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Hattab J, Marruchella G, Sibra A, Tiscar PG, Todisco G. Canaries' Microbiota: The Gut Bacterial Communities along One Female Reproductive Cycle. Microorganisms 2023; 11:2289. [PMID: 37764133 PMCID: PMC10537324 DOI: 10.3390/microorganisms11092289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 08/31/2023] [Accepted: 09/09/2023] [Indexed: 09/29/2023] Open
Abstract
Investigations of bacterial communities are on the rise both in human and veterinary medicine. Their role in health maintenance and pathogenic mechanisms is in the limelight of infectious, metabolic, and cancer research. Among the most considered, gut bacterial communities take the cake. Their part in animals was assessed mainly to improve animal production, public health, and pet management. In this regard, canaries deserve attention, being a popular pet and source of economic income for bird-keepers, for whom breeding represents a pivotal point. Thus, the present work aimed to follow gut bacterial communities' evolution along on whole reproductive cycle of 12 healthy female canaries. Feces were collected during parental care, molting, and resting phase, and submitted for 16S rRNA sequencing. Data were analyzed and a substantial presence of Lactobacillus aviarius along all the phases, and a relevant shift of microbiota during molting and rest due to an abrupt decrease of the Vermiphilaceae family were detected. Although the meaning of such change is not clear, future research may highlight unforeseen scenarios. Moreover, Lactobacillus aviarius may be deemed for normal bacteria flora restoration in debilitated birds, perhaps improving their health and productivity.
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Affiliation(s)
- Jasmine Hattab
- Department of Veterinary Medicine, University of Teramo, SP18 Piano d’Accio, 64100 Teramo, Italy; (J.H.); (G.M.)
| | - Giuseppe Marruchella
- Department of Veterinary Medicine, University of Teramo, SP18 Piano d’Accio, 64100 Teramo, Italy; (J.H.); (G.M.)
| | - Alessandra Sibra
- APHA—Animal & Plant Health Agency, Building 1, Sevington Inland Border Facility, Ashford TN25 6GE, UK;
| | - Pietro Giorgio Tiscar
- Department of Veterinary Medicine, University of Teramo, SP18 Piano d’Accio, 64100 Teramo, Italy; (J.H.); (G.M.)
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Minich D, Madden C, Navarro MA, Glowacki L, French-Kim K, Chan W, Evans MV, Soares K, Mrofchak R, Madan R, Ballash GA, LaPerle K, Paul S, Vodovotz Y, Uzal FA, Martinez M, Hausmann J, Junge RE, Hale VL. Gut microbiota and age shape susceptibility to clostridial enteritis in lorikeets under human care. Anim Microbiome 2022; 4:7. [PMID: 35000619 PMCID: PMC8744333 DOI: 10.1186/s42523-021-00148-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 12/07/2021] [Indexed: 12/14/2022] Open
Abstract
Background Enteritis is a common cause of morbidity and mortality in lorikeets that can be challenging to diagnose and treat. In this study, we examine gut microbiota in two lorikeet flocks with enteritis (Columbus Zoo and Aquarium—CZA; Denver Zoo—DZ). Since 2012, the CZA flock has experienced repeated outbreaks of enteritis despite extensive diet, husbandry, and clinical modifications. In 2018, both CZA and DZ observed a spike in enteritis. Recent research has revealed that the gut microbiota can influence susceptibility to enteropathogens. We hypothesized that a dysbiosis, or alteration in the gut microbial community, was making some lorikeets more susceptible to enteritis, and our goal was to characterize this dysbiosis and determine the features that predicted susceptibility.
