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Xiong Q, Wan ATY, Liu X, Fung CSH, Xiao X, Malainual N, Hou J, Wang L, Wang M, Yang KY, Cui Y, Leung ELH, Nong W, Shin SK, Au SWN, Jeong KY, Chew FT, Hui JHL, Leung TF, Tungtrongchitr A, Zhong N, Liu Z, Tsui SKW. Comparative Genomics Reveals Insights into the Divergent Evolution of Astigmatic Mites and Household Pest Adaptations. Mol Biol Evol 2022; 39:6582989. [PMID: 35535514 PMCID: PMC9113151 DOI: 10.1093/molbev/msac097] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Highly diversified astigmatic mites comprise many medically important human household pests such as house dust mites causing ∼1–2% of all allergic diseases globally; however, their evolutionary origin and diverse lifestyles including reversible parasitism have not been illustrated at the genomic level, which hampers allergy prevention and our exploration of these household pests. Using six high-quality assembled and annotated genomes, this study not only refuted the monophyly of mites and ticks, but also thoroughly explored the divergence of Acariformes and the diversification of astigmatic mites. In monophyletic Acariformes, Prostigmata known as notorious plant pests first evolved, and then rapidly evolving Astigmata diverged from soil oribatid mites. Within astigmatic mites, a wide range of gene families rapidly expanded via tandem gene duplications, including ionotropic glutamate receptors, triacylglycerol lipases, serine proteases and UDP glucuronosyltransferases. Gene diversification after tandem duplications provides many genetic resources for adaptation to sensing environmental signals, digestion, and detoxification in rapidly changing household environments. Many gene decay events only occurred in the skin-burrowing parasitic mite Sarcoptes scabiei. Throughout the evolution of Acariformes, massive horizontal gene transfer events occurred in gene families such as UDP glucuronosyltransferases and several important fungal cell wall lytic enzymes, which enable detoxification and digestive functions and provide perfect drug targets for pest control. This comparative study sheds light on the divergent evolution and quick adaptation to human household environments of astigmatic mites and provides insights into the genetic adaptations and even control of human household pests.
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Affiliation(s)
- Qing Xiong
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong.,Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong
| | - Angel Tsz-Yau Wan
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong.,Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong
| | - Xiaoyu Liu
- Shenzhen Key Laboratory of Allergy and Immunology, School of Medicine, Shenzhen University, China
| | - Cathy Sin-Hang Fung
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong
| | - Xiaojun Xiao
- Shenzhen Key Laboratory of Allergy and Immunology, School of Medicine, Shenzhen University, China
| | - Nat Malainual
- Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Jinpao Hou
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong.,Centre for Microbial Genomics and Proteomics, The Chinese University of Hong Kong, Hong Kong
| | - Lingyi Wang
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong
| | - Mingqiang Wang
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong.,Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong
| | - Kevin Yi Yang
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong.,Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong
| | - Yubao Cui
- Department of Clinical Laboratory, Wuxi People's Hospital Affiliated to Nanjing Medical University, Wuxi, China
| | - Elaine Lai-Han Leung
- Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau
| | - Wenyan Nong
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong
| | - Soo-Kyung Shin
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong
| | | | - Kyoung Yong Jeong
- Institute of Allergy, Department of Internal Medicine, College of Medicine, Yonsei University, Seoul, Korea
| | - Fook-Tim Chew
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Jerome Ho-Lam Hui
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong
| | - Ting-Fan Leung
- Department of Paediatrics, The Chinese University of Hong Kong, Hong Kong
| | - Anchalee Tungtrongchitr
- Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Nanshan Zhong
