC infections and developing new methods for its effective treatment and elimination.
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Affiliation(s)
- Yukiko Nishiuchi
- Toneyama Institute for Tuberculosis Research, Osaka City University Medical School , Toyonaka , Japan
| | - Tomotada Iwamoto
- Department of Infectious Diseases, Kobe Institute of Health , Kobe , Japan
| | - Fumito Maruyama
- Section of Microbiology, Graduate School of Medicine and Faculty of Medicine, Kyoto University , Kyoto , Japan
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49
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Roobthaisong A, Aikawa C, Nozawa T, Maruyama F, Nakagawa I. YvqE and CovRS of Group A Streptococcus Play a Pivotal Role in Viability and Phenotypic Adaptations to Multiple Environmental Stresses. PLoS One 2017; 12:e0170612. [PMID: 28122066 PMCID: PMC5266302 DOI: 10.1371/journal.pone.0170612] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 01/06/2017] [Indexed: 01/14/2023] Open
Abstract
Streptococcus pyogenes (group A Streptococcus, or GAS) is a human pathogen that causes a wide range of diseases. For successful colonization within a variety of host niches, GAS utilizes TCSs to sense and respond to environmental changes and adapts its pathogenic traits accordingly; however, many GAS TCSs and their interactions remain uncharacterized. Here, we elucidated the roles of a poorly characterized TCS, YvqEC, and a well-studied TCS, CovRS, in 2 different GAS strain SSI-1 and JRS4, respectively. Deletion of yvqE and yvqC in JRS4 resulted in lower cell viability and abnormality of cell division when compared to the wild-type strain under standard culture conditions, demonstrating an important role for YvqEC. Furthermore, a double-deletion of yvqEC and covRS in SSI-1 and JRS4 resulted in a significantly impaired ability to survive under various stress conditions, as well as an increased sensitivity to cell wall-targeting antibiotics compared to that observed in either single mutant or wild-type strains suggesting synergistic interactions. Our findings provide new insights into the impact of poorly characterized TCS (YvqEC) and potential synergistic interactions between YvqEC and CovRS and reveal their potential role as novel therapeutic targets against GAS infection.
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Affiliation(s)
- Amonrattana Roobthaisong
- Section of Molecular Craniofacial Embryology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
- Department of Microbiology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Chihiro Aikawa
- Department of Microbiology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Takashi Nozawa
- Department of Microbiology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Fumito Maruyama
- Department of Microbiology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Ichiro Nakagawa
- Department of Microbiology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- * E-mail:
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50
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Jorquera MA, Maruyama F, Ogram AV, Navarrete OU, Lagos LM, Inostroza NG, Acuña JJ, Rilling JI, de La Luz Mora M. Erratum to: Rhizobacterial Community Structures Associated with Native Plants Grown in Chilean Extreme Environments. Microb Ecol 2017; 73:253. [PMID: 27538874 DOI: 10.1007/s00248-016-0830-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Affiliation(s)
- Milko A Jorquera
- Center of Plant, Soil interaction and Natural Resources, Biotechnology, Scientific and Technological Bioresource Nucleus, Ave. Francisco Salazar, 01145, Temuco, Chile.
| | - Fumito Maruyama
- Section of Microbiology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Andrew V Ogram
- Soil and Water Science Department, University of Florida, 2181 McCarty Hall, PO Box 110290, Gainesville, FL, 32611, USA
| | - Oscar U Navarrete
- Center of Plant, Soil interaction and Natural Resources, Biotechnology, Scientific and Technological Bioresource Nucleus, Ave. Francisco Salazar, 01145, Temuco, Chile
| | - Lorena M Lagos
- Programa de Doctorado en Ciencias de Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile
| | - Nitza G Inostroza
- Center of Plant, Soil interaction and Natural Resources, Biotechnology, Scientific and Technological Bioresource Nucleus, Ave. Francisco Salazar, 01145, Temuco, Chile
| | - Jacquelinne J Acuña
- Center of Plant, Soil interaction and Natural Resources, Biotechnology, Scientific and Technological Bioresource Nucleus, Ave. Francisco Salazar, 01145, Temuco, Chile
| | - Joaquín I Rilling
- Programa de Doctorado en Ciencias de Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile
| | - María de La Luz Mora
- Center of Plant, Soil interaction and Natural Resources, Biotechnology, Scientific and Technological Bioresource Nucleus, Ave. Francisco Salazar, 01145, Temuco, Chile
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