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      The fecal bacterial microbiota of bats; Slovenia

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          Abstract

          Methods

          Fecal samples were collected from 92 bats in Slovenia, consisting of 12 different species, and the bacterial microbiota was assessed via next generation sequencing of the 16S rRNA gene V4 region.

          Results

          Sequences were assigned to 28 different phyla, but only Proteobacteria, Firmicutes, Bacteroidetes and Actinobacteria accounted for ≥1% of sequences. One phylum (Proteobacteria), one class (Gammaproteobacteria), three orders (Pseudomonadales, Lactobacillales, Bacillales), four families (Enterobacteriaceae, Pseudomonadaceae, Staphylococcaceae, Carnobacteriaceae), and five genera ( Pseudomonas, Staphylococcus, Carnobacterium, an unclassified Enterobacteriaceae, Acinetobacter) accounted for 50% of sequences. There were no significant differences in the relative abundances of any phyla between bat species, but various differences were noted at lower taxonomic levels, such as Enterobacteriaceae ( P = 0.007, most abundant in M. blythii), Pseudomonadaceae ( P = 0.007, most abundant in Rhinolophus hipposideros) and Chlamydiaceae ( P = 0.04, most abundant in Myotis myotis). There were significant differences in richness between species in both adults and juveniles/subadults, but there was no impact of sex on any alpha diversity index. When only adults are considered, there were significant differences in community membership between M. blythii and M. emarginatus ( P = 0.011), and M. blythii and R. hipposideros ( P = 0.004). There were also significant differences in community structure between M. blythii and M. emarginatus ( P = 0.025), and M. blythii and R. hipposideros ( P = 0.026). When adults of the four main species were compared, 14 OTUs were identified as differentially abundant using LEfSe. Only one difference was identified when comparing R. hipposideros adults and juvenile/subadults, with Klebsiella over-represented in the younger bats.

          Conclusions

          Bats have a complex and diverse microbiota with a high relative abundance of Proteobacteria. The relevance of this difference is unclear and requires further study. Differences in the microbiota were observed between bat species, perhaps reflecting different diets and environmental exposures.

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          Most cited references37

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          Dirichlet Multinomial Mixtures: Generative Models for Microbial Metagenomics

          We introduce Dirichlet multinomial mixtures (DMM) for the probabilistic modelling of microbial metagenomics data. This data can be represented as a frequency matrix giving the number of times each taxa is observed in each sample. The samples have different size, and the matrix is sparse, as communities are diverse and skewed to rare taxa. Most methods used previously to classify or cluster samples have ignored these features. We describe each community by a vector of taxa probabilities. These vectors are generated from one of a finite number of Dirichlet mixture components each with different hyperparameters. Observed samples are generated through multinomial sampling. The mixture components cluster communities into distinct ‘metacommunities’, and, hence, determine envirotypes or enterotypes, groups of communities with a similar composition. The model can also deduce the impact of a treatment and be used for classification. We wrote software for the fitting of DMM models using the ‘evidence framework’ (http://code.google.com/p/microbedmm/). This includes the Laplace approximation of the model evidence. We applied the DMM model to human gut microbe genera frequencies from Obese and Lean twins. From the model evidence four clusters fit this data best. Two clusters were dominated by Bacteroides and were homogenous; two had a more variable community composition. We could not find a significant impact of body mass on community structure. However, Obese twins were more likely to derive from the high variance clusters. We propose that obesity is not associated with a distinct microbiota but increases the chance that an individual derives from a disturbed enterotype. This is an example of the ‘Anna Karenina principle (AKP)’ applied to microbial communities: disturbed states having many more configurations than undisturbed. We verify this by showing that in a study of inflammatory bowel disease (IBD) phenotypes, ileal Crohn's disease (ICD) is associated with a more variable community.
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            Bats as ‘special’ reservoirs for emerging zoonotic pathogens

            Highlights • Bats experience morbidity to many extracellular but few intracellular infections. • Bats control intracellular pathogens via cellular pathways to apoptosis/autophagy. • These ROS mitigation pathways promote longevity and tumor avoidance. • Extracellular pathogen-associated morbidity in bats results from immunopathology.
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              Bat Flight and Zoonotic Viruses

