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Těšický M, Schmiedová L, Krajzingrová T, Samblas MG, Bauerová P, Kreisinger J, Vinkler M. Nearly (?) sterile avian egg in a passerine bird. FEMS Microbiol Ecol 2024; 100:fiad164. [PMID: 38115624 PMCID: PMC10791042 DOI: 10.1093/femsec/fiad164] [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: 02/14/2023] [Revised: 12/02/2023] [Accepted: 12/18/2023] [Indexed: 12/21/2023] Open
Abstract
During early ontogeny, microbiome affects development of the gastrointestinal tract, immunity, and survival in vertebrates. Bird eggs are thought to be (1) initially sterile (sterile egg hypothesis) and (2) colonized after oviposition through horizontal trans-shell migration, or (3) initially seeded with bacteria by vertical transfer from mother oviduct. To date, however, little empirical data illuminate the contribution of these mechanisms to gut microbiota formation in avian embryos. We investigated microbiome of the egg content (day 0; E0-egg), embryonic gut at day 13 (E13) and female faeces in a free-living passerine, the great tit (Parus major), using a methodologically advanced procedure combining 16S rRNA gene sequencing and microbe-specific qPCR assays. Our metabarcoding revealed that the avian egg is (nearly) sterile, but acquires a slightly richer microbiome during the embryonic development. Of the three potentially pathogenic bacteria targeted by qPCR, only Dietzia was found in E0-egg (yet also in negative controls), E13 gut and female samples, which might indicate possible vertical transfer. Unlike in poultry, we have shown that major bacterial colonization of the gut in passerines does not occur before hatching. We emphasize that protocols that carefully check for environmental contamination are critical in studies with low-bacterial biomass samples.
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Affiliation(s)
- Martin Těšický
- Faculty of Science, Department of Zoology, Charles University, Viničná 7, 128 43 Prague, Czech Republic
- Institute of Vertebrate Biology, v.v.i., The Czech Academy of Sciences, Květná 8, Brno 603 65, Czech Republic
- Institute of Paleonatomy, Domestification Research and History of Veterinary Medicine, Ludwig Maxmilian University of Munich, Kaulbachstr. 37 III, 80539 Munich, Germany
| | - Lucie Schmiedová
- Faculty of Science, Department of Zoology, Charles University, Viničná 7, 128 43 Prague, Czech Republic
- Institute of Vertebrate Biology, v.v.i., The Czech Academy of Sciences, Květná 8, Brno 603 65, Czech Republic
| | - Tereza Krajzingrová
- Faculty of Science, Department of Zoology, Charles University, Viničná 7, 128 43 Prague, Czech Republic
| | - Mercedes Gomez Samblas
- Faculty of Science, Department of Zoology, Charles University, Viničná 7, 128 43 Prague, Czech Republic
- Faculty of Science, Department of Parasitology, Campus Universitario de Fuentenueva, University of Granada, Profesor Adolfo Rancano, 18071 Granada, Spain
| | - Petra Bauerová
- Division of Air Quality, Czech Hydrometeorological Institute
, Tušimice Observatory, Tušimice 6, 432 01 Kadaň, Czech Republic
| | - Jakub Kreisinger
- Faculty of Science, Department of Zoology, Charles University, Viničná 7, 128 43 Prague, Czech Republic
| | - Michal Vinkler
- Faculty of Science, Department of Zoology, Charles University, Viničná 7, 128 43 Prague, Czech Republic
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2
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Girgis MM, Christodoulides M. Vertebrate and Invertebrate Animal and New In Vitro Models for Studying Neisseria Biology. Pathogens 2023; 12:782. [PMID: 37375472 DOI: 10.3390/pathogens12060782] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/03/2023] [Accepted: 05/18/2023] [Indexed: 06/29/2023] Open
Abstract
The history of Neisseria research has involved the use of a wide variety of vertebrate and invertebrate animal models, from insects to humans. In this review, we itemise these models and describe how they have made significant contributions to understanding the pathophysiology of Neisseria infections and to the development and testing of vaccines and antimicrobials. We also look ahead, briefly, to their potential replacement by complex in vitro cellular models.
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Affiliation(s)
- Michael M Girgis
- Neisseria Research Group, Molecular Microbiology, School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK
- Department of Microbiology and Immunology, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Myron Christodoulides
- Neisseria Research Group, Molecular Microbiology, School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK
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3
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Rothia nasimurium as a Cause of Disease: First Isolation from Farmed Chickens. Vet Sci 2022; 9:vetsci9120653. [PMID: 36548814 PMCID: PMC9783258 DOI: 10.3390/vetsci9120653] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/17/2022] [Accepted: 11/18/2022] [Indexed: 11/24/2022] Open
Abstract
Rothia nasimurium is a facultative anaerobic Gram-positive coccus belonging to the Rothia genus of the Micrococcaceae family. While Rothia nasimurium is considered an opportunistic pathogen, to date few studies have investigated its pathogenicity and drug resistance. In January 2022, chickens at a poultry farm in China's Xinjiang Uygur Autonomous Region became ill and died. Treatment with commonly used Chinese medicines and antibiotics was ineffective, causing economic losses to the poultry farm. In order to determine the cause of the disease in these poultry farm chickens, the isolation and identification of the pathogens in the livers and other internal organs of the sick and dead chickens were performed. Further, animal pathogenicity tests, antibiotic susceptibility tests, and the detection of antibiotic resistance genes were carried out to analyze the pathogenicity and drug resistance of the identified pathogens. A Gram-positive coccus was isolated from the livers of the diseased chickens. The isolate was resistant to 17 antibiotics, including ciprofloxacin, chloramphenicol, and florfenicol, and was only sensitive to penicillin, amikacin, and tigecycline, to varying degrees. The results of the drug resistance gene testing indicated that the isolated bacterium carried 13 kinds of resistance genes. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, morphological observations, biochemical tests, and 16S rRNA gene sequence analysis were performed on the isolated bacterium, and it was determined that the isolated bacterial strain was Rothia nasimurium. The animal pathogenicity tests showed that the isolate caused feather loss and death in chicks; the clinical symptoms and necropsy lesions of the test chicks were consistent with those observed in the farmed chickens. A review of the literature revealed that, to date, there are no reports of infection with Rothia nasimurium in chickens. Thus, in this study, Rothia nasimurium was isolated from chickens for the first time and an investigation of the biological characteristics of the bacterium was carried out in order to provide a reference for the clinical treatment, prevention, and control of Rothia nasimurium infection.
