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Bean TG, Chadwick EA, Herrero-Villar M, Mateo R, Naidoo V, Rattner BA. Do Pharmaceuticals in the Environment Pose a Risk to Wildlife? ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2024; 43:595-610. [PMID: 36398854 DOI: 10.1002/etc.5528] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/29/2022] [Accepted: 11/14/2022] [Indexed: 06/16/2023]
Abstract
The vast majority of knowledge related to the question "To what extent do pharmaceuticals in the environment pose a risk to wildlife?" stems from the Asian vulture crisis (>99% decline of some species of Old World vultures on the Indian subcontinent related to the veterinary use of the nonsteroidal anti-inflammatory drug [NSAID] diclofenac). The hazard of diclofenac and other NSAIDs (carprofen, flunixin, ketoprofen, nimesulide, phenylbutazone) to vultures and other avian species has since been demonstrated; indeed, only meloxicam and tolfenamic acid have been found to be vulture-safe. Since diclofenac was approved for veterinary use in Spain and Italy in 2013 (home to ~95% of vultures in Europe), the risk of NSAIDs to vultures in these countries has become one of the principal concerns related to pharmaceuticals and wildlife. Many of the other bodies of work on pharmaceutical exposure, hazard and risk to wildlife also relate to adverse effects in birds (e.g., poisoning of scavenging birds in North America and Europe from animal carcasses containing pentobarbital, secondary and even tertiary poisoning of birds exposed to pesticides used in veterinary medicine as cattle dips, migratory birds as a vector for the transfer of antimicrobial and antifungal resistance). Although there is some research related to endocrine disruption in reptiles and potential exposure of aerial insectivores, there remain numerous knowledge gaps for risk posed by pharmaceuticals to amphibians, reptiles, and mammals. Developing noninvasive sampling techniques and new approach methodologies (e.g., genomic, in vitro, in silico, in ovo) is important if we are to bridge the current knowledge gaps without extensive vertebrate testing. Environ Toxicol Chem 2024;43:595-610. © 2022 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA.
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Affiliation(s)
| | | | - Marta Herrero-Villar
- Instituto de Investigación en Recursos Cinegéticos, Ciudad Real, Castilla-La-Mancha, Spain
| | - Rafael Mateo
- Instituto de Investigación en Recursos Cinegéticos, Ciudad Real, Castilla-La-Mancha, Spain
| | - Vinny Naidoo
- Department of Paraclinical Sciences, Faculty of Veterinary Science, University of Pretoria, Pretoria, Gauteng, South Africa
| | - Barnett A Rattner
- Eastern Ecological Science Center at the Patuxent Research Refuge, US Geological Survey, Laurel, Maryland, USA
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2
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Sauer EL, Connelly C, Perrine W, Love AC, DuRant SE. Male pathology regardless of behaviour drives transmission in an avian host-pathogen system. J Anim Ecol 2024; 93:36-44. [PMID: 38044497 DOI: 10.1111/1365-2656.14026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 10/04/2023] [Indexed: 12/05/2023]
Abstract
Host sex is an important source of heterogeneity in the severity of epidemics. Pinpointing the mechanisms causing this heterogeneity can be difficult because differences in behaviour among sexes (e.g. greater territorial aggression in males) can bias exposure risk, obfuscating the role of immune function, which can lead to differences in pathology, in driving differential susceptibility between sexes. Thus, sex-biased transmission driven by differences in immune function independent of behaviour is poorly understood, especially in non-mammalian systems. Here we examine the previously unexplored potential for male-biased pathology to affect transmission using an avian host-pathogen system. We employ a sex-dependent multistate transmission model parameterized with isolated, individual-based experimental exposures of domestic canaries and experimental transmission data of house finches. The experiment revealed that male birds have shorter incubation periods, longer recovery periods, higher pathogen burdens and greater disease pathology than females. Our model revealed that male-biased pathology led to epidemic size rapidly increasing with the proportion of male birds, with a nearly 10-fold increase in total epidemic size from an all-female to an all-male simulation. Our results demonstrate that female-biased resistance, independent of male behaviour, can drive sex-dependent transmission in wildlife, indicating that sex-based differences in immune function, not just differences in exposure risk, can shape epidemic dynamics.
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Affiliation(s)
- Erin L Sauer
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, USA
| | - Chloe Connelly
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, USA
| | - Weston Perrine
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, USA
| | - Ashely C Love
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, USA
- Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Sarah E DuRant
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, USA
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3
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Dhivahar J, Parthasarathy A, Krishnan K, Kovi BS, Pandian GN. Bat-associated microbes: Opportunities and perils, an overview. Heliyon 2023; 9:e22351. [PMID: 38125540 PMCID: PMC10730444 DOI: 10.1016/j.heliyon.2023.e22351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 09/21/2023] [Accepted: 11/09/2023] [Indexed: 12/23/2023] Open
Abstract
The potential biotechnological uses of bat-associated bacteria are discussed briefly, indicating avenues for biotechnological applications of bat-associated microbes. The uniqueness of bats in terms of their lifestyle, genomes and molecular immunology may predispose bats to act as disease reservoirs. Molecular phylogenetic analysis has shown several instances of bats harbouring the ancestral lineages of bacterial (Bartonella), protozoal (Plasmodium, Trypanosoma cruzi) and viral (SARS-CoV2) pathogens infecting humans. Along with the transmission of viruses from bats, we also discuss the potential roles of bat-associated bacteria, fungi, and protozoan parasites in emerging diseases. Current evidence suggests that environmental changes and interactions between wildlife, livestock, and humans contribute to the spill-over of infectious agents from bats to other hosts. Domestic animals including livestock may act as intermediate amplifying hosts for bat-origin pathogens to transmit to humans. An increasing number of studies investigating bat pathogen diversity and infection dynamics have been published. However, whether or how these infectious agents are transmitted both within bat populations and to other hosts, including humans, often remains unknown. Metagenomic approaches are uncovering the dynamics and distribution of potential pathogens in bat microbiomes, which might improve the understanding of disease emergence and transmission. Here, we summarize the current knowledge on bat zoonoses of public health concern and flag the gaps in the knowledge to enable further research and allocation of resources for tackling future outbreaks.