Results We employed 16S rRNA sequencing to characterize the cloacal microbiota in lorikeets (CZA n = 67, DZ n = 24) over time. We compared the microbiota of healthy lorikeets, to lorikeets with enteritis, and lorikeets susceptible to enteritis, with “susceptible” being defined as healthy birds that subsequently developed enteritis. Based on sequencing data, culture, and toxin gene detection in intestinal contents, we identified Clostridium perfringens type A (CZA and DZ) and C. colinum (CZA only) at increased relative abundances in birds with enteritis. Histopathology and immunohistochemistry further identified the presence of gram-positive bacilli and C. perfringens, respectively, in the necrotizing intestinal lesions. Finally, using Random Forests and LASSO models, we identified several features (young age and the presence of Rhodococcus fascians and Pseudomonas umsongensis) associated with susceptibility to clostridial enteritis. Conclusions We identified C. perfringens type A and C. colinum associated with lorikeet necrohemorrhagic enteritis at CZA and DZ. Susceptibility testing of isolates lead to an updated clinical treatment plan which ultimately resolved the outbreaks at both institutions. This work provides a foundation for understanding gut microbiota features that are permissive to clostridial colonization and host factors (e.g. age, prior infection) that shape responses to infection. Supplementary Information The online version contains supplementary material available at 10.1186/s42523-021-00148-7.
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Affiliation(s)
- David Minich
- Department of Veterinary Preventive Medicine, Ohio State University College of Veterinary Medicine, 1902 Coffey Rd., Columbus, OH, 43210, USA
| | - Christopher Madden
- Department of Veterinary Preventive Medicine, Ohio State University College of Veterinary Medicine, 1902 Coffey Rd., Columbus, OH, 43210, USA
| | - Mauricio A Navarro
- California Animal Health & Food Safety Lab, University of California, Davis, San Bernardino, CA, USA.,Instituto de Patología Animal, Facultad de Ciencias Veterinarias, Universidad Austral de Chile, Valdivia, Chile
| | - Leo Glowacki
- Ohio State University College of Arts and Sciences, Columbus, OH, USA
| | - Kristen French-Kim
- Department of Veterinary Preventive Medicine, Ohio State University College of Veterinary Medicine, 1902 Coffey Rd., Columbus, OH, 43210, USA
| | - Willow Chan
- Ohio State University College of Food, Agricultural, and Environmental Sciences, Columbus, OH, USA
| | - Morgan V Evans
- Department of Veterinary Preventive Medicine, Ohio State University College of Veterinary Medicine, 1902 Coffey Rd., Columbus, OH, 43210, USA.,Ohio State University College of Public Health, Columbus, OH, USA
| | - Kilmer Soares
- Department of Veterinary Preventive Medicine, Ohio State University College of Veterinary Medicine, 1902 Coffey Rd., Columbus, OH, 43210, USA.,Department of Animal Science, College of Agricultural Sciences (CCA), Federal University of Paraiba (UFPB), Areia, PB, Brazil
| | - Ryan Mrofchak
- Department of Veterinary Preventive Medicine, Ohio State University College of Veterinary Medicine, 1902 Coffey Rd., Columbus, OH, 43210, USA
| | - Rushil Madan
- Department of Veterinary Preventive Medicine, Ohio State University College of Veterinary Medicine, 1902 Coffey Rd., Columbus, OH, 43210, USA
| | - Gregory A Ballash
- Department of Veterinary Preventive Medicine, Ohio State University College of Veterinary Medicine, 1902 Coffey Rd., Columbus, OH, 43210, USA
| | - Krista LaPerle
- Department of Veterinary Preventive Medicine, Ohio State University College of Veterinary Medicine, 1902 Coffey Rd., Columbus, OH, 43210, USA.,Comparative Pathology & Digital Imaging Shared Resource, Ohio State University, Columbus, OH, USA
| | - Subhadeep Paul
- Ohio State University College of Arts and Sciences, Columbus, OH, USA
| | - Yael Vodovotz
- Ohio State University College of Food, Agricultural, and Environmental Sciences, Columbus, OH, USA
| | - Francisco A Uzal
- California Animal Health & Food Safety Lab, University of California, Davis, San Bernardino, CA, USA
| | - Margaret Martinez
- Department of Veterinary Preventive Medicine, Ohio State University College of Veterinary Medicine, 1902 Coffey Rd., Columbus, OH, 43210, USA.,The Marine Mammal Center, Sausalito, CA, USA
| | | | | | - Vanessa L Hale
- Department of Veterinary Preventive Medicine, Ohio State University College of Veterinary Medicine, 1902 Coffey Rd., Columbus, OH, 43210, USA.