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Li T, Yang Y, Li H, Li C. Mixed-Mode Bacterial Transmission via Eggshells in an Oviparous Reptile Without Parental Care. Front Microbiol 2022; 13:911416. [PMID: 35836422 PMCID: PMC9273969 DOI: 10.3389/fmicb.2022.911416] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Accepted: 05/23/2022] [Indexed: 11/13/2022] Open
Abstract
Symbiotic microorganisms play important roles in maintaining health and facilitating the adaptation of the host. We know little about the origin and transgenerational transmission of symbiotic bacteria, especially in egg-laying species without parental care. Here, we investigated the transmission of bacterial symbionts in the Chinese three-keeled pond turtle (Mauremys reevesii), a species with no post-oviposition parental care, by evaluating contributions from potential maternal and environmental sources to eggshell bacterial communities. Using 16S rRNA amplicon sequencing, we established that the bacterial communities of eggshells were similar to those of the maternal cloaca, maternal skin, and nest soil, but distinct from those of surface soil around nest and pond water. Phylogenetic structure analysis and source-tracking models revealed the deterministic assembly process of eggshell microbiota and high contributions of the maternal cloaca, maternal skin, and nest soil microbiota to eggshell bacterial communities. Moreover, maternal cloaca showed divergent contribution to eggshell microbiota compared with two other main sources in phylogenesis and taxonomic composition. The results demonstrate a mixture of horizontal and vertical transmission of symbiotic bacteria across generations in an oviparous turtle without parental care and provide insight into the significance of the eggshell microbiome in embryo development.
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5
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Kang Y, Zhou H, Jin W. Rothia nasimurium as a Cause of Disease: First Isolation from Farmed Geese. Vet Sci 2022; 9:vetsci9050197. [PMID: 35622725 PMCID: PMC9145032 DOI: 10.3390/vetsci9050197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/13/2022] [Accepted: 04/15/2022] [Indexed: 11/29/2022] Open
Abstract
Rothia nasimurium was known previously as an opportunistic pathogen of animals. However, there are few reports regarding the pathogenicity of Rothia nasimurium. In September 2020, geese contracted a disease of unknown cause which brought economic losses to a farm in Jiangsu Province, China, prompting a series of investigations. The bacterium was isolated, cultured, and purified, and then identified using Gram staining, biochemical tests, matrix-assisted laser desorption/ionization time of flight mass spectrometry, and 16S rRNA sequence analysis. After determining the obtained bacteria species, antibiotic susceptibility tests and animal regression experiments were carried out. A strain of bacterium was successfully isolated from the livers of the diseased geese, which was identified as a strain of the Gram-positive bacterium Rothia nasimurium according to the 16S rRNA sequencing results. By indexing references, no goose was reported to have been infected with Rothia nasimurium. The antibiotic susceptibility testing showed that only four antibiotics (amikacin, cefazolin, fosfomycin, and ampicillin/sulbactam) could effectively inhibit the growth of the Rothia nasimurium strain. The animal regression experiments showed that the novel isolated strain could infect goslings, and it also causes serious depilation of goslings. The results of the manuscript expanded the range of pathogenic microorganisms in geese, which is helpful to develop methods for avian endemic control.
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Affiliation(s)
- Yuhui Kang
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (Y.K.); (H.Z.)
| | - Hongshan Zhou
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (Y.K.); (H.Z.)
| | - Wenjie Jin
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (Y.K.); (H.Z.)
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou 225009, China
- Ministry of Education Key Laboratory of Poultry Preventive Medicine, Yangzhou 225009, China
- Correspondence:
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Egg-laying increases body temperature to an annual maximum in a wild bird. Sci Rep 2022; 12:1681. [PMID: 35102175 PMCID: PMC8803923 DOI: 10.1038/s41598-022-05516-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 01/12/2022] [Indexed: 12/04/2022] Open
Abstract
Most birds, unlike reptiles, lay eggs successively to form a full clutch. During egg-laying, birds are highly secretive and prone to disturbance and predation. Using multisensor data loggers, we show that average daily body temperature during egg-laying is significantly increased (1 °C) in wild eider ducks (Somateria mollissima). Strikingly, this increase corresponds to the annual maximum body temperature (40.7 °C), representing a severe annual thermogenic challenge. This egg-laying-induced rise in body temperature may prove to be a common feature of wild birds and could be caused by habitat-related thermoregulatory adjustments and hormonal modulation of reproduction. We conclude our findings with new perspectives of the benefits of high body temperature associated with egg-laying of birds and the potential effect of heat stress that may occur with the future advent of heatwaves.
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Attard MRG, Bowen J, Corado R, Hall LS, Dorey RA, Portugal SJ. Ecological drivers of eggshell wettability in birds. J R Soc Interface 2021; 18:20210488. [PMID: 34637642 PMCID: PMC8510701 DOI: 10.1098/rsif.2021.0488] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Accepted: 09/13/2021] [Indexed: 01/22/2023] Open
Abstract
Complex and at times extreme environments have pushed many bird species to develop unique eggshell surface properties to protect the embryo from external threats. Because microbes are usually transmitted into eggs by moisture, some species have evolved hydrophobic shell surfaces that resist water absorption, while also regulating heat loss and the exchange of gases. Here, we investigate the relationship between the wettability of eggshells from 441 bird species and their life-history traits. We measured the initial contact angle between sessile water droplets and the shell surface, and how far the droplet spread. Using phylogenetic comparative methods, we show that body mass, annual temperature and eggshell maculation primarily explained variance in water contact angle across eggshells. Species nesting in warm climates were more likely to exhibit highly hydrophobic eggshells than those nesting in cold climates, potentially to reduce microbial colonization. In non-passerines, immaculate eggs were found to have more hydrophobic surfaces than maculate eggshells. Droplets spread more quickly on eggshells incubated in open nests compared to domed nests, likely to decrease heat transfer from the egg. Here, we identify clear adaptations of eggshell wettability across a diverse range of nesting environments, driven by the need to retain heat and prevent microbial adhesion.