              Bats are a major source of zoonotic viruses worldwide ( 1 – 3 ). Molecular studies have demonstrated that bats are natural host reservoirs for several recently emerged high-profile zoonotic viruses, including sudden acute respiratory syndrome–like coronaviruses ( 4 ); Ebola and Marburg hemorrhagic fever filoviruses ( 5 , 6 ); rabies and rabies-related lyssaviruses; and many paramyxoviruses, including rubulaviruses and Nipah and Hendra viruses ( 7 – 9 ). Identification of a diverse range of bat paramyxoviruses, including those conspecific with human mumps virus, and phylogenetic reconstruction of host associations suggests numerous host switches of paramyxoviruses from bats to other mammals and birds ( 9 ). Bats infected with these viruses seem to show no overt signs of disease ( 10 , 11 ) and, in some cases, appear to be persistently infected ( 12 ). In the aggregate, zoonotic viruses in >15 virus families have been identified in at least 200 species in 12 bat families around the world ( 3 , 9 , 11 ). In a recent comparative analysis, Luis et al. ( 3 ) showed bats to be more likely to be infected with more zoonotic viruses per host species than were rodents, thus adding weight to the suggestion that bats might in some way be unique as sources of emerging zoonoses. In areas where these viruses have been studied, some viral groups (e.g., coronaviruses, astroviruses, paramyxoviruses) have much higher viral diversity and prevalence in bats than in sympatric species of rodents ( 9 , 11 ). Although bats serve as reservoir hosts with great viral diversity, little evidence exists for corresponding death or illness of bats from viruses (other than lyssaviruses) that have spread into humans and domesticated mammals with high virulence ( 9 , 10 ). This statement also can be true for some viruses from other groups of mammals that serve as reservoirs of viruses, particularly rodents. However, low virulence coupled with high diversity has led to the suggestion that bats might have evolved mechanisms to control viral replication more effectively than have most other mammals ( 10 , 13 ) and that some attribute common to all bats (a very widely distributed and diverse group) also might explain the apparent low virulence of viral infections in these animals ( 1 , 2 ). We hypothesize that the increased metabolism and higher body temperatures of bats during flight might serve as an evolutionary adjuvant to their immune systems, providing a powerful selective force against virulence and promoting the diversity of viruses that infect bat populations. Perhaps counter-intuitively, this would enable bats to tolerate a greater diversity of viruses that have a high potential for virulence when transmitted to other mammals. The hypothesis also might help explain why co-evolved bat viruses cause high pathogenicity when they spill over into other mammals because the bat-derived viruses might survive well under both febrile and cooler conditions. Are Bats Special As Viral Hosts? Three recent reports provide especially noteworthy background for this perspective. Luis et al. ( 3 ) performed a comparative analysis of viruses in bats and rodents (the most speciose group of mammals) and associated ecologic factors. The analysis indicated that bats are indeed special in hosting more viruses per species than rodents, despite twice as many rodent species in the world, and that certain ecologic factors are associated with the hosting of more viruses by bats ( 3 ). Through an extensive genomic analysis of 2 divergent species of bats, Zhang et al. ( 13 ) found that flight evolved in tandem with concomitant genetic changes to their innate immune systems. These changes were consistent with the need for DNA damage repair because of high metabolic rates during flight ( 13 ). Baker et al. ( 10 ) reviewed antiviral immune responses in bats and suggested the possibility that bats might be able to control viral replication through innate immunity. They summarized research indicating that bats have immune elements found in most other mammals, including pattern recognition receptors and multiple interferons, and show complement activity ( 10 ). Many standard elements of the adaptive immune system also have been described in bats, including multiple immunoglobulins, antibody responses, interleukins and other cytokines, and cell-mediated T-cell responses (although investigations of the latter have been limited [ 10 ]). However, genes that code for some immune elements are notably lacking in bats and indicate permanent change to the bat immune system ( 13 ). Fever, Flight, and Metabolic Rate Fever in mammals is accompanied by an initially high metabolic rate associated with beneficial immune responses ( 14 , 15 ). During flight, bats exhibit a high increase in metabolic rate over the resting metabolic rate of normeothermic, otherwise active bats. This increase is estimated to be 15–16-fold ( 16 ), in comparison with the 7-fold increase in metabolic rates of rodents running to exhaustion ( 17 ) or the 2-fold increase in metabolic rates of most flying birds ( 18 ). Strains of laboratory mice that are inbred for higher metabolic rates show stronger immune responses to immune challenge (keyhole limpet hemocyanin antigen) with stronger antigen-specific IgM production than strains bred for lower metabolic rates; leukocyte counts and mass of lymphatic organs that are the sources of immune cells involved in antigen recognition and elimination also are elevated in the strains with higher