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      Expanded diversity of novel hemoplasmas in rare and undersampled Neotropical bats

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          Abstract

          Hemotropic mycoplasmas are emerging as a model system for studying bacterial pathogens in bats, but taxonomic coverage of sampled host species remains biased. We leveraged a long-term field study in Belize to uncover novel hemoplasma diversity in bats by analyzing 80 samples from 19 species, most of which are infrequently encountered. PCR targeting the partial 16S rRNA gene found 41% of bats positive for hemoplasmas. Phylogenetic analyses found two novel host shifts of hemoplasmas, four entirely new hemoplasma genotypes, and the first hemoplasma detections in four bat species. One of these novel hemoplasmas (from Neoeptesicus furinalis) shared 97.6% identity in the partial 16S rRNA gene to a human hemoplasma ( Candidatus Mycoplasma haemohominis). Additional analysis of the partial 23S rRNA gene allowed us to also designate two novel hemoplasma species, in Myotis elegans and Phyllostomus discolor, with the proposed names Candidatus Mycoplasma haematomyotis sp. nov. and Candidatus Mycoplasma haematophyllostomi sp. nov., respectively. Our analyses show that additional hemoplasma diversity in bats can be uncovered by targeting rare or undersampled host species.

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          NGPhylogeny.fr: new generation phylogenetic services for non-specialists

          Abstract Phylogeny.fr, created in 2008, has been designed to facilitate the execution of phylogenetic workflows, and is nowadays widely used. However, since its development, user needs have evolved, new tools and workflows have been published, and the number of jobs has increased dramatically, thus promoting new practices, which motivated its refactoring. We developed NGPhylogeny.fr to be more flexible in terms of tools and workflows, easily installable, and more scalable. It integrates numerous tools in their latest version (e.g. TNT, FastME, MrBayes, etc.) as well as new ones designed in the last ten years (e.g. PhyML, SMS, FastTree, trimAl, BOOSTER, etc.). These tools cover a large range of usage (sequence searching, multiple sequence alignment, model selection, tree inference and tree drawing) and a large panel of standard methods (distance, parsimony, maximum likelihood and Bayesian). They are integrated in workflows, which have been already configured (‘One click’), can be customized (‘Advanced’), or are built from scratch (‘A la carte’). Workflows are managed and run by an underlying Galaxy workflow system, which makes workflows more scalable in terms of number of jobs and size of data. NGPhylogeny.fr is deployable on any server or personal computer, and is freely accessible at https://ngphylogeny.fr.
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            Bat-borne virus diversity, spillover and emergence

            Most viral pathogens in humans have animal origins and arose through cross-species transmission. Over the past 50 years, several viruses, including Ebola virus, Marburg virus, Nipah virus, Hendra virus, severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory coronavirus (MERS-CoV) and SARS-CoV-2, have been linked back to various bat species. Despite decades of research into bats and the pathogens they carry, the fields of bat virus ecology and molecular biology are still nascent, with many questions largely unexplored, thus hindering our ability to anticipate and prepare for the next viral outbreak. In this Review, we discuss the latest advancements and understanding of bat-borne viruses, reflecting on current knowledge gaps and outlining the potential routes for future research as well as for outbreak response and prevention efforts.
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              • Article: not found

              Calibrating bacterial evolution.

              Attempts to calibrate bacterial evolution have relied on the assumption that rates of molecular sequence divergence in bacteria are similar to those of higher eukaryotes, or to those of the few bacterial taxa for which ancestors can be reliably dated from ecological or geological evidence. Despite similarities in the substitution rates estimated for some lineages, comparisons of the relative rates of evolution at different classes of nucleotide sites indicate no basis for their universal application to all bacteria. However, there is evidence that bacteria have a constant genome-wide mutation rate on an evolutionary time scale but that this rate differs dramatically from the rate estimated by experimental methods.
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                Author and article information

                Contributors
                Journal
                One Health
                One Health
                One Health
                Elsevier
                2352-7714
                21 September 2023
                December 2023
                21 September 2023
                : 17
                : 100633
                Affiliations
                [a ]Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
                [b ]School of Biological Sciences, University of Oklahoma, Norman, OK, USA
                [c ]Department of Environmental Biology, SUNY College of Environmental Science and Forestry, Syracuse, NY, USA
                [d ]Department of Biological Sciences, University of Arkansas, Fayetteville, AR, USA
                [e ]Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN, USA
                [f ]Smithsonian Tropical Research Institute, Balboa, Ancón, Panama
                [g ]Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA
                [h ]Department of Biology, University of Western Ontario, London, Ontario, Canada
                [i ]Department of Mammalogy, Division of Vertebrate Zoology, American Museum of Natural History, New York, NY, USA
                Author notes
                [* ]Corresponding author. danbeck@ 123456ou.edu
                Article
                S2352-7714(23)00153-2 100633
                10.1016/j.onehlt.2023.100633
                10618802
                a9b9baea-11c4-4914-bc84-09af1e3f23be
                © 2023 The Authors

                This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).

                History
                : 12 June 2023
                : 19 August 2023
                : 21 September 2023
                Categories
                Short Communication

                hemotropic mycoplasma,chiroptera,belize,16s rrna gene,23s rrna gene

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