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Affiliation(s)
- Marie R. G. Attard
- Department of Biological Sciences, School of Life and Environmental Sciences, Royal Holloway University of London, Egham, Surrey TW20 0EX, UK
- School of Engineering and Innovation, Open University, Milton Keynes MK7 6AA, UK
| | - James Bowen
- School of Engineering and Innovation, Open University, Milton Keynes MK7 6AA, UK
| | - René Corado
- Western Foundation of Vertebrate Zoology, Camarillo, CA 93012-8506, USA
| | - Linnea S. Hall
- Western Foundation of Vertebrate Zoology, Camarillo, CA 93012-8506, USA
| | - Robert A. Dorey
- Department of Mechanical Engineering Sciences, University of Surrey, Guildford, Surrey GU2 7XH, UK
| | - Steven J. Portugal
- Department of Biological Sciences, School of Life and Environmental Sciences, Royal Holloway University of London, Egham, Surrey TW20 0EX, UK
- The Natural History Museum, Tring, Herts HP23 6AP, UK
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Wang X, Howe S, Deng F, Zhao J. Current Applications of Absolute Bacterial Quantification in Microbiome Studies and Decision-Making Regarding Different Biological Questions. Microorganisms 2021; 9:1797. [PMID: 34576694 PMCID: PMC8467167 DOI: 10.3390/microorganisms9091797] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/16/2021] [Accepted: 08/21/2021] [Indexed: 11/17/2022] Open
Abstract
High throughput sequencing has emerged as one of the most important techniques for characterizing microbial dynamics and revealing bacteria and host interactions. However, data interpretation using this technique is mainly based on relative abundance and ignores total bacteria load. In certain cases, absolute abundance is more important than compositional relative data, and interpretation of microbiota data based solely on relative abundance can be misleading. The available approaches for absolute quantification are highly diverse and challenging, especially for quantification in differing biological situations, such as distinguishing between live and dead cells, quantification of specific taxa, enumeration of low biomass samples, large sample size feasibility, and the detection of various other cellular features. In this review, we first illustrate the importance of integrating absolute abundance into microbiome data interpretation. Second, we briefly discuss the most widely used cell-based and molecular-based bacterial load quantification methods, including fluorescence spectroscopy, flow cytometry, 16S qPCR, 16S qRT-PCR, ddPCR, and reference spike-in. Last, we present a specific decision-making scheme for absolute quantification methods based on different biological questions and some of the latest quantitative methods and procedure modifications.
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Affiliation(s)
- Xiaofan Wang
- Department of Animal Science, Division of Agriculture, University of Arkansas, Fayetteville, AR 72701, USA
| | - Samantha Howe
- Department of Animal Science, Division of Agriculture, University of Arkansas, Fayetteville, AR 72701, USA
| | - Feilong Deng
- Department of Animal Science, Division of Agriculture, University of Arkansas, Fayetteville, AR 72701, USA
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, College of Life Science and Engineering, Foshan University, Foshan 528225, China
| | - Jiangchao Zhao
- Department of Animal Science, Division of Agriculture, University of Arkansas, Fayetteville, AR 72701, USA
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9
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Genetic characterization, mechanisms and dissemination risk of antibiotic resistance of multidrug-resistant Rothia nasimurium. INFECTION GENETICS AND EVOLUTION 2021; 90:104770. [PMID: 33588066 DOI: 10.1016/j.meegid.2021.104770] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 01/14/2021] [Accepted: 02/09/2021] [Indexed: 12/11/2022]
Abstract
Rothia nasimurium is part of the commensal flora of humans and other animals and has recently received increasing attention for its multidrug-resistance (MDR) and pathogenicity. Currently, no systematic reports characterize the genetics, mechanisms, and dissemination risks of antibiotic resistance in MDR R. nasimurium. Here, we present the first report outlining a MDR strain of R. nasimurium, E1706032a, isolated from ducks exhibiting clinical sickness. Phylogenetic analysis indicates that E1706032a mostly likely originated in the commensal bacteria of Amazona aestiva in Florida. E1706032a is resistant to beta-lactams, aminoglycosides, macrolides, sulfonamides, fluoroquinolones, rifamycins, tetracyclines, lincosamides and chloramphenicol. Genetic sequences related to drug resistance were detected, including resistance genes (aac(6')-Ib, ant(3″)-Ia, sul1, dfrA7, erm(X)), efflux pumps (tetZ, qacEΔ1, cmx, phosphate ABC transporter ATP-binding protein), and resistance-related proteins (hydrolase of the metallo-beta-lactamase (MBLs), mycinamicin resistance protein (myrA), DNA-directed RNA polymerase subunit beta (rpoB) variants, etc). E1706032a carries an IS481-like element, IS5564 and IS6-like elements, and IS6100 along with several novel transposases of the IS3 family. E1706032a also carries the class 1 integron gene IntI1, which is downstream adjacent to the gene cassettes aac(6')-Ib, tetZ, dfrA27, ant(3″)-Ia, qacEΔ1, sul1, cmx and upstream adjacent to gene tnpA of IS6100. Genetic analysis suggests that E1706032a carries wide antibiotic resistance and dissemination potential through movable elements and thus has the potential to cause difficult-to-treat infections in animals and humans. The dissemination of E1706032a from parrots in Florida to ducks in eastern China indicates a cross-regional public health infection risk that should be evaluated for risk of global spreading.