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Zhigang Liu
- Shenzhen Key Laboratory of Allergy and Immunology, School of Medicine, Shenzhen University, China
| | - Stephen Kwok-Wing Tsui
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong.,Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong.,Centre for Microbial Genomics and Proteomics, The Chinese University of Hong Kong, Hong Kong
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Characterisation of Bacteriophage vB_SmaM_Ps15 Infective to Stenotrophomonas maltophilia Clinical Ocular Isolates. Viruses 2022; 14:v14040709. [PMID: 35458438 PMCID: PMC9025141 DOI: 10.3390/v14040709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 03/18/2022] [Accepted: 03/24/2022] [Indexed: 11/16/2022] Open
Abstract
Recent acknowledgment that multidrug resistant Stenotrophomonas maltophilia strains can cause severe infections has led to increasing global interest in addressing its pathogenicity. While being primarily associated with hospital-acquired respiratory tract infections, this bacterial species is also relevant to ophthalmology, particularly to contact lens-related diseases. In the current study, the capacity of Stenotrophomonas phage vB_SmaM_Ps15 to infect ocular S. maltophilia strains was investigated to explore its future potential as a phage therapeutic. The phage proved to be lytic to a range of clinical isolates collected in Australia from eye swabs, contact lenses and contact lens cases that had previously shown to be resistant to several antibiotics and multipurpose contact lenses disinfectant solutions. Morphological analysis by transmission electron microscopy placed the phage into the Myoviridae family. Its genome size was 161,350 bp with a G + C content of 54.2%, containing 276 putative protein-encoding genes and 24 tRNAs. A detailed comparative genomic analysis positioned vB_SmaM_Ps15 as a new species of the Menderavirus genus, which currently contains six very similar globally distributed members. It was confirmed as a virulent phage, free of known lysogenic and pathogenicity determinants, which supports its potential use for the treatment of S. maltophilia eye infections.
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Samba-Louaka A, Delafont V, Rodier MH, Cateau E, Héchard Y. Free-living amoebae and squatters in the wild: ecological and molecular features. FEMS Microbiol Rev 2019; 43:415-434. [DOI: 10.1093/femsre/fuz011] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 04/30/2019] [Indexed: 02/06/2023] Open
Abstract
ABSTRACT
Free-living amoebae are protists frequently found in water and soils. They feed on other microorganisms, mainly bacteria, and digest them through phagocytosis. It is accepted that these amoebae play an important role in the microbial ecology of these environments. There is a renewed interest for the free-living amoebae since the discovery of pathogenic bacteria that can resist phagocytosis and of giant viruses, underlying that amoebae might play a role in the evolution of other microorganisms, including several human pathogens. Recent advances, using molecular methods, allow to bring together new information about free-living amoebae. This review aims to provide a comprehensive overview of the newly gathered insights into (1) the free-living amoeba diversity, assessed with molecular tools, (2) the gene functions described to decipher the biology of the amoebae and (3) their interactions with other microorganisms in the environment.
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Affiliation(s)
- Ascel Samba-Louaka
- Laboratoire Ecologie et Biologie des Interactions (EBI), Equipe Microbiologie de l'Eau, Université de Poitiers, UMR CNRS 7267, 1 rue Georges Bonnet, TSA51106, 86073 POITIERS Cedex 9, France
| | - Vincent Delafont
- Laboratoire Ecologie et Biologie des Interactions (EBI), Equipe Microbiologie de l'Eau, Université de Poitiers, UMR CNRS 7267, 1 rue Georges Bonnet, TSA51106, 86073 POITIERS Cedex 9, France
| | - Marie-Hélène Rodier
- Laboratoire Ecologie et Biologie des Interactions (EBI), Equipe Microbiologie de l'Eau, Université de Poitiers, UMR CNRS 7267, 1 rue Georges Bonnet, TSA51106, 86073 POITIERS Cedex 9, France
- Laboratoire de Parasitologie et Mycologie, CHU La Milétrie, 2 rue de la Milétrie, 86021 Poitiers Cedex, France
| | - Estelle Cateau