metabolic rates ( 19 ). The metabolic cost of raising an immune response to experimental stimulation typically results in a general increase of ≈10%–30% of resting metabolic rates in a variety of nonvolant small mammals ( 20 , 21 ). When a bat is confronted by a viral antigen, the proportional increase in metabolism for raising an immune response may be trivial compared with the very large increase in the metabolic costs of flight (the proportional increase for flight may even be greater, given the wider metabolic scope of many species of bats that undergo shallow daily torpor). Thus, we hypothesize that the higher metabolic rates during flight in bats may enhance, facilitate, or perhaps subsidize any inherent cost of raising metabolism to activate an immune response. The daily cyclical nature of raised metabolism during flight also might enable some viruses to persist within the bats and perhaps become resistant to this part of the innate immune response. Bat Flight and Elevated Body Temperatures Canale and Henry ( 22 ) stated, “The heat of fever forestalls pathogen replication and increases the efficiency of the immune responses. Such body warming is associated with shortened disease duration and improved survival in most animals.” Although fever has been associated with improved recovery, very little is known about mechanisms, including whether the impact involves thresholds or average rates of immune response. During fever, mammalian core body temperatures can vary but typically are 38°C–41°C ( 14 ). The high metabolic demands of bat flight result in core body temperatures that commonly reach the ranges of core temperatures typical of fever. High body temperatures during flight have been demonstrated in multiple species of bats within several families (Table 1), and such high body temperature ranges increase the rate of multiple immune responses in mammals, including components of the innate and adaptive immune systems (Table 2). Daily high body temperatures thus might arm bats against some pathogens during the early stages of infection. An exception to the daily high body temperatures during flight occurs during hibernation in temperate zones: although bats rouse from hibernation multiple times each winter ( 35 ), replication of most mammalian adapted pathogens is expected to be markedly reduced by the lower core body temperatures of hibernation. Table 1 Examples of elevated core body temperature in flying bats* Bat species (family) Core temperature during flight, °C Source Eidolon helvum (Pteropidae) 36.9–40.8 ( 23 ) Hypsignathus monstrosus (Pteropidae) 37.2–40.0 ( 23 ) Rousettus aegyptiacus (Pteropidae) 38.2–41.2 ( 23 ) Rhinolophus ferrumequinum (Rhinolophidae) 41† ( 24 ) Miniopterus sp. (Miniopteridae) 41.1 ± 0.45 ( 25 ) Phyllostomus hastatus (Phyllostomidae) 41.2–42.1 ( 17 ) Carollia perspicillata (Phyllostomidae) 40.2 ± 0.8 ( 26 ) Artibeus lituratus (Phyllostomidae) c. 41.2 ± 1 ( 27 ) Sturnira lilium (Phyllostomidae) c. 40.5 ± 0.3 ( 27 ) Noctilio albiventris (Noctilionidae) 35.5–40.6 ( 28 ) Myotis yumanensis (Vespertilionidae) 40.0–40.8 ( 29 ) Eptesicus fuscus (Vespertilionidae) 41.3 ± 2.1†, 37–39.5‡ ( 30 ) Mops condylurus (Molossidae) 40.5 ± 1.1 ( 31 ) Tadarida brasiliensis (Molossidae) 35–42 ( 32 ) Eumops perotis (Molossidae) 37.8–39.3 ( 33 ) Myotis volans (Vespertilionidae) 37.4 ( 34 ) Myotis evotis (Vespertilionidae) 38.3 ( 34 ) Myotis californicus (Vespertilionidae) 38.4 ( 34 ) Parastrellus Hesperus (Vespertilionidae) 38.8 ( 34 ) Eptesicus fuscus (Vespertilionidae) 41.0 ( 34 ) Lasiurus cinereus (Vespertilionidae) 40.2 ( 34 ) Antrozous pallidus (Vespertilionidae) 40.6 ( 34 ) Tadarida brasiliensis (Molossidae) 38.0 ( 34 ) *Data available from original sources are given as ranges or means ±1 SD.
†Skin temperature.
‡Body temperature. Table 2 Favorable innate and adaptive immune responses associated with the high body temperature of fever in mammals* Enhanced neutrophil and monocyte motility and emigration Enhanced phagocytosis and pinocytosis Increased oxygen radical production by phagocytes Increased interferon production Increased antiviral, antitumor, or antiproliferative, and natural killer cell stimulating activities of interferon Potentiated interferon-induced anti-anaphylaxis (anergy) Enhanced natural killer complement activation Enhanced expression of Fc receptors Increased T-helper cell activation, expression, recruitment, and cytotoxic activity Blocked T-suppressor cell activity Increased antibody production Enhanced tumor necrosis factor-α Increased T-cell proliferative response to nonspecific mitogens, interleukin-1 and −2, and allogeneic lymphocytes Increased killing of intracellular bacteria Increased bactericidal effect of antimicrobial agents Induced cytoprotective heat-shock proteins in host cells Induced pathogen heat-shock proteins, which activate host defenses Induced cytoprotective heat-shock proteins in host cells *See reviews in ( 14 , 15 ). A Speculative Hypothesis If the elevated metabolic rates and body temperatures accompanying flight facilitate activation of the immune system of bats on a daily cycle, then flight could be the ultimate explanatory variable for the evolution of viral infections without overt signs of illness in bats. Zhang et al. ( 13 ) showed that the evolution of flight in bats has been accompanied by genetic changes to their immune systems to accommodate high metabolic rates. Theoretical models of the evolution of parasite virulence show that intermediate levels of virulence are a typical