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10
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Methicillin-Resistant Macrococcus bohemicus Encoding a Divergent SCC mecB Element. Antibiotics (Basel) 2020; 9:antibiotics9090590. [PMID: 32927653 PMCID: PMC7560078 DOI: 10.3390/antibiotics9090590] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 09/02/2020] [Accepted: 09/07/2020] [Indexed: 11/22/2022] Open
Abstract
A methicillin-resistant Macrococcus isolate from canine otitis, H889678/16/1, was whole-genome sequenced using HiSeq technology to identify the species, antimicrobial resistance determinates and their genomic context. H889678/16/1 belonged to the newly described species Macrococcus bohemicus. It encoded mecB within a novel SCCmec element most similar to that of Macrococcus canis KM45013T. This SCCmecH889678/16/1 element also encoded blaZm and fusC, but no other resistance determinates were found in the H889678/16/1 genome. The ccrA and ccrB recombinase genes within SCCmecH889678/16/1 were distinct from those previously described in staphylococci and macrococci and therefore designated here as ccrAm3 and ccrBm3. Our study represents, to the best of our knowledge, the first description of mecB being encoded by M. bohemicus and of methicillin resistance in this species. Furthermore, the SCCmec described here is highly dissimilar to other such elements and encodes novel ccr genes. Our report demonstrates a wider distribution of mecB among Macrococcus species and expands the genomic context in which mecB may be found. The potential for dissemination of mec genes from Macrococcus to related but more pathogenic Staphylococcus species highlights the need to understand the epidemiology of these genes in macrococci.
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Svobodová J, Šmídová L, Javůrková VG. Different incubation patterns affect selective antimicrobial properties of the egg interior: experimental evidence from eggs of precocial and altricial birds. ACTA ACUST UNITED AC 2019; 222:jeb.201442. [PMID: 30814292 DOI: 10.1242/jeb.201442] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 02/22/2019] [Indexed: 12/14/2022]
Abstract
Avian eggs contend with omnipresent microorganisms entering the egg interior, where they affect embryo viability and hatchling phenotype. The incubation behaviour and deposition of egg white antimicrobial proteins (AMPs) vary highly across the avian altricial-precocial spectrum. Experimental evidence of how these alterations in avian reproductive strategies affect the antimicrobial properties of the precocial and altricial egg interior is lacking, however. Here, we tested the egg white antimicrobial activity in eggs of two representative model species, from each end of the avian altricial-precocial spectrum, against potentially pathogenic and beneficial probiotic microorganisms. Eggs were experimentally treated to mimic un-incubated eggs in the nest, partial incubation during the egg-laying period, the onset of full incubation and the increased deposition of two main egg white AMPs, lysozyme and ovotransferrin. We moreover assessed to what extent egg antimicrobial components, egg white pH and AMP concentrations varied as a result of different incubation patterns. Fully incubated precocial and altricial eggs decreased their antimicrobial activity against a potentially pathogenic microorganism, whereas partial incubation significantly enhanced the persistence of a beneficial probiotic microorganism in precocial eggs. These effects were most probably conditioned by temperature-dependent alterations in egg white pH and AMP concentrations. While lysozyme concentration and pH decreased in fully incubated precocial but not altricial eggs, egg white ovotransferrin increased along with the intensity of incubation in both precocial and altricial eggs. This study is the first to experimentally demonstrate that different incubation patterns may have selective antimicrobial potential mediated by species-specific effects on antimicrobial components in the egg white.
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Affiliation(s)
- Jana Svobodová
- Czech University of Life Sciences, Faculty of Environmental Sciences, Department of Ecology, Kamýcká 1176, 165 21 Prague 6, Czech Republic
| | - Lucie Šmídová
- Charles University, Faculty of Science, Department of Zoology, Viničná 7, 128 44 Prague 2, Czech Republic
| | - Veronika Gvoždíková Javůrková
- Czech University of Life Sciences, Faculty of Agrobiology, Food and Natural Resources, Department of Animal Science, Kamýcká 957, 165 21 Prague 6, Czech Republic
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12
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Peralta-Sánchez JM, Martín-Platero AM, Wegener-Parfrey L, Martínez-Bueno M, Rodríguez-Ruano S, Navas-Molina JA, Vázquez-Baeza Y, Martín-Gálvez D, Martín-Vivaldi M, Ibáñez-Álamo JD, Knight R, Soler JJ. Bacterial density rather than diversity correlates with hatching success across different avian species. FEMS Microbiol Ecol 2019; 94:4847879. [PMID: 29438507 DOI: 10.1093/femsec/fiy022] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 02/07/2018] [Indexed: 01/09/2023] Open
Abstract
Bacterial communities within avian nests are considered an important determinant of egg viability, potentially selecting for traits that confer embryos with protection against trans-shell infection. A high bacterial density on the eggshell increases hatching failure, whether this effect could be due to changes in bacterial community or just a general increase in bacterial density. We explored this idea using intra- and interspecific comparisons of the relationship between hatching success and eggshell bacteria characterized by culture and molecular techniques (fingerprinting and high-throughput sequencing). We collected information for 152 nests belonging to 17 bird species. Hatching failures occurred more frequently in nests with higher density of aerobic mesophilic bacteria on their eggshells. Bacterial community was also related to hatching success, but only when minority bacterial operational taxonomic units were considered. These findings support the hypothesis that bacterial density is a selective agent of embryo viability, and hence a proxy of hatching failure only within species. Although different avian species hold different bacterial densities or assemblages on their eggs, the association between bacteria and hatching success was similar for different species. This result suggests that interspecific differences in antibacterial defenses are responsible for keeping the hatching success at similar levels in different species.