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Affiliation(s)
- J. Dhivahar
- Research Department of Zoology, St. Johns College, Palayamkottai, 627002, India
- Department of Plant Biology and Biotechnology, Laboratory of Microbial Ecology, Loyola College, Chennai, 600034, India
- Department of Biotechnology, Laboratory of Virology, University of Madras, Chennai, 600025, India
| | - Anutthaman Parthasarathy
- Department of Chemistry and Biosciences, Richmond Building, University of Bradford, Bradford, West Yorkshire, BD7 1DP, United Kingdom
| | - Kathiravan Krishnan
- Department of Biotechnology, Laboratory of Virology, University of Madras, Chennai, 600025, India
| | - Basavaraj S. Kovi
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Yoshida Ushinomiyacho, 69, Sakyo Ward, 606-8501, Kyoto, Japan
| | - Ganesh N. Pandian
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Yoshida Ushinomiyacho, 69, Sakyo Ward, 606-8501, Kyoto, Japan
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4
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White A, Giannetto M, Mulla L, Del Rosario A, Lim T, Culver E, Timmer M, Bushell J, Lambert MR, Hernández-Gómez O. Bacterial communities of the threatened Western Pond Turtle may be impacted by land use. FEMS Microbiol Ecol 2023; 99:fiad143. [PMID: 37950563 DOI: 10.1093/femsec/fiad143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 11/05/2023] [Accepted: 11/08/2023] [Indexed: 11/12/2023] Open
Abstract
As semi-aquatic species that use both terrestrial and aquatic habitats, freshwater turtles and their microbial communities are especially sensitive to the impacts of habitat disturbance. In this study, we use 16S rRNA amplicon sequencing to characterize the shell and cloacal bacterial communities of turtles in the San Francisco Bay Area. We captured western pond turtles (Actinemys/Emys marmorata) across eight sites located in urban and rural environments, along with invasive red-eared sliders (Trachemys scripta elegans). We assessed differences in western pond turtle bacterial communities diversity/composition between shell and cloacal samples and evaluated how alpha/beta diversity metrics were influenced by habitat quality. We found phylum-level bacterial taxonomic turnover in the bacterial communities of western pond turtles relative to the host tissue substrate samples. Our findings indicate that location identity elicits a high degree of lower-level (i.e. species/genus) bacterial taxonomic turnover. Further, we found that samples originating from good quality habitat had poorer shell bacterial communities but more diverse cloacal ones. The shell bacterial communities of red-eared sliders overlapped with those western pond turtles suggesting the existence of microbial dispersal between these two species. Our results add to our current understanding of turtle symbiont microbial ecology by establishing patterns of bacterial symbiont variation in an urban to rural gradient.
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Affiliation(s)
- Alison White
- Department of Natural Sciences and Mathematics, Dominican University of California, San Rafael, CA 94901, United States
| | - Madison Giannetto
- Department of Natural Sciences and Mathematics, Dominican University of California, San Rafael, CA 94901, United States
| | - Lubna Mulla
- Department of Natural Sciences and Mathematics, Dominican University of California, San Rafael, CA 94901, United States
| | - Amber Del Rosario
- Department of Natural Sciences and Mathematics, Dominican University of California, San Rafael, CA 94901, United States
| | - Tammy Lim
- East Bay Regional Parks, Oakland, CA 94605, United States
| | - Edward Culver
- East Bay Regional Parks, Oakland, CA 94605, United States
| | - Matthew Timmer
- Land Trust of Santa Cruz County, Santa Cruz, CA 95060, United States
| | - Jessie Bushell
- San Francisco Zoo and Gardens, San Francisco, CA 94132, United States
| | - Max R Lambert
- Washington Department of Fish and Wildlife, Olympia, WA 98501, United States
| | - Obed Hernández-Gómez
- Department of Natural Sciences and Mathematics, Dominican University of California, San Rafael, CA 94901, United States
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5
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Fieldman T. Evolutionary principles for modifying pathogen virulence. Crit Rev Microbiol 2023:1-12. [PMID: 37146153 DOI: 10.1080/1040841x.2023.2203766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Current methods for combatting infectious diseases are largely limited to the prevention of infection, enhancing host immunity (via vaccination), and administration of small molecules to slow the growth of or kill pathogens (e.g. antimicrobials). Beyond efforts to deter the rise of antimicrobial resistance, little consideration is given to pathogen evolution. Natural selection will favor different levels of virulence under different circumstances. Experimental studies and a wealth of theoretical work have identified many likely evolutionary determinants of virulence. Some of these, such as transmission dynamics, are amenable to modification by clinicians and public health practitioners. In this article, we provide a conceptual overview of virulence, followed by the analysis of modifiable evolutionary determinants of virulence including vaccinations, antibiotics, and transmission dynamics. Finally, we discuss both the importance and limitations of taking an evolutionary approach to reducing pathogen virulence.
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Affiliation(s)
- Tom Fieldman
- Clinical Microbiology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
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6
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Dallas JW, Warne RW. Captivity and Animal Microbiomes: Potential Roles of Microbiota for Influencing Animal Conservation. MICROBIAL ECOLOGY 2023; 85:820-838. [PMID: 35316343 DOI: 10.1007/s00248-022-01991-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 03/07/2022] [Indexed: 05/04/2023]
Abstract
During the ongoing biodiversity crisis, captive conservation and breeding programs offer a refuge for species to persist and provide source populations for reintroduction efforts. Unfortunately, captive animals are at a higher disease risk and reintroduction efforts remain largely unsuccessful. One potential factor in these outcomes is the host microbiota which includes a large diversity and abundance of bacteria, fungi, and viruses that play an essential role in host physiology. Relative to wild populations, the generalized pattern of gut and skin microbiomes in captivity are reduced alpha diversity and they exhibit a significant shift in community composition and/or structure which often correlates with various physiological maladies. Many conditions of captivity (antibiotic exposure, altered diet composition, homogenous environment, increased stress, and altered intraspecific interactions) likely lead to changes in the host-associated microbiome. To minimize the problems arising from captivity, efforts can be taken to manipulate microbial diversity and composition to be comparable with wild populations through methods such as increasing dietary diversity, exposure to natural environmental reservoirs, or probiotics. For individuals destined for reintroduction, these strategies can prime the microbiota to buffer against novel pathogens and changes in diet and improve reintroduction success. The microbiome is a critical component of animal physiology and its role in species conservation should be expanded and included in the repertoire of future management practices.