result of the trade-off between the opposing selective forces of host death and parasite transmission ( 36 ). However, heightened host adaptive immune responses that might be facilitated in bats during flight also can result in harmful immunopathologic changes and disease. (A nonviral example of such harmful immunopathology in bats seems to occur during infection by the fungal pathogen causing white-nose syndrome (Pseudogymnoascus destructans) when hibernating bats resume flight [ 37 ]). In systems in which disease organisms cause major immunopathologic changes, theoretical analyses suggest that natural selection can favor decreased virulence and incomplete clearance of parasites ( 36 , 38 ). Through heightened immunopathologic responses, flight might have been a potent selective factor for the reduced virulence to the natural hosts seen in the pool of emerging viruses recently discovered in bats. It also is notable that there are few reports of mass deaths from diseases in bats (except for the novel white-nose syndrome fungus), despite reports of bat die-offs due largely to other causes that have appeared in the literature over the years (e.g., review in 39 ). The evolution of flight in conjunction with the bat’s speculated heightened potential for immune vigilance might have predisposed bats to be reservoir hosts to a preponderance of viruses that now lack major effects on bats as the natural host populations but that can emerge into populations of humans and domesticated mammals with greater virulence. Consideration of the role of torpor is also germane to our hypothesis. As noted by Luis et al. ( 3 ), “more research is needed to determine the relationship between torpor, host competence as related to within-host viral persistence and population viral perpetuation processes.” Viral replication is dampened under the cooler host body temperatures that prevail during prolonged torpor, and hypothermia has been considered to be a host strategy that is adaptive against pathogens ( 40 ). Luis et al. ( 3 ) hypothesized that the negative correlation identified between the use of torpor and zoonotic viral richness may be due to lower contact rates, yet in bats it is also consistent with longer periods with no or lower flight activity and, consequently, lower frequency of the hypothesized heightened vigilance against invading viruses during the course of host–parasite co-evolution. On the other hand, reduced immune system activity during torpor may enable cold-adapted pathogens to persist ( 40 ), as in the case of the novel fungal pathogen causing white-nose syndrome. As a group, bats show a wide range of adaptations involving torpor that varies with latitude and phylogeny, ranging from prolonged deep winter hibernation through shallow daily torpor to year-round homeothermy. Viruses that have co-evolved with bats under these conditions might have properties that can favor survival under a wider scope of temperatures, possibly facilitating spillover to novel hosts. Testing the Hypothesis In their review of bat immunology and viral diversity, Wang et al. ( 11 ) posed the question “Flight capability, longevity and innate immunity—are they linked?” and noted that “data in this field are so limited that it is … important to provoke original, speculative or even controversial ideas or theories in this important field of research.” Our “flight-as-fever” hypothesis suggests 1 mechanism unique to bats that might be key in the flight capability–innate immunity linkage question raised by Wang et al. ( 11 ). Researchers interested in testing this hypothesis will find it challenging and demanding of creativity. Unfortunately, no prior studies have investigated the effect of the high body temperatures and metabolic rates associated with flight on host–virus interactions in bats. However, we suggest that a variety of in vivo, in vitro, and in silico approaches be considered. For example, in vivo approaches could rely on the experimental techniques that were used decades ago in the pioneering studies of bat flight physiology ( 16 , 17 ). As in these prior physiologic studies, captive bats can be trained to fly in wind tunnels. Experiments could be designed to determine whether trained bats allowed to fly show heightened immune responses compared with when they were not flying. These experiments could begin with determining immune responses after exposure to harmless antigens and then progress to experiments involving exposure to viruses. In vitro studies could determine the comparative susceptibility of bat viruses and nonbat viruses grown in culture to altered and variable thermal regimes typical of the body temperatures of bats during flight, as well as bats in torpor. (In this regard, we note that most bat viruses that have been identified by using genetic techniques have not been isolated, described morphologically, or grown in culture; additional research using techniques of classical virology are certainly needed to improve the understanding of bat virology). Finally, in silico techniques of modeling and simulation would be helpful in understanding the likely co-evolution of bat viruses and their hosts when subject to daily fever-like thermal and metabolic regimes. Regimes of such frequency might accelerate the pace of co-evolution in the otherwise slowly evolving hosts, and favor the development of low pathogenicity in their much more rapidly evolving viruses.
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                Author and article information

