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Pilgrim J. Comparative genomics of a novel Erwinia species associated with the Highland midge ( Culicoides impunctatus). Microb Genom 2024; 10. [PMID: 38630610 DOI: 10.1099/mgen.0.001242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2024] Open
Abstract
Erwinia (Enterobacterales: Erwiniaceae) are a group of cosmopolitan bacteria best known as the causative agents of various plant diseases. However, other species in this genus have been found to play important roles as insect endosymbionts supplementing the diet of their hosts. Here, I describe Candidatus Erwinia impunctatus (Erwimp) associated with the Highland midge Culicoides impunctatus (Diptera: Ceratopogonidae), an abundant biting pest in the Scottish Highlands. The genome of this new Erwinia species was assembled using hybrid long and short read techniques, and a comparative analysis was undertaken with other members of the genus to understand its potential ecological niche and impact. Genome composition analysis revealed that Erwimp is similar to other endophytic and ectophytic species in the genus and is unlikely to be restricted to its insect host. Evidence for an additional plant host includes the presence of a carotenoid synthesis operon implicated as a virulence factor in plant-associated members in the sister genus Pantoea. Unique features of Erwimp include several copies of intimin-like proteins which, along with signs of genome pseudogenization and a loss of certain metabolic pathways, suggests an element of host restriction seen elsewhere in the genus. Furthermore, a screening of individuals over two field seasons revealed the absence of the bacteria in Culicoides impunctatus during the second year indicating this microbe-insect interaction is likely to be transient. These data suggest that Culicoides impunctatus may have an important role to play beyond a biting nuisance, as an insect vector transmitting Erwimp alongside any conferred impacts to surrounding biota.
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Affiliation(s)
- Jack Pilgrim
- Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
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Fiebig A, Schnizlein MK, Pena-Rivera S, Trigodet F, Dubey AA, Hennessy MK, Basu A, Pott S, Dalal S, Rubin D, Sogin ML, Eren AM, Chang EB, Crosson S. Bile acid fitness determinants of a Bacteroides fragilis isolate from a human pouchitis patient. mBio 2024; 15:e0283023. [PMID: 38063424 PMCID: PMC10790697 DOI: 10.1128/mbio.02830-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 10/26/2023] [Indexed: 12/19/2023] Open
Abstract
IMPORTANCE The Gram-negative bacterium Bacteroides fragilis is a common member of the human gut microbiota that colonizes multiple host niches and can influence human physiology through a variety of mechanisms. Identification of genes that enable B. fragilis to grow across a range of host environments has been impeded in part by the relatively limited genetic tractability of this species. We have developed a high-throughput genetic resource for a B. fragilis strain isolated from a UC pouchitis patient. Bile acids limit microbial growth and are altered in abundance in UC pouches, where B. fragilis often blooms. Using this resource, we uncovered pathways and processes that impact B. fragilis fitness in bile and that may contribute to population expansions during bouts of gut inflammation.
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Affiliation(s)
- Aretha Fiebig
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Matthew K. Schnizlein
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Selymar Pena-Rivera
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Florian Trigodet
- Department of Medicine, University of Chicago, Chicago, Illinois, USA
- Helmholtz Institute for Functional Marine Biodiversity, University of Oldenburg, Oldenburg, Germany
| | - Abhishek Anil Dubey
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Miette K. Hennessy
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Anindita Basu
- Department of Medicine, University of Chicago, Chicago, Illinois, USA
| | - Sebastian Pott
- Department of Medicine, University of Chicago, Chicago, Illinois, USA
| | - Sushila Dalal
- Department of Medicine, University of Chicago, Chicago, Illinois, USA
| | - David Rubin
- Department of Medicine, University of Chicago, Chicago, Illinois, USA
| | | | - A. Murat Eren
- Department of Medicine, University of Chicago, Chicago, Illinois, USA
- Helmholtz Institute for Functional Marine Biodiversity, University of Oldenburg, Oldenburg, Germany
| | - Eugene B. Chang
- Department of Medicine, University of Chicago, Chicago, Illinois, USA
| | - Sean Crosson
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
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