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Affiliation(s)
- Jason W Dallas
- Department of Biological Sciences, Southern Illinois University, 1125 Lincoln Drive, Carbondale, IL, 62901, USA.
| | - Robin W Warne
- Department of Biological Sciences, Southern Illinois University, 1125 Lincoln Drive, Carbondale, IL, 62901, USA
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7
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Sun W, Zheng Z. Research on removal of fluoroquinolones in rural domestic wastewater by vertical flow constructed wetlands under different hydraulic loads. CHEMOSPHERE 2022; 303:135100. [PMID: 35644233 DOI: 10.1016/j.chemosphere.2022.135100] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 04/08/2022] [Accepted: 05/22/2022] [Indexed: 06/15/2023]
Abstract
Antibiotics had attracted more and more attention in recent years due to their harmfulness. Fluoroquinolones (FQs), one class of antibiotics widely used in human and veterinary medicine, were found in various water bodies in China. Therefore, in order to found an efficient method for removing FQs in rural domestic wastewater and optimize the process parameters, ceramsite and soil were applied in vertical flow constructed wetlands (VFCWs) to study the effects of different hydraulic loads and different substrates on the removal of FQs and conventional pollutants. The results showed the VFCW-D filled with 45 cm soil layer and 15 cm ceramasite layer had the highest removal efficiency of conventional pollutants and FQs under low hydraulic load. Nevertheless, the removal efficiency of conventional pollutants was significantly declined for the VFCWs which contained soil substrates under high hydraulic load due to the soil pores were clogged by the accumulation of organic matter. Finally, VFCW-A filled with 60 cm ceramasite layer revealed good ability to remove conventional pollutants and FQs under high hydraulic load. Deinococcus played a vital role here due to its excellent removal effect on conventional pollutants. The microbial composition in the substrate changed greatly after adding antibiotics under high hydraulic load. Devosia, Pseudorhodoferax, Cellvibrio, Bosea, Caulobacter, Acinetobacter, Zoogloea, Arcobacter, Dechloromonas, Flavobacterium, Nakamurella, Chloroplast, Clostridium_sensu_stricto_1, Pelosinus, UTCFX1 and Hypnocyclicus became the new dominated genera and were essential to remove pollutants. In summary, VFCW was an effective system to remove fluoroquinolones in rural domestic wastewater.
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Affiliation(s)
- Wenjing Sun
- Department of Environmental Science and Engineering, Fudan University, Shanghai, 200438, China
| | - Zheng Zheng
- Department of Environmental Science and Engineering, Fudan University, Shanghai, 200438, China.
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8
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Sandmeier FC, Leonard KL, Weitzman CL, Tracy CR. Potential Facilitation Between a Commensal and a Pathogenic Microbe in a Wildlife Disease. ECOHEALTH 2022; 19:427-438. [PMID: 35752710 DOI: 10.1007/s10393-022-01603-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 05/16/2022] [Indexed: 06/15/2023]
Abstract
We assessed the potential for microbial interactions influencing a well-documented host-pathogen system. Mycoplasma agassizii is the known etiological agent of upper respiratory tract disease in Mojave desert tortoises (Gopherus agassizii), but disease in wild animals is extremely heterogeneous. For example, a much larger proportion of animals harbor M. agassizii than those that develop disease. With the availability of a new quantitative PCR assay for a microbe that had previously been implicated in disease, Pasteurella testudinis, we tested 389 previously collected samples of nasal microbes from tortoise populations across the Mojave desert. We showed that P. testudinis is a common commensal microbe. However, we did find that its presence was associated with higher levels of M. agassizii among the tortoises positive for this pathogen. The best predictor of P. testudinis prevalence in tortoise populations was average size of tortoises, suggesting that older populations have higher levels of P. testudinis. The prevalence of co-infection in populations was associated with the prevalence of URTD, providing additional evidence for an indirect interaction between the two microbes and inflammatory disease. We showed that URTD, like many chronic, polymicrobial diseases involving mucosal surfaces, shows patterns of a polymicrobial etiology.
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Affiliation(s)
- Franziska C Sandmeier
- Biology Department, LS 210, Colorado State University - Pueblo, 2100 Bonforte Blvd, Pueblo, CO, 81001, USA.
| | - Kendra L Leonard
- Biology Department, LS 210, Colorado State University - Pueblo, 2100 Bonforte Blvd, Pueblo, CO, 81001, USA
| | - Chava L Weitzman
- Biology Department, Virginia Polytechnic Institute and State University, Blacksburg, USA
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9
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Temporal impacts of topical ceftazidime and tobramycin-vancomycin mixtures on the ocular surface microbiota in rabbits. Exp Eye Res 2022; 220:109098. [PMID: 35513041 DOI: 10.1016/j.exer.2022.109098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 04/16/2022] [Accepted: 04/25/2022] [Indexed: 11/20/2022]
Abstract
Antibiotics are one of the important factors that can alter the diversity and composition of ocular surface microbiota. At present, there are a few studies about the antibiotic effect on ocular surface microbiota, including its time-dependent changes. However, these limited studies have revealed various results, and more experiments are required. In this study, we used 16 S rRNA sequencing method to investigate the effects of topical ceftazidime and tobramycin-vancomycin mixtures on the ocular surface microbiota and the temporal changes of the microbiota after discontinuing antibiotic treatment in rabbits. Seventeen healthy rabbits were treated with 5% ceftazidime and a mixture of 0.3% tobramycin-5% vancomycin (CTV) eye drops on one eye four times a day for 7 days. Swab samples of conjunctiva sacs were collected before antibiotic treatment (D0), 12 h after the last antibiotic treatment (D8) and two further time points on Day 15 (D15) and Day 30 (D30). We found that the species diversity of the ocular surface microbiota increased significantly at D8 and was restored at D15, namely, one week after antibiotic cessation. The community structure of the ocular surface microbiota changed after treatment with CTV but recovered at D30. At D8, the relative abundances of 13 bacterial phyla of the initial top 20 phyla and 11 bacterial genera of the initial top 20 genera were significantly different from the relative abundances of the phyla and genera at D0. Furthermore, the relative abundance of the dominant phylum Epsilonbacteraeota obviously decreased, while Proteobacteria and Bacteroidetes markedly increased. For dominant genera, the relative abundance of Helicobacter notably decreased, while Acinetobacter and Pasteurella greatly increased. Thirteen altered bacterial phyla and 7 of 11 altered bacterial genera recovered to preantibiotic levels at D30. In addition, there was a group of nondominant and rare bacteria enriched at D8, and most of them were restored at D30. In conclusion, the species diversity, community structure and composition of the ocular surface microbiota changed greatly after exposure to CTV, but they tended to be restored within weeks after discontinuing antibiotic treatment.