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Affiliation(s)
- Juan Manuel Peralta-Sánchez
- Departamento de Microbiología, Universidad de Granada, Calle Fuentenueva, s/n, E-18071 Granada, Spain.,Department of Integrative Ecology, Estación Biológica de Doñana, C.S.I.C. Avda. Américo Vespucio s/n, E-41092 Seville, Spain
| | | | | | - Manuel Martínez-Bueno
- Departamento de Microbiología, Universidad de Granada, Calle Fuentenueva, s/n, E-18071 Granada, Spain
| | - Sonia Rodríguez-Ruano
- Departamento de Microbiología, Universidad de Granada, Calle Fuentenueva, s/n, E-18071 Granada, Spain.,Faculty of Science, University of South Bohemia, Branisovska 1760, 370 05 Ceske Budejovice, Czech Republic
| | - José Antonio Navas-Molina
- Department of Computer Science & Engineering University of California San Diego, La Jolla, CA 92093, USA
| | - Yoshiki Vázquez-Baeza
- Department of Computer Science & Engineering University of California San Diego, La Jolla, CA 92093, USA
| | - David Martín-Gálvez
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD, UK
| | - Manuel Martín-Vivaldi
- Departamento de Zoología, Universidad de Granada, Campus de Fuentenueva, s/n, E-18071 Granada, Spain
| | - Juan Diego Ibáñez-Álamo
- Groningen Institute for Evolutionary Life Sciences, University of Groningen. 9700 CC Groningen, The Netherlands
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA.,Center for Microbiome Innovation, University of California San Diego, La Jolla, CA 92093, USA
| | - Juan José Soler
- Departamento de Ecología Funcional y Evolutiva. Estación Experimental de Zonas Áridas, C.S.I.C., E-04120 Almería, Spain
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13
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Reproductive success related to uropygial gland volume varies with abundance of conspecifics in barn swallows Hirundo rustica. Behav Ecol Sociobiol 2018. [DOI: 10.1007/s00265-018-2598-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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14
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Mašlaňová I, Wertheimer Z, Sedláček I, Švec P, Indráková A, Kovařovic V, Schumann P, Spröer C, Králová S, Šedo O, Krištofová L, Vrbovská V, Füzik T, Petráš P, Zdráhal Z, Ružičková V, Doškař J, Pantuček R. Description and Comparative Genomics of Macrococcus caseolyticus subsp. hominis subsp. nov., Macrococcus goetzii sp. nov., Macrococcus epidermidis sp. nov., and Macrococcus bohemicus sp. nov., Novel Macrococci From Human Clinical Material With Virulence Potential and Suspected Uptake of Foreign DNA by Natural Transformation. Front Microbiol 2018; 9:1178. [PMID: 29951040 PMCID: PMC6008420 DOI: 10.3389/fmicb.2018.01178] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 05/15/2018] [Indexed: 11/30/2022] Open
Abstract
The genus Macrococcus is a close relative of the genus Staphylococcus. Whilst staphylococci are widespread as human pathogens, macrococci have not yet been reported from human clinical specimens. Here we investigated Gram-positive and catalase-positive cocci recovered from human clinical material and identified as Macrococcus sp. by a polyphasic taxonomic approach and by comparative genomics. Relevant phenotypic, genotypic and chemotaxonomic methods divided the analyzed strains into two separate clusters within the genus Macrococcus. Comparative genomics of four representative strains revealed enormous genome structural plasticity among the studied isolates. We hypothesize that high genomic variability is due to the presence of a com operon, which plays a key role in the natural transformation of bacilli and streptococci. The possible uptake of exogenous DNA by macrococci can contribute to a different mechanism of evolution from staphylococci, where phage-mediated horizontal gene transfer predominates. The described macrococcal genomes harbor novel plasmids, genomic islands and islets, as well as prophages. Capsule gene clusters, intracellular protease, and a fibronectin-binding protein enabling opportunistic pathogenesis were found in all four strains. Furthermore, the presence of a CRISPR-Cas system with 90 spacers in one of the sequenced genomes corresponds with the need to limit the burden of foreign DNA. The highly dynamic genomes could serve as a platform for the exchange of virulence and resistance factors, as was described for the methicillin resistance gene, which was found on the novel composite SCCmec-like element containing a unique mec gene complex that is considered to be one of the missing links in SCC evolution. The phenotypic, genotypic, chemotaxonomic and genomic results demonstrated that the analyzed strains represent one novel subspecies and three novel species of the genus Macrococcus, for which the names Macrococcus caseolyticus subsp. hominis subsp. nov. (type strain CCM 7927T = DSM 103682T), Macrococcus goetzii sp. nov. (type strain CCM 4927T = DSM 103683T), Macrococcus epidermidis sp. nov. (type strain CCM 7099T = DSM 103681T), and Macrococcus bohemicus sp. nov. (type strain CCM 7100T = DSM 103680T) are proposed. Moreover, a formal description of Macrococcus caseolyticus subsp. caseolyticus subsp. nov. and an emended description of the genus Macrococcus are provided.