                Contributors
                Role: ConceptualizationRole: Funding acquisitionRole: InvestigationRole: MethodologyRole: Project administrationRole: Writing – review & editing
                Role: ConceptualizationRole: InvestigationRole: MethodologyRole: ResourcesRole: Writing – review & editing
                Role: Data curationRole: Formal analysisRole: MethodologyRole: SoftwareRole: ValidationRole: Writing – original draftRole: Writing – review & editing
                Role: Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                23 May 2018
                2018
                : 13
                : 5
                : e0196728
                Affiliations
                [1 ] Veterinary Faculty, University of Ljubljana, Ljubljana, Slovenia
                [2 ] Slovenian Museum of Natural History, Ljubljana, Slovenija
                [3 ] Dept of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
                Free University of Bozen/Bolzano, ITALY
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                Author information
                http://orcid.org/0000-0003-1896-1937
                Article
                PONE-D-17-25578
                10.1371/journal.pone.0196728
                5965822
                29791473
                6bda198e-eec7-4905-90f5-482c57564a36
                © 2018 Vengust et al

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 6 July 2017
                : 18 April 2018
                Page count
                Figures: 5, Tables: 5, Pages: 15
                Funding
                Funded by: Slovenian National Research Agency
                Award ID: PR-0053
                Award Recipient :
                Funded by: Slovenian Ministry of Environmental and Spatial Planning
                Award ID: JN4310/2014
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100000038, Natural Sciences and Engineering Research Council of Canada;
                Award Recipient : Scott Weese
                This work was financed with the support of Slovenian National Research Agency (Grant no. P4-0053) and Ministry of the Environment and Spatial Planning (JN4310/2014). Additional support was provided by the Canadian Natural Sciences and Engineering Research Council (Discovery Grant)( http://www.nserc-crsng.gc.ca/index_eng.asp). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
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                Biology and Life Sciences
                Organisms
                Eukaryota
                Animals
                Vertebrates
                Amniotes
                Mammals
                Bats
                Biology and Life Sciences
                Microbiology
                Medical Microbiology
                Microbiome
                Biology and Life Sciences
                Genetics
                Genomics
                Microbial Genomics
                Microbiome
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                Microbiology
                Microbial Genomics
                Microbiome
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                Enterobacteriaceae
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                Pseudomonas
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                Biology and Life Sciences
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                Biology and Life Sciences
                Microbiology
                Medical Microbiology
                Microbial Pathogens
                Bacterial Pathogens
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                Medicine and Health Sciences
                Pathology and Laboratory Medicine
                Pathogens
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                Data has been uploaded to the Scholars Portal Dataverse https://dataverse.scholarsportal.info/dataverse/guelph DOI: 10.5683/SP/RAJQ2P.

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