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10
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Nieto-Claudin A, Esperón F, Apakupakul K, Peña I, Deem SL. Health assessments uncover novel viral sequences in five species of Galapagos tortoises. Transbound Emerg Dis 2021; 69:e1079-e1089. [PMID: 34784447 DOI: 10.1111/tbed.14391] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 10/27/2021] [Accepted: 11/07/2021] [Indexed: 01/06/2023]
Abstract
Emerging infectious diseases (EIDs) have been reported as causes of morbidity and mortality in free-living animal populations, including turtles and tortoises, and they have even resulted in species extinctions, with human activities contributing to the spread of many of these diseases. In the Galapagos, giant tortoises are endangered due to habitat change, invasive species, and other human impacts; however, the impact of EIDs on Galapagos tortoise conservation remains understudied. To fill this gap, we conducted health assessments of five tortoise species from the islands of Santa Cruz, Isabela and Española. We performed health evaluations of 454 animals and PCR testing for pathogens known to be relevant in other tortoise species. We identified two novel sequences of adenoviruses and four of herpesviruses. Based on alignments of the DNA polymerase gene and maximum likelihood phylogenetic analyses, we found both novel adenoviruses to be most closely related to red footed tortoise adenovirus 2, by nucleotide sequence and red footed tortoise adenovirus 1, based on amino acid sequence. Three of the herpesvirus sequences translated into the same deduced amino acid sequence; therefore, they may be considered the same viral species, closely related to terrapene herpesvirus 2. The fourth herpesvirus sequence was highly divergent from any sequence previously detected and is related to an eagle owl herpesvirus based on nucleotide sequence and to loggerhead oro-cutaneous herpesvirus based on amino acids. These novel viruses may be pathogenic for giant tortoises under specific conditions (e.g., stress). Continued screening is crucial to determine if these viruses play a role in tortoise fitness, morbidity and survival. This information allows us to provide recommendations to the Galapagos National Park Directorate and other institutions to improve the management of these unique species both in Galapagos and globally, and for tortoise reintroduction plans throughout the archipelago.
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Affiliation(s)
- Ainoa Nieto-Claudin
- Charles Darwin Research Station, Charles Darwin Foundation, Santa Cruz, Galapagos, Ecuador.,Veterinary Faculty, Complutense University of Madrid, Puerta de Hierro Av, Madrid, Spain.,Saint Louis Zoo Institute for Conservation Medicine, One Government Drive, Saint Louis, Missouri
| | - Fernando Esperón
- Veterinary Faculty, Complutense University of Madrid, Puerta de Hierro Av, Madrid, Spain.,INIA, CISA, Algete-El Casar Road, Valdeolmos, Spain.,Veterinary Department, School of Biomedical and Health Sciences, Universidad Europea de Madrid, Madrid, Spain
| | - Kathleen Apakupakul
- Saint Louis Zoo Institute for Conservation Medicine, One Government Drive, Saint Louis, Missouri
| | - Irene Peña
- Charles Darwin Research Station, Charles Darwin Foundation, Santa Cruz, Galapagos, Ecuador
| | - Sharon L Deem
- Charles Darwin Research Station, Charles Darwin Foundation, Santa Cruz, Galapagos, Ecuador.,Saint Louis Zoo Institute for Conservation Medicine, One Government Drive, Saint Louis, Missouri
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11
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Weitzman CL, Rostama B, Thomason CA, May M, Belden LK, Hawley DM. Experimental test of microbiome protection across pathogen doses reveals importance of resident microbiome composition. FEMS Microbiol Ecol 2021; 97:6385755. [PMID: 34626186 DOI: 10.1093/femsec/fiab141] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 10/07/2021] [Indexed: 01/04/2023] Open
Abstract
The commensal microbes inhabiting a host tissue can interact with invading pathogens and host physiology in ways that alter pathogen growth and disease manifestation. Prior work in house finches (Haemorhous mexicanus) found that resident ocular microbiomes were protective against conjunctival infection and disease caused by a relatively high dose of Mycoplasma gallisepticum. Here, we used wild-caught house finches to experimentally examine whether protective effects of the resident ocular microbiome vary with the dose of invading pathogen. We hypothesized that commensal protection would be strongest at low M. gallisepticum inoculation doses because the resident microbiome would be less disrupted by invading pathogen. Our five M. gallisepticum dose treatments were fully factorial with an antibiotic treatment to perturb resident microbes just prior to M. gallisepticum inoculation. Unexpectedly, we found no indication of protective effects of the resident microbiome at any pathogen inoculation dose, which was inconsistent with the prior work. The ocular bacterial communities at the beginning of our experiment differed significantly from those previously reported in local wild-caught house finches, likely causing this discrepancy. These variable results underscore that microbiome-based protection in natural systems can be context dependent, and natural variation in community composition may alter the function of resident microbiomes in free-living animals.