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Affiliation(s)
- Ivana Mašlaňová
- Division of Genetics and Molecular Biology, Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Zuzana Wertheimer
- Division of Genetics and Molecular Biology, Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Ivo Sedláček
- Czech Collection of Microorganisms, Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Pavel Švec
- Czech Collection of Microorganisms, Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Adéla Indráková
- Division of Genetics and Molecular Biology, Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Vojtěch Kovařovic
- Division of Genetics and Molecular Biology, Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Peter Schumann
- Leibniz Institute Deutsche Sammlung von Mikroorganismen und Zellkulturen—German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Cathrin Spröer
- Leibniz Institute Deutsche Sammlung von Mikroorganismen und Zellkulturen—German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Stanislava Králová
- Czech Collection of Microorganisms, Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Ondrej Šedo
- Central European Institute of Technology, Masaryk University, Brno, Czechia
| | - Lucie Krištofová
- Czech Collection of Microorganisms, Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Veronika Vrbovská
- Division of Genetics and Molecular Biology, Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Tibor Füzik
- Central European Institute of Technology, Masaryk University, Brno, Czechia
| | - Petr Petráš
- Reference Laboratory for Staphylococci, National Institute of Public Health, Prague, Czechia
| | - Zbyněk Zdráhal
- Central European Institute of Technology, Masaryk University, Brno, Czechia
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czechia
| | - Vladislava Ružičková
- Division of Genetics and Molecular Biology, Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Jiří Doškař
- Division of Genetics and Molecular Biology, Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Roman Pantuček
- Division of Genetics and Molecular Biology, Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
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15
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Li G, Du X, Zhou D, Li C, Huang L, Zheng Q, Cheng Z. Emergence of pathogenic and multiple-antibiotic-resistant Macrococcus caseolyticus in commercial broiler chickens. Transbound Emerg Dis 2018; 65:1605-1614. [PMID: 29799666 DOI: 10.1111/tbed.12912] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Revised: 04/26/2018] [Accepted: 04/29/2018] [Indexed: 11/27/2022]
Abstract
Macrococcus caseolyticus is generally considered to be a non-pathogenic bacterium that does not cause human or animal diseases. However, recently, a strain of M. caseolyticus (SDLY strain) that causes high mortality rates was isolated from commercial broiler chickens in China. The main pathological changes caused by SDLY included caseous exudation in cranial cavities, inflammatory infiltration, haemorrhages and multifocal necrosis in various organs. The whole genome of the SDLY strain was sequenced and was compared with that of the non-pathogenic JCSC5402 strain of M. caseolyticus. The results showed that the SDLY strain harboured a large quantity of mutations, antibiotic resistance genes and numerous insertions and deletions of virulence genes. In particular, among the inserted genes, there is a cluster of eight connected genes associated with the synthesis of capsular polysaccharide. This cluster encodes a transferase and capsular polysaccharide synthase, promotes the formation of capsules and causes changes in pathogenicity. Electron microscopy revealed a distinct capsule surrounding the SDLY strain. The pathogenicity test showed that the SDLY strain could cause significant clinical symptoms and pathological changes in both SPF chickens and mice. In addition, these clinical symptoms and pathological changes were the same as those observed in field cases. Furthermore, the anti-microbial susceptibility test demonstrated that the SDLY strain exhibits multiple-antibiotic resistance. The emergence of pathogenic M. caseolyticus indicates that more attention should be paid to the effects of this micro-organism on both poultry and public health.
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Affiliation(s)
- Gen Li
- College of Veterinary Medicine, Shandong Agricultural University, Tai'an City, China
| | - Xusheng Du
- College of Veterinary Medicine, Shandong Agricultural University, Tai'an City, China
| | - Defang Zhou
- College of Veterinary Medicine, Shandong Agricultural University, Tai'an City, China
| | - Chengui Li
- College of Veterinary Medicine, Shandong Agricultural University, Tai'an City, China
| | - Libo Huang
- College of Veterinary Medicine, Shandong Agricultural University, Tai'an City, China
| | | | - Ziqiang Cheng
- College of Veterinary Medicine, Shandong Agricultural University, Tai'an City, China
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16
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Volokhov DV, Amselle M, Bodeis-Jones S, Delmonte P, Zhang S, Davidson MK, Gulland FM, Chizhikov VE. Neisseria zalophi sp. nov., isolated from oral cavity of California sea lions (Zalophus californianus). Arch Microbiol 2018; 200:819-828. [DOI: 10.1007/s00203-018-1499-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 02/21/2018] [Accepted: 02/22/2018] [Indexed: 12/18/2022]
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17
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Graczyk M, Andres K, Kapkowska E, Szwaczkowski T. Genetic evaluation of reproductive potential in the Zatorska goose under a conservation program. Anim Sci J 2018; 89:752-759. [DOI: 10.1111/asj.12990] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 12/21/2017] [Indexed: 11/27/2022]
Affiliation(s)
- Magdalena Graczyk
- Department of Genetics and Animal Breeding; Poznan University of Life Sciences; Poznan Poland
| | - Krzysztof Andres
- Department of Swine and Small Animal Breeding; Institute of Animal Science; University of Agriculture in Cracow; Cracow Poland
| | - Ewa Kapkowska
- Department of Swine and Small Animal Breeding; Institute of Animal Science; University of Agriculture in Cracow; Cracow Poland
| | - Tomasz Szwaczkowski
- Department of Genetics and Animal Breeding; Poznan University of Life Sciences; Poznan Poland
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18
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van Veelen HPJ, Salles JF, Tieleman BI. Microbiome assembly of avian eggshells and their potential as transgenerational carriers of maternal microbiota. ISME JOURNAL 2018; 12:1375-1388. [PMID: 29445132 DOI: 10.1038/s41396-018-0067-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 12/01/2017] [Accepted: 12/21/2017] [Indexed: 02/07/2023]
Abstract
The microbiome is essential for development, health and homeostasis throughout an animal's life. Yet, the origins and transmission processes governing animal microbiomes remain elusive for non-human vertebrates, oviparous vertebrates in particular. Eggs may function as transgenerational carriers of the maternal microbiome, warranting characterisation of egg microbiome assembly. Here, we investigated maternal and environmental contributions to avian eggshell microbiota in wild passerine birds: woodlark Lullula arborea and skylark Alauda arvensis. Using 16S rRNA gene sequencing, we demonstrated in both lark species, at the population and within-nest levels, that bacterial communities of freshly laid eggs were distinct from the female cloacal microbiome. Instead, soil-borne bacteria appeared to thrive on freshly laid eggs, and eggshell microbiota composition strongly resembled maternal skin, body feather and nest material communities, sources in direct contact with laid eggs. Finally, phylogenetic structure analysis and microbial source tracking underscored species sorting from directly contacting sources rather than in vivo-transferred symbionts. The female-egg-nest system allowed an integrative assessment of avian egg microbiome assembly, revealing mixed modes of symbiont acquisition not previously documented for vertebrate eggs. Our findings illuminated egg microbiome origins, which suggested a limited potential of eggshells for transgenerational transmission, encouraging further investigation of eggshell microbiome functions in vertebrates.