- Laboratoire Ecologie et Biologie des Interactions (EBI), Equipe Microbiologie de l'Eau, Université de Poitiers, UMR CNRS 7267, 1 rue Georges Bonnet, TSA51106, 86073 POITIERS Cedex 9, France
- Laboratoire de Parasitologie et Mycologie, CHU La Milétrie, 2 rue de la Milétrie, 86021 Poitiers Cedex, France
| | - Yann Héchard
- Laboratoire Ecologie et Biologie des Interactions (EBI), Equipe Microbiologie de l'Eau, Université de Poitiers, UMR CNRS 7267, 1 rue Georges Bonnet, TSA51106, 86073 POITIERS Cedex 9, France
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Thomas S, Izard J, Walsh E, Batich K, Chongsathidkiet P, Clarke G, Sela DA, Muller AJ, Mullin JM, Albert K, Gilligan JP, DiGuilio K, Dilbarova R, Alexander W, Prendergast GC. The Host Microbiome Regulates and Maintains Human Health: A Primer and Perspective for Non-Microbiologists. Cancer Res 2017; 77:1783-1812. [PMID: 28292977 PMCID: PMC5392374 DOI: 10.1158/0008-5472.can-16-2929] [Citation(s) in RCA: 215] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 12/19/2016] [Accepted: 12/21/2016] [Indexed: 02/07/2023]
Abstract
Humans consider themselves discrete autonomous organisms, but recent research is rapidly strengthening the appreciation that associated microorganisms make essential contributions to human health and well being. Each person is inhabited and also surrounded by his/her own signature microbial cloud. A low diversity of microorganisms is associated with a plethora of diseases, including allergy, diabetes, obesity, arthritis, inflammatory bowel diseases, and even neuropsychiatric disorders. Thus, an interaction of microorganisms with the host immune system is required for a healthy body. Exposure to microorganisms from the moment we are born and appropriate microbiome assembly during childhood are essential for establishing an active immune system necessary to prevent disease later in life. Exposure to microorganisms educates the immune system, induces adaptive immunity, and initiates memory B and T cells that are essential to combat various pathogens. The correct microbial-based education of immune cells may be critical in preventing the development of autoimmune diseases and cancer. This review provides a broad overview of the importance of the host microbiome and accumulating knowledge of how it regulates and maintains a healthy human system. Cancer Res; 77(8); 1783-812. ©2017 AACR.
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Affiliation(s)
- Sunil Thomas
- Lankenau Institute for Medical Research, Wynnewood, Pennsylvania.
| | - Jacques Izard
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, Nebraska
| | - Emily Walsh
- Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, Massachusetts
| | - Kristen Batich
- Department of Neurosurgery, Duke Brain Tumor Immunotherapy Program, Duke University Medical Center, Durham, North Carolina
- Department of Surgery, Duke Brain Tumor Immunotherapy Program, Duke University Medical Center, Durham, North Carolina
- Department of Pathology, Duke University Medical Center, Durham, North Carolina
| | - Pakawat Chongsathidkiet
- Department of Neurosurgery, Duke Brain Tumor Immunotherapy Program, Duke University Medical Center, Durham, North Carolina
- Department of Surgery, Duke Brain Tumor Immunotherapy Program, Duke University Medical Center, Durham, North Carolina
- Department of Pathology, Duke University Medical Center, Durham, North Carolina
| | - Gerard Clarke
- Department of Psychiatry and Neurobehavioural Science, APC Microbiome Institute University College Cork, Cork, Ireland
| | - David A Sela
- Department of Food Science, University of Massachusetts, Amherst, Massachusetts
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts
- Center for Microbiome Research, University of Massachusetts Medical School, Worcester, Massachusetts
| | | | - James M Mullin
- Lankenau Institute for Medical Research, Wynnewood, Pennsylvania
| | - Korin Albert
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, Massachusetts
- Department of Food Science, University of Massachusetts, Amherst, Massachusetts
| | - John P Gilligan
- Lankenau Institute for Medical Research, Wynnewood, Pennsylvania
| | | | - Rima Dilbarova
- Lankenau Institute for Medical Research, Wynnewood, Pennsylvania
| | - Walker Alexander
- Lankenau Institute for Medical Research, Wynnewood, Pennsylvania
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