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Affiliation(s)
- Chava L Weitzman
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24060, USA
| | - Bahman Rostama
- Department of Biomedical Sciences, University of New England, Biddeford - 04005, ME, USA
| | - Courtney A Thomason
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24060, USA.,Division of Remediation, Tennessee Department of Environment and Conservation, Oak Ridge - 37830, TN, USA
| | - Meghan May
- Department of Biomedical Sciences, University of New England, Biddeford - 04005, ME, USA
| | - Lisa K Belden
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24060, USA
| | - Dana M Hawley
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24060, USA
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12
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Slowinski S, Ramirez I, Narayan V, Somayaji M, Para M, Pi S, Jadeja N, Karimzadegan S, Pees B, Shapira M. Interactions with a Complex Microbiota Mediate a Trade-Off between the Host Development Rate and Heat Stress Resistance. Microorganisms 2020; 8:microorganisms8111781. [PMID: 33202910 PMCID: PMC7697855 DOI: 10.3390/microorganisms8111781] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 11/09/2020] [Accepted: 11/11/2020] [Indexed: 12/28/2022] Open
Abstract
Animals and plants host diverse communities of microorganisms, and these microbiotas have been shown to influence host life history traits. Much has been said about the benefits that host-associated microbiotas bestow on the host. However, life history traits often demonstrate tradeoffs among one another. Raising Caenorhabditis elegans nematodes in compost microcosms emulating their natural environment, we examined how complex microbiotas affect host life history traits. We show that soil microbes usually increase the host development rate but decrease host resistance to heat stress, suggesting that interactions with complex microbiotas may mediate a tradeoff between host development and stress resistance. What element in these interactions is responsible for these effects is yet unknown, but experiments with live versus dead bacteria suggest that such effects may depend on bacterially provided signals.
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Affiliation(s)
- Samuel Slowinski
- Department of Integrative Biology, 3040 Valley Life Sciences Building, University of California, Berkeley, CA 94720-3140, USA; (I.R.); (V.N.); (M.S.); (M.P.); (S.P.); (N.J.); (S.K.); (B.P.)
- Department of Biology, 4223 Biology-Psychology Bldg., University of Maryland, College Park, MD 20742, USA
- Correspondence: (S.S.); (M.S.)
| | - Isabella Ramirez
- Department of Integrative Biology, 3040 Valley Life Sciences Building, University of California, Berkeley, CA 94720-3140, USA; (I.R.); (V.N.); (M.S.); (M.P.); (S.P.); (N.J.); (S.K.); (B.P.)
| | - Vivek Narayan
- Department of Integrative Biology, 3040 Valley Life Sciences Building, University of California, Berkeley, CA 94720-3140, USA; (I.R.); (V.N.); (M.S.); (M.P.); (S.P.); (N.J.); (S.K.); (B.P.)
| | - Medha Somayaji
- Department of Integrative Biology, 3040 Valley Life Sciences Building, University of California, Berkeley, CA 94720-3140, USA; (I.R.); (V.N.); (M.S.); (M.P.); (S.P.); (N.J.); (S.K.); (B.P.)
| | - Maya Para
- Department of Integrative Biology, 3040 Valley Life Sciences Building, University of California, Berkeley, CA 94720-3140, USA; (I.R.); (V.N.); (M.S.); (M.P.); (S.P.); (N.J.); (S.K.); (B.P.)
| | - Sarah Pi
- Department of Integrative Biology, 3040 Valley Life Sciences Building, University of California, Berkeley, CA 94720-3140, USA; (I.R.); (V.N.); (M.S.); (M.P.); (S.P.); (N.J.); (S.K.); (B.P.)
| | - Niharika Jadeja
- Department of Integrative Biology, 3040 Valley Life Sciences Building, University of California, Berkeley, CA 94720-3140, USA; (I.R.); (V.N.); (M.S.); (M.P.); (S.P.); (N.J.); (S.K.); (B.P.)
| | - Siavash Karimzadegan
- Department of Integrative Biology, 3040 Valley Life Sciences Building, University of California, Berkeley, CA 94720-3140, USA; (I.R.); (V.N.); (M.S.); (M.P.); (S.P.); (N.J.); (S.K.); (B.P.)
| | - Barbara Pees
- Department of Integrative Biology, 3040 Valley Life Sciences Building, University of California, Berkeley, CA 94720-3140, USA; (I.R.); (V.N.); (M.S.); (M.P.); (S.P.); (N.J.); (S.K.); (B.P.)
| | - Michael Shapira
- Department of Integrative Biology, 3040 Valley Life Sciences Building, University of California, Berkeley, CA 94720-3140, USA; (I.R.); (V.N.); (M.S.); (M.P.); (S.P.); (N.J.); (S.K.); (B.P.)
- Correspondence: (S.S.); (M.S.)
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13
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Microbiome dynamics and genomic determinants of bovine mastitis. Genomics 2020; 112:5188-5203. [PMID: 32966856 DOI: 10.1016/j.ygeno.2020.09.039] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/24/2020] [Accepted: 09/19/2020] [Indexed: 01/21/2023]
Abstract
The milk of lactating cows presents a complex ecosystem of interconnected microbial communities which can influence the pathophysiology of mastitis. We hypothesized possible dynamic shifts of microbiome composition and genomic features with different pathological conditions of mastitis (Clinical Mastitis; CM, Recurrent CM; RCM, Subclinical Mastitis; SCM). To evaluate this hypothesis, we employed whole metagenome sequencing (WMS) in 20 milk samples (CM, 5; RCM, 6; SCM, 4; H, 5) to unravel the microbiome dynamics, interrelation, and relevant metabolic functions. The WMS data mapped to 442 bacterial, 58 archaeal and 48 viral genomes with distinct variation in microbiome composition (CM > H > RCM > SCM). Furthermore, we identified a number of microbial genomic features, including 333, 304, 183 and 50 virulence factors-associated genes (VFGs) and 48, 31, 11 and 6 antibiotic resistance genes (ARGs) in CM, RCM, SCM, and H-microbiomes, respectively. We also detected different metabolic pathway and functional genes associated with mastitis pathogenesis. Therefore, profiling microbiome dynamics in different conditions of mastitis and associated microbial genomic features contributes to developing microbiome-based diagnostics and therapeutics for bovine mastitis.