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Affiliation(s)
- H Pieter J van Veelen
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, P.O. box 11103, 9700 CC, Groningen, The Netherlands.
| | - Joana Falcão Salles
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, P.O. box 11103, 9700 CC, Groningen, The Netherlands
| | - B Irene Tieleman
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, P.O. box 11103, 9700 CC, Groningen, The Netherlands
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19
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Lee SI, Lee H, Jablonski PG, Choe JC, Husby M. Microbial abundance on the eggs of a passerine bird and related fitness consequences between urban and rural habitats. PLoS One 2017; 12:e0185411. [PMID: 28953940 PMCID: PMC5617198 DOI: 10.1371/journal.pone.0185411] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 09/12/2017] [Indexed: 11/18/2022] Open
Abstract
Urban environments present novel and challenging habitats to wildlife. In addition to well-known difference in abiotic factors between rural and urban environments, the biotic environment, including microbial fauna, may also differ significantly. In this study, we aimed to compare the change in microbial abundance on eggshells during incubation between urban and rural populations of a passerine bird, the Eurasian Magpie (Pica pica), and examine the consequences of any differences in microbial abundances in terms of hatching success and nestling survival. Using real-time PCR, we quantified the abundances of total bacteria, Escherichia coli/Shigella spp., surfactin-producing Bacillus spp. and Candida albicans on the eggshells of magpies. We found that urban magpie eggs harboured greater abundances of E. coli/Shigella spp. and C. albicans before incubation than rural magpie eggs. During incubation, there was an increase in the total bacterial load, but a decrease in C. albicans on urban eggs relative to rural eggs. Rural eggs showed a greater increase in E. coli/Shigella spp. relative to their urban counterpart. Hatching success of the brood was generally lower in urban than rural population. Nestling survival was differentially related with the eggshell microbial abundance between urban and rural populations, which was speculated to be the result of the difference in the strength of the interaction among the microbes. This is the first demonstration that avian clutches in urban and rural populations differ in eggshell microbial abundance, which can be further related to the difference in hatching success and nestling survival in these two types of environments. We suggest that future studies on the eggshell microbes should investigate the interaction among the microbes, because the incubation and/or environmental factors such as urbanization or climate condition can influence the dynamic interactions among the microbes on the eggshells which can further determine the breeding success of the parents.
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Affiliation(s)
- Sang-im Lee
- School of Undergraduate Studies, Daegu Gyeongbuk Institute of Science and Technology, Daegu, Korea
| | - Hyunna Lee
- Laboratory of Behavior and Ecology, EcoCreative Program, Ewha Womans University, Seoul, Korea
| | - Piotr G. Jablonski
- Laboratory of Behavioral Ecology and Evolution, School of Biological Sciences, Seoul National University, Seoul, Korea
- Museum and Institute of Zoology, Polish Academy of Sciences, Warsaw, Poland
| | - Jae Chun Choe
- Laboratory of Behavior and Ecology, EcoCreative Program, Ewha Womans University, Seoul, Korea
| | - Magne Husby
- Department of Science, Nord University, Levanger, Norway
- * E-mail:
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20
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Hansen CM, Himschoot EA, Hare RF, Meixell BW, Hemert CV, Hueffer K. Neisseria arctica sp. nov., isolated from nonviable eggs of greater white-fronted geese (Anser albifrons) in Arctic Alaska. Int J Syst Evol Microbiol 2017; 67:1115-1119. [PMID: 28056218 PMCID: PMC5775901 DOI: 10.1099/ijsem.0.001773] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 01/02/2017] [Indexed: 11/18/2022] Open
Abstract
During the summers of 2013 and 2014, isolates of a novel Gram-stain-negative coccus in the genus Neisseriawere obtained from the contents of nonviable greater white-fronted goose (Anseralbifrons) eggs on the Arctic Coastal Plain of Alaska. We used a polyphasic approach to determine whether these isolates represent a novel species. 16S rRNA gene sequences, 23S rRNA gene sequences, and chaperonin 60 gene sequences suggested that these Alaskan isolates are members of a distinct species that is most closely related to Neisseria canis, Neisseriaanimaloris and Neisseriashayeganii. Analysis of the rplF gene additionally showed that the isolates are unique and most closely related to Neisseriaweaveri. Average nucleotide identity of the whole genome sequence of the type strain was between 71.5 and 74.6 % compared to close relatives, further supporting designation as a novel species. Fatty acid methyl ester analysis showed a predominance of C14 : 0, C16 : 0 and C16 : 1ω7c fatty acids. Finally, biochemical characteristics distinguished the isolates from other species of the genus Neisseria. On the basis of these combined data, the isolates are proposed to represent a novel species of the genus Neisseria, with the name Neisseria arctica sp. nov. The type strain is KH1503T (=ATCC TSD-57T=DSM 103136T).
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Affiliation(s)
- Cristina M Hansen
- Department of Veterinary Medicine, University of Alaska Fairbanks, Fairbanks, AK, USA
| | - Elizabeth A Himschoot
- Department of Veterinary Medicine, University of Alaska Fairbanks, Fairbanks, AK, USA
| | - Rebekah F Hare
- Department of Veterinary Medicine, University of Alaska Fairbanks, Fairbanks, AK, USA
| | - Brandt W Meixell
- U.S. Geological Survey, Alaska Science Center, Anchorage, AK, USA
| | | | - Karsten Hueffer
- Department of Veterinary Medicine, University of Alaska Fairbanks, Fairbanks, AK, USA
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21
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Wang C, Luo J, Wang H, Amer S, Ding H, Dong Y, He H. Isolation and characterization of a Neisseria sp. from the captive wild goose (Anser anser). Integr Zool 2016; 11:128-33. [PMID: 26767581 DOI: 10.1111/1749-4877.12181] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The present study investigated 15 dead cases of captive wild goslings (Anser anser), which were bred in a small poultry farm in Shandong Province, China. The examined cases presented diverse clinical signs accompanied with neurological manifestations and fatal outcomes. Bacterial culture identified the gram-negative Neisseria sp. from the brain homogenate of most examined cases (10/15, 66.7%). The isolated bacteria were identified based on morphologic characteristics, biochemical tests and 16S rDNA typing. Results proved that 1 identical bacterial strain (BNO09-3) was isolated from the positive cases. The phylogeny based on the 16S rDNA gene sequences indicated that this isolate has a close relationship with various strains of genus Neisseria sp. isolated from liver and feces of duck. This is the first report of Neisseria sp. causing fatality in captive wild geese in China.
