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      Presence and diversity of Chlamydiae bacteria in Spinturnix myoti, an ectoparasite of bats Translated title: Présence et diversité des bactéries Chlamydiae chez Spinturnix myoti, un acarien ectoparasite de chauve-souris

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          Abstract

          Chlamydia spp. and Chlamydia-like organisms are able to infect vertebrates such as mammals, reptiles and birds, but also arthropods and protozoans. Since they have been detected in bats and bat feces, we expected Chlamydiae bacteria to also be present in the mite Spinturnix myoti, an ectoparasite of mouse-eared bats ( Myotis spp.). The prevalence of Chlamydiales in 88 S. myoti was 57.95% and significantly depended on bat host species. In addition, the prevalence was significantly different between bat species living in sympatry or in allopatry. While there was uninterpretable sequencing for 16 samples, eight showed best BLAST hit identities lower than 92.5% and thus corresponded to new family-level lineages according to the established taxonomy cut-off. The four remaining sequences exhibited best BLAST hit identities ranging from 94.2 to 97.4% and were taxonomically assigned to three different family-level lineages, with two of them belonging to the Parachlamydiaceae, one to the Simkaniaceae, and one to the Chlamydiaceae. These results highlighted for the first time the presence of Chlamydia-like organisms and the possible zoonotic origin of Chlamydia sp. in S. myoti ectoparasites of bats, and therefore suggest that these ectoparasites may play a role in maintaining and/or transmitting members of the Chlamydiae phylum within Myotis spp. bat populations. Our results further highlight that the wide diversity of bacteria belonging to the Chlamydiae phylum is largely underestimated.

          Translated abstract

          Les Chlamydia spp. et les organismes apparentés aux Chlamydia sont capables d’infecter des vertébrés tels que les mammifères, les reptiles et les oiseaux mais aussi des arthropodes et des protozoaires. Puisqu’elles ont été détectées dans des chauves-souris et des excréments de chauves-souris, nous nous attendions à ce que les bactéries du phylum Chlamydiae soient également présentes dans des Spinturnix myoti, des acariens ectoparasites de chauves-souris du groupe des murins ( Myotis spp.). La prévalence des Chlamydiales dans 88 S. myoti était de 57,95 % et dépendait de manière significative des espèces hôtes de chauves-souris. De plus, la prévalence était significativement différente entre les chauves-souris vivant en sympatrie ou en allopatrie. Alors qu’il y avait un séquençage ininterprétable pour 16 échantillons, huit présentaient des résultats d’analyse de type de type BLAST avec une similarité inférieure à 92.5% et à 92,5 % et correspondaient donc à de nouvelles familles selon les seuils utilisés en taxonomie par les chlamydiologistes. Les quatre séquences restantes présentaient des résultats BLAST allant de 94,2 à 97,4 % et ont été taxonomiquement attribuées à trois familles ; deux d’entre elles appartenant aux Parachlamydiaceae, une aux Simkaniaceae et enfin une aux Chlamydiaceae. Ces résultats ont mis en évidence pour la première fois la présence d’organismes de type Chlamydia mais aussi d’organisme pouvant amener à des zoonoses tel que Chlamydia sp. chez Spinturnix myoti, un ectoparasite de chauves-souris. Ces résultats suggèrent donc que ces ectoparasites pourraient jouer un rôle dans le maintien et/ou la transmission des membres de l’embranchement des Chlamydiae au sein des populations de chauves-souris du genre Myotis. Nos résultats soulignent en outre que la grande diversité des bactéries appartenant à l’embranchement des Chlamydiae est largement sous-estimée.

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          Most cited references61

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          We describe MUSCLE, a new computer program for creating multiple alignments of protein sequences. Elements of the algorithm include fast distance estimation using kmer counting, progressive alignment using a new profile function we call the log-expectation score, and refinement using tree-dependent restricted partitioning. The speed and accuracy of MUSCLE are compared with T-Coffee, MAFFT and CLUSTALW on four test sets of reference alignments: BAliBASE, SABmark, SMART and a new benchmark, PREFAB. MUSCLE achieves the highest, or joint highest, rank in accuracy on each of these sets. Without refinement, MUSCLE achieves average accuracy statistically indistinguishable from T-Coffee and MAFFT, and is the fastest of the tested methods for large numbers of sequences, aligning 5000 sequences of average length 350 in 7 min on a current desktop computer. The MUSCLE program, source code and PREFAB test data are freely available at http://www.drive5. com/muscle.
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            Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

            Summary: The two main functions of bioinformatics are the organization and analysis of biological data using computational resources. Geneious Basic has been designed to be an easy-to-use and flexible desktop software application framework for the organization and analysis of biological data, with a focus on molecular sequences and related data types. It integrates numerous industry-standard discovery analysis tools, with interactive visualizations to generate publication-ready images. One key contribution to researchers in the life sciences is the Geneious public application programming interface (API) that affords the ability to leverage the existing framework of the Geneious Basic software platform for virtually unlimited extension and customization. The result is an increase in the speed and quality of development of computation tools for the life sciences, due to the functionality and graphical user interface available to the developer through the public API. Geneious Basic represents an ideal platform for the bioinformatics community to leverage existing components and to integrate their own specific requirements for the discovery, analysis and visualization of biological data. Availability and implementation: Binaries and public API freely available for download at http://www.geneious.com/basic, implemented in Java and supported on Linux, Apple OSX and MS Windows. The software is also available from the Bio-Linux package repository at http://nebc.nerc.ac.uk/news/geneiousonbl. Contact: peter@biomatters.com
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                Author and article information

                Journal
                parasite
                https://www.parasite-journal.org
                Parasite
                Parasite
                EDP Sciences
                1776-1042
                02 November 2020
                2020
                02 November 2020
                02 November 2020
                : 27
                : ( publisher-idID: parasite/2020/01 )
                : 54
                Affiliations
                [1 ] Center for Research on Intracellular Bacteria (CRIB), Institute of Microbiology, University Hospital Center and University of Lausanne, , 1011 Lausanne, Switzerland,
                [2 ] Museum of Zoology, , 1005 Lausanne, Switzerland,
                [3 ] Department of Ecology and Evolution, University of Lausanne, , 1015 Lausanne, Switzerland,
                Author notes
                [* ]Corresponding author: gilbert.greub@ 123456chuv.ch
                Author information
                https://orcid.org/0000-0001-9529-3317
                Article
                parasite200054
                10.1051/parasite/2020052
                838965e3-0aca-4d1a-840b-d318a597559a
                © K. Thiévent et al., published by EDP Sciences, 2020

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( https://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 31 March 2020
                : 07 October 2020
                Page count
                Figures: 2, Tables: 1, Equations: 0, References: 60, Pages: 8
                Categories
                Research Article
                Custom metadata
                Parasite 27, 54 (2020)
                2020
                2020
                2020
                yes

                Parasitology,Life sciences
                Epidemiology,Vector,Bats,Phylogenetic analysis,Chlamydiae,Mites
                Parasitology, Life sciences
                Epidemiology, Vector, Bats, Phylogenetic analysis, Chlamydiae, Mites

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