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14
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Kruger A. Frog Skin Microbiota Vary With Host Species and Environment but Not Chytrid Infection. Front Microbiol 2020; 11:1330. [PMID: 32670233 PMCID: PMC7328345 DOI: 10.3389/fmicb.2020.01330] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 05/25/2020] [Indexed: 01/15/2023] Open
Abstract
Describing the structure and function of the amphibian cutaneous microbiome has gained importance with the spread of Batrachochytrium dendrobatidis (Bd), the fungal pathogen that can cause the skin disease chytridiomycosis. Sampling amphibian skin microbiota is needed to characterize current infection status and to help predict future susceptibility to Bd based on microbial composition since some skin microbes have antifungal capabilities that may confer disease resistance. Here, I use 16S rRNA sequencing to describe the composition and structure of the cutaneous microbiota of six species of amphibians. Frog skin samples were also tested for Bd, and I found 11.8% Bd prevalence among all individuals sampled (n = 76). Frog skin microbiota varied by host species and sampling site, but did not differ among Bd-positive and Bd-negative individuals. These results suggest that bacterial composition reflects host species and the environment, but does not reflect Bd infection among the species sampled here. Of the bacterial OTUs identified using an indicator species analysis as strongly associated with amphibians, significantly more indicator OTUs were putative anti-Bd taxa than would be expected based on the proportion of anti-Bd OTUs among all frog OTUs, suggesting strong associations between host species and anti-Bd OTUs. This relationship may partially explain why some of these frogs are asymptomatic carriers of Bd, but more work is needed to determine the other factors that contribute to interspecific variation in Bd susceptibility. This work provides important insights on inter- and intra-specific variation in microbial community composition, putative function, and disease dynamics in populations of amphibians that appear to be coexisting with Bd.
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Affiliation(s)
- Ariel Kruger
- Department of Ecology, Evolution, and Natural Resources, Rutgers University, New Brunswick, NJ, United States
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15
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Respiratory and Gut Microbiota in Commercial Turkey Flocks with Disparate Weight Gain Trajectories Display Differential Compositional Dynamics. Appl Environ Microbiol 2020; 86:AEM.00431-20. [PMID: 32276973 DOI: 10.1128/aem.00431-20] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 04/01/2020] [Indexed: 12/11/2022] Open
Abstract
Communities of gut bacteria (microbiota) are known to play roles in resistance to pathogen infection and optimal weight gain in turkey flocks. However, knowledge of turkey respiratory microbiota and its link to gut microbiota is lacking. This study presents a 16S rRNA gene-based census of the turkey respiratory microbiota (nasal cavity and trachea) alongside gut microbiota (cecum and ileum) in two identical commercial Hybrid Converter turkey flocks raised in parallel under typical field commercial conditions. The flocks were housed in adjacent barns during the brood stage and in geographically separated farms during the grow-out stage. Several bacterial taxa, primarily Staphylococcus, that were acquired in the respiratory tract at the beginning of the brood stage persisted throughout the flock cycle. Late-emerging predominant taxa in the respiratory tract included Deinococcus and Corynebacterium Tracheal and nasal microbiota of turkeys were identifiably distinct from one another and from gut microbiota. Nevertheless, gut and respiratory microbiota changed in parallel over time and appeared to share many taxa. During the brood stage, the two flocks generally acquired similar gut and respiratory microbiota, and their average body weights were comparable. However, there were qualitative and quantitative differences in microbial profiles and body weight gain trajectories after the flocks were transferred to geographically separated grow-out farms. Lower weight gain corresponded to the emergence of Deinococcus and Ornithobacterium in the respiratory tract and Fusobacterium and Parasutterella in gut. This study provides an overview of turkey microbiota under field conditions and suggests several hypotheses concerning the respiratory microbiome.IMPORTANCE Turkey meat is an important source of animal protein, and the industry around its production contributes significantly to the agricultural economy. The microorganisms present in the gut of turkeys are known to impact bird health and flock performance. However, the respiratory microbiota in turkeys is entirely unexplored. This study has elucidated the microbiota of respiratory tracts of turkeys from two commercial flocks raised in parallel throughout a normal flock cycle. Further, the study suggests that bacteria originating in the gut or in poultry house environments influence respiratory communities; consequently, they induce poor performance, either directly or indirectly. Future attempts to develop microbiome-based interventions for turkey health should delimit the contributions of respiratory microbiota and aim to limit disturbances to those communities.
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16
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Perez K, Mullen N, Canter JA, Ley DH, May M. Phenotypic diversity in an emerging mycoplasmal disease. Microb Pathog 2019; 138:103798. [PMID: 31639466 DOI: 10.1016/j.micpath.2019.103798] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 10/08/2019] [Accepted: 10/11/2019] [Indexed: 11/27/2022]
Abstract
The avian pathogen Mycoplasma gallisepticum (MG) is a known pathogen of poultry, and newly emerged pathogen of house finches wherein it is associated with lethal conjunctivitis. Factors present in MG that are known to mediate virulence include cytadherence, sialidase activity, peroxide production, and biofilm formation. We have quantitatively assessed these factors for MG isolates from house finches from a temporal and geographic distribution across the continental United States that show differing capacity for virulence in vivo. Statistically significant (P < 0.05) differences were observed across strains for sialidase activity, cytadherence, and hydrogen peroxide production. Sialidase activity increased over time in geographically static populations, but did not correlate with time overall. All strains were able to bind α-2,6-linked sialic acid. No strains were found to bind α-2,3-linked sialic acid. All strains produced biofilms in vitro; however, no significant differences were observed in the density of biofilms across strains. Quantitative variance in virulence-associated traits is consistent with within-host evolutionary adaptation in response to a change in ecological niche by a parasitic pathogen.
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Affiliation(s)
- Kailey Perez
- Department of Biomedical Sciences, University of New England, Biddeford, ME, USA
| | - Nathan Mullen
- Department of Biomedical Sciences, University of New England, Biddeford, ME, USA
| | - Jessica A Canter
- Department of Pathobiology and Veterinary Science, University of Connecticut, Storrs, CT, USA
| | - David H Ley
- Department of Population Health and Pathobiology, North Carolina State University, Raleigh, NC, USA
| | - Meghan May
- Department of Biomedical Sciences, University of New England, Biddeford, ME, USA.