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Affiliation(s)
- Chengmin Wang
- National Research Center For Wildlife Born Diseases, Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Jing Luo
- National Research Center For Wildlife Born Diseases, Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Haijing Wang
- National Research Center For Wildlife Born Diseases, Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Said Amer
- National Research Center For Wildlife Born Diseases, Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Department of Zoology, Faculty of Science, Kafr El Sheikh University, Kafr El Sheikh, Egypt
| | - Hua Ding
- Department of Infectious Diseases, Hangzhou Center for Disease Control and Prevention, Hangzhou, China
| | - Ying Dong
- Department of Medical Oncology, the Second Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Hongxuan He
- National Research Center For Wildlife Born Diseases, Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
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22
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Forde TL, Orsel K, Zadoks RN, Biek R, Adams LG, Checkley SL, Davison T, De Buck J, Dumond M, Elkin BT, Finnegan L, Macbeth BJ, Nelson C, Niptanatiak A, Sather S, Schwantje HM, van der Meer F, Kutz SJ. Bacterial Genomics Reveal the Complex Epidemiology of an Emerging Pathogen in Arctic and Boreal Ungulates. Front Microbiol 2016; 7:1759. [PMID: 27872617 PMCID: PMC5097903 DOI: 10.3389/fmicb.2016.01759] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2016] [Accepted: 10/19/2016] [Indexed: 12/20/2022] Open
Abstract
Northern ecosystems are currently experiencing unprecedented ecological change, largely driven by a rapidly changing climate. Pathogen range expansion, and emergence and altered patterns of infectious disease, are increasingly reported in wildlife at high latitudes. Understanding the causes and consequences of shifting pathogen diversity and host-pathogen interactions in these ecosystems is important for wildlife conservation, and for indigenous populations that depend on wildlife. Among the key questions are whether disease events are associated with endemic or recently introduced pathogens, and whether emerging strains are spreading throughout the region. In this study, we used a phylogenomic approach to address these questions of pathogen endemicity and spread for Erysipelothrix rhusiopathiae, an opportunistic multi-host bacterial pathogen associated with recent mortalities in arctic and boreal ungulate populations in North America. We isolated E. rhusiopathiae from carcasses associated with large-scale die-offs of muskoxen in the Canadian Arctic Archipelago, and from contemporaneous mortality events and/or population declines among muskoxen in northwestern Alaska and caribou and moose in western Canada. Bacterial genomic diversity differed markedly among these locations; minimal divergence was present among isolates from muskoxen in the Canadian Arctic, while in caribou and moose populations, strains from highly divergent clades were isolated from the same location, or even from within a single carcass. These results indicate that mortalities among northern ungulates are not associated with a single emerging strain of E. rhusiopathiae, and that alternate hypotheses need to be explored. Our study illustrates the value and limitations of bacterial genomic data for discriminating between ecological hypotheses of disease emergence, and highlights the importance of studying emerging pathogens within the broader context of environmental and host factors.
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Affiliation(s)
- Taya L. Forde
- Faculty of Veterinary Medicine, University of CalgaryCalgary, AB, Canada
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of GlasgowGlasgow, UK
| | - Karin Orsel
- Faculty of Veterinary Medicine, University of CalgaryCalgary, AB, Canada
| | - Ruth N. Zadoks
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of GlasgowGlasgow, UK
| | - Roman Biek
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of GlasgowGlasgow, UK
| | - Layne G. Adams
- Alaska Science Center, U.S. Geological SurveyAnchorage, AK, USA
| | - Sylvia L. Checkley
- Faculty of Veterinary Medicine, University of CalgaryCalgary, AB, Canada
| | - Tracy Davison
- Environment and Natural Resources, Government of Northwest TerritoriesInuvik, NT, Canada
| | - Jeroen De Buck
- Faculty of Veterinary Medicine, University of CalgaryCalgary, AB, Canada
| | - Mathieu Dumond
- Department of Environment, Government of NunavutKugluktuk, NU, Canada
| | - Brett T. Elkin
- Environment and Natural Resources, Government of Northwest TerritoriesYellowknife, NT, Canada
| | | | - Bryan J. Macbeth
- Faculty of Veterinary Medicine, University of CalgaryCalgary, AB, Canada
| | - Cait Nelson
- Ministry of Forests, Lands and Natural Resource Operations, Government of British ColumbiaNanaimo, BC, Canada
| | | | - Shane Sather
- Department of Environment, Government of NunavutCambridge Bay, Nunavut, Canada
| | - Helen M. Schwantje
- Ministry of Forests, Lands and Natural Resource Operations, Government of British ColumbiaNanaimo, BC, Canada
| | - Frank van der Meer
- Faculty of Veterinary Medicine, University of CalgaryCalgary, AB, Canada
| | - Susan J. Kutz
- Faculty of Veterinary Medicine, University of CalgaryCalgary, AB, Canada
- Canadian Wildlife Health CooperativeCalgary, AB, Canada
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23
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Rothrock M, Locatelli A, Glenn T, Thomas J, Caudill A, Kiepper B, Hiett K. Assessing the microbiomes of scalder and chiller tank waters throughout a typical commercial poultry processing day. Poult Sci 2016; 95:2372-82. [DOI: 10.3382/ps/pew234] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 05/16/2016] [Indexed: 12/22/2022] Open
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24
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Draft Genome Sequence of a Taxonomically Unique Neisseria Strain Isolated from a Greater White-Fronted Goose (Anser albifrons) Egg on the North Slope of Alaska. GENOME ANNOUNCEMENTS 2015; 3:3/4/e00772-15. [PMID: 26184936 PMCID: PMC4505124 DOI: 10.1128/genomea.00772-15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We report here the draft genome sequence of a unique Neisseria strain that was isolated from a greater white-fronted goose (Anser albifrons) egg. The sequencing was performed with an Illumina MiSeq system, and the sequence consists of 275 contigs. The total genome is 2,397,978 bp long and has a G+C content of 46.4%.
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