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17
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Metcalf CJE, Koskella B. Protective microbiomes can limit the evolution of host pathogen defense. Evol Lett 2019; 3:534-543. [PMID: 31636945 PMCID: PMC6791398 DOI: 10.1002/evl3.140] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 08/22/2019] [Accepted: 08/28/2019] [Indexed: 12/17/2022] Open
Abstract
The evolution of host immunity occurs in the context of the microbiome, but little theory exists to predict how resistance against pathogens might be influenced by the need to tolerate and regulate commensal microbiota. We present a general model to explore the optimal investment in host immunity under conditions in which the host can, versus cannot easily distinguish among commensal versus pathogenic bacteria, and when commensal microbiota can, versus cannot protect the host against the impacts of pathogen infection. We find that a loss of immune vigilance associated with innate immunity over evolutionary time can occur due to the challenge of discriminating between pathogenic and other microbe species. Further, we find the greater the protective effect of microbiome species, acting either directly or via competition with a pathogen, or the higher the costs of immunity, the more likely the loss of immune vigilance is. Conversely, this effect can be reversed when pathogens increase host mortality. Generally, the magnitude of costs of immunity required to allow evolution of decreased immune vigilance are predicted to be lowest when microbiome and pathogen species most resemble each other (in terms of host recognition), and when immune effects on the pathogen are weak. Our model framework makes explicit the core trade‐offs likely to shape the evolution of immunity in the context of microbiome/pathogen discrimination. We discuss how this informs interpretation of patterns and process in natural systems, including vulnerability to pathogen emergence.
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Affiliation(s)
- C Jessica E Metcalf
- Department of Ecology and Evolutionary Princeton University Princeton New Jersey 08540
| | - Britt Koskella
- Department of Integrative Biology University of California Berkeley Berkeley California 94720
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18
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Ingala MR, Becker DJ, Bak Holm J, Kristiansen K, Simmons NB. Habitat fragmentation is associated with dietary shifts and microbiota variability in common vampire bats. Ecol Evol 2019; 9:6508-6523. [PMID: 31236240 PMCID: PMC6580296 DOI: 10.1002/ece3.5228] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 04/12/2019] [Accepted: 04/15/2019] [Indexed: 12/28/2022] Open
Abstract
Host ecological factors and external environmental factors are known to influence the structure of gut microbial communities, but few studies have examined the impacts of environmental changes on microbiotas in free-ranging animals. Rapid land-use change has the potential to shift gut microbial communities in wildlife through exposure to novel bacteria and/or by changing the availability or quality of local food resources. The consequences of such changes to host health and fitness remain unknown and may have important implications for pathogen spillover between humans and wildlife. To better understand the consequences of land-use change on wildlife microbiotas, we analyzed long-term dietary trends, gut microbiota composition, and innate immune function in common vampire bats (Desmodus rotundus) in two nearby sites in Belize that vary in landscape structure. We found that vampire bats living in a small forest fragment had more homogenous diets indicative of feeding on livestock and shifts in microbiota heterogeneity, but not overall composition, compared to those living in an intact forest reserve. We also found that irrespective of sampling site, vampire bats which consumed relatively more livestock showed shifts in some core bacteria compared with vampire bats which consumed relatively less livestock. The relative abundance of some core microbiota members was associated with innate immune function, suggesting that future research should consider the role of the host microbiota in immune defense and its relationship to zoonotic infection dynamics. We suggest that subsequent homogenization of diet and habitat loss through livestock rearing in the Neotropics may lead to disruption to the microbiota that could have downstream impacts on host immunity and cross-species pathogen transmission.
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Affiliation(s)
- Melissa R. Ingala
- Richard Gilder Graduate SchoolAmerican Museum of Natural HistoryNew YorkNew York
- Division of Vertebrate Zoology, Department of MammalogyAmerican Museum of Natural HistoryNew YorkNew York
| | - Daniel J. Becker
- Odum School of EcologyUniversity of GeorgiaAthensGeorgia
- Center for the Ecology of Infectious DiseaseUniversity of GeorgiaAthensGeorgia
- Department of BiologyIndiana UniversityBloomingtonIndiana
| | - Jacob Bak Holm
- Department of BiologyUniversity of CopenhagenCopenhagenDenmark
- Clinical‐MicrobiomicsCopenhagenDenmark
| | - Karsten Kristiansen
- Department of BiologyUniversity of CopenhagenCopenhagenDenmark
- BGIShenzhenChina
| | - Nancy B. Simmons
- Division of Vertebrate Zoology, Department of MammalogyAmerican Museum of Natural HistoryNew YorkNew York
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Correa-Fiz F, Gonçalves Dos Santos JM, Illas F, Aragon V. Antimicrobial removal on piglets promotes health and higher bacterial diversity in the nasal microbiota. Sci Rep 2019; 9:6545. [PMID: 31024076 PMCID: PMC6484018 DOI: 10.1038/s41598-019-43022-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 04/12/2019] [Indexed: 01/28/2023] Open
Abstract
The view on antimicrobials has dramatically changed due to the increased knowledge on the importance of microbiota composition in different body parts. Antimicrobials can no longer be considered only beneficial, but also potentially deleterious for favourable bacterial populations. Still, the use of metaphylactic antimicrobial treatment at early stages of life is a practice in use in porcine production. Many reports have shown that antibiotics can critically affect the gut microbiota, however the effect of perinatal antimicrobial treatment on the nasal microbiota has not been explored yet. To gain insights on the potential changes in nasal microbial composition due to antimicrobial treatments, piglets from two different farms were sampled at weaning. The nasal microbiota was analysed when antimicrobial treatment was used early in life, and later, when no antimicrobial treatment was used during the lactation period. Removal of perinatal antimicrobials resulted in an increased bacterial diversity in nasal microbiota at weaning. Concurrently, elimination of antimicrobials produced an increase in the relative abundance of Prevotella and Lactobacillus, and a decrease in Moraxella and Bergeyella. These changes in microbiota composition were accompanied by an improvement of the piglets' health and a higher productivity in the nursery phase.
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Affiliation(s)
- Florencia Correa-Fiz
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain.
| | | | - Francesc Illas
- Selección Batallé, Avinguda dels segadors, 17421, Riudarenes, Spain
| | - Virginia Aragon
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
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20
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Menke S, Heurich M, Henrich M, Wilhelm K, Sommer S. Impact of winter enclosures on the gut bacterial microbiota of red deer in the Bavarian Forest National Park. WILDLIFE BIOLOGY 2019. [DOI: 10.2981/wlb.00503] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Sebastian Menke
- S. Menke, K. Wilhelm and S. Sommer , Inst. of Ecology and Conservation Genomics, Univ. of Ulm, Albert-Einstein Allee 11, DE-89081 Ulm, Germany
| | - Marco Heurich
- M. Heurich and M. Henrich, Dept of Conservation and Research, Bavarian Forest National Park, Zoology, Grafenau, Germany
| | - Maik Henrich
- M. Heurich and M. Henrich, Dept of Conservation and Research, Bavarian Forest National Park, Zoology, Grafenau, Germany
| | - Kerstin Wilhelm
- S. Menke, K. Wilhelm and S. Sommer , Inst. of Ecology and Conservation Genomics, Univ. of Ulm, Albert-Einstein Allee 11, DE-89081 Ulm, Germany
| | - Simone Sommer
- S. Menke, K. Wilhelm and S. Sommer , Inst. of Ecology and Conservation Genomics, Univ. of Ulm, Albert-Einstein Allee 11, DE-89081 Ulm, Germany
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21
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Leis ML, Costa MO. Initial description of the core ocular surface microbiome in dogs: Bacterial community diversity and composition in a defined canine population. Vet Ophthalmol 2018; 22:337-344. [PMID: 30095241 DOI: 10.1111/vop.12599] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
OBJECTIVE To characterize the bacterial community residing on the conjunctiva of clinically healthy dogs. METHODS Bacterial DNA from conjunctival swabs of 10 dogs with normal ocular examinations (both OD and OS, n = 20) was extracted, and 16S rRNA amplicons were sequenced using Illumina MiSeq 600. Resulting data were subjected to quality control steps, and analyzed for bacterial community richness and diversity, within- and between-group dissimilarity, and relative taxonomic composition. RESULTS High-quality reads (2.22 million bp) resulted in a mean of 159 068 sequences per sample. Bacterial community evenness and diversity was high when compared to other species, and did not significantly differ when samples were grouped by dogs or eyes. As expected, within-dog samples were more similar than between-dog samples. Taxonomic classification revealed that >95% of the community consisted of Firmicutes (34.9 ± 8.8%), Actinobacteria (26.3 ± 7.1%), Proteobacteria (26.2 ± 6.6%), and Bacteroidetes (9.4 ± 2.4%). Key members of the dog ocular surface microbiome, found in all dogs and corresponding to >25% of all identified OTUs (operational taxonomic units), were part of the Bifidobacteriaceae, Lachnospiraceae, Moraxellaceae, Corynebacteriaceae families. Genera previously thought to account for the majority of the core ocular surface microbiome in the dog (Staphylococcus sp., Streptococcus sp., and Bacillus sp.) were associated with only 2.63% of overall reads. CONCLUSIONS This study shows the feasibility of conjunctival swabs and high-throughput sequencing to profile the bacterial community structure of the canine ocular surface. A core ocular surface microbiome was identified for this canine population.
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Affiliation(s)
- Marina L Leis
- Small Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Matheus O Costa
- Faculty of Veterinary Medicine, Department of Farm Animal Health, Utrecht University, Utrecht, Netherlands.,Large Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
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22
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Knutie SA. Relationships among introduced parasites, host defenses, and gut microbiota of Galapagos birds. Ecosphere 2018. [DOI: 10.1002/ecs2.2286] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Affiliation(s)
- Sarah A. Knutie
- Department of Ecology and Evolutionary Biology University of Connecticut Storrs Connecticut 06269 USA
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23
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Kim D, Kwon SJ, Wu X, Sauve J, Lee I, Nam J, Kim J, Dordick JS. Selective Killing of Pathogenic Bacteria by Antimicrobial Silver Nanoparticle-Cell Wall Binding Domain Conjugates. ACS APPLIED MATERIALS & INTERFACES 2018; 10:13317-13324. [PMID: 29619821 DOI: 10.1021/acsami.8b00181] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Broad-spectrum antibiotics indiscriminately kill bacteria, removing nonpathogenic microorganisms and leading to evolution of antibiotic resistant strains. Specific antimicrobials that could selectively kill pathogenic bacteria without targeting other bacteria in the natural microbial community or microbiome may be able to address this concern. In this work, we demonstrate that silver nanoparticles, suitably conjugated to a selective cell wall binding domain (CBD), can efficiently target and selectively kill bacteria. As a relevant example, CBDBA from Bacillus anthracis selectively bound to B. anthracis in a mixture with Bacillus subtilis, as well in a mixture with Staphylococcus aureus. This new biologically-assisted hybrid strategy, therefore, has the potential to provide selective decontamination of pathogenic bacteria with minimal impact on normal microflora.
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Affiliation(s)
- Domyoung Kim
- Department of Chemical and Biological Engineering , Rensselaer Polytechnic Institute , 110 8th Street , Troy , New York 12180 , United States
| | - Seok-Joon Kwon
- Department of Chemical and Biological Engineering , Rensselaer Polytechnic Institute , 110 8th Street , Troy , New York 12180 , United States
| | - Xia Wu
- Department of Chemical and Biological Engineering , Rensselaer Polytechnic Institute , 110 8th Street , Troy , New York 12180 , United States
| | - Jessica Sauve
- Department of Chemical and Biological Engineering , Rensselaer Polytechnic Institute , 110 8th Street , Troy , New York 12180 , United States
| | - Inseon Lee
- Department of Chemical and Biological Engineering , Korea University , 145 Anam-ro , Seongbuk-gu , Seoul 02841 , Republic of Korea
| | - Jahyun Nam
- Department of Chemical and Biological Engineering , Korea University , 145 Anam-ro , Seongbuk-gu , Seoul 02841 , Republic of Korea
| | - Jungbae Kim
- Department of Chemical and Biological Engineering , Korea University , 145 Anam-ro , Seongbuk-gu , Seoul 02841 , Republic of Korea
| | - Jonathan S Dordick
- Department of Chemical and Biological Engineering , Rensselaer Polytechnic Institute , 110 8th Street , Troy , New York 12180 , United States
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