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Characterization of the microbiome along the gastrointestinal tracts of semi-artificially reared bar-headed geese (Anser indicus). Folia Microbiol (Praha) 2019; 65:533-543. [PMID: 31768913 DOI: 10.1007/s12223-019-00758-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 11/01/2019] [Indexed: 10/25/2022]
Abstract
As one of the dominant waterfowl species of wetland areas in the Qinghai-Tibet Plateau, since 2003, artificial rearing of bar-headed geese (Anser indicus) has increased in several provinces of China for the purpose of conservation and economic development. In this study, we systematically characterized the microbial community diversity, compositions and predicted functions of semi-artificially reared bar-headed geese by sampling five different gut locations (the oropharynxs, crops, gizzards, ceca, and cloacae) along the gastrointestinal tracts of three individuals. Alpha diversity analyses showed that the gizzards had the richest species diversity and that the ceca had the least. Beta diversity analyses showed that the cecal samples formed their own cluster, while samples from the oropharynxs, crops, gizzards, and cloacae overlapped with each other. At the phylum level, Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, and Fusobacteria constituted the top five dominant phyla among all five gastrointestinal sections. At the genus level, a total of 10 genera with proportions above 2.5% were found to be significantly different among the gastrointestinal sections. Furthermore, 53 genera were detected in all gastrointestinal sections of bar-headed geese. PICRUSt data also predicted a group of microbial functions overrepresented in the different segments of the gastrointestinal tracts. Understanding the microbiota along the bar-headed geese gastrointestinal tracts is essential for future microbiological study of this bird and may contribute to the development of geese husbandry.
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Wang W, Wang A, Yang Y, Wang F, Liu Y, Zhang Y, Sharshov K, Gui L. Composition, diversity and function of gastrointestinal microbiota in wild red-billed choughs (Pyrrhocorax pyrrhocorax). Int Microbiol 2019; 22:491-500. [PMID: 31020476 DOI: 10.1007/s10123-019-00076-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 02/27/2019] [Accepted: 04/01/2019] [Indexed: 12/15/2022]
Abstract
Hitherto, virtually nothing is known about the microbial communities related to the bird species in the family Corvidae. To fill this gap, the present study was conducted to provide a baseline description of the gut microbiota of wild red-billed choughs (Pyrrhocorax pyrrhocorax). In this study, microbiota from four gastrointestinal locations (oropharynx, gizzard, small intestine, and large intestine) of three wild red-billed choughs were analyzed using the Illumina MiSeq sequencing platform by targeting the V4-V5 regions of the 16S rRNA genes. The gut microbiota of the red-billed choughs were dominated by the phylum Firmicutes (59.56%), followed by Proteobacteria (16.56%), Bacteroidetes (13.86%), and Actinobacteria (7.03%), which were commonly detected in avian gut ecosystems. Genus-level compositions were found to be largely dominated by Lactobacillus (18.21%), Weissella (12.37%), Erysipelatoclostridium (6.94%), Bacteroides (6.63%), Escherichia-Shigella (5.15%), Leuconostoc (4.60%), Proteus (3.33%), Carnobacterium (2.71%), Lactococcus (1.69%), and Enterococcus (1.63%). The overall intestinal microbiota was enriched with functions related to ATP-binding cassette (ABC) transporters, DNA repair and recombination proteins, purine metabolism, ribosome, transcription factors, pyrimidine metabolism, peptidases, and two-component system. In terms of four different gastrointestinal locations, hierarchical clustering analysis and principal coordinate analysis showed that microbial communities of the oropharynx, gizzard, small intestine, and large intestine formed four separated clusters. A total of 825 OTUs and 382 genera were detected in all four gastrointestinal locations, which were considered as the major microbes in the intestines of red-billed choughs. Coexistence of lactic acid bacteria and potential pathogens in the gut environments of red-billed choughs required further investigations.
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Affiliation(s)
- Wen Wang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xi'ning, 810016, China
| | - Aizhen Wang
- College of Eco-Environmental Engineering, Qinghai University, Xi'ning, 810016, China
| | - Yongsheng Yang
- Chinese Academy of Sciences, Northwest Institute of Plateau Biology, Xi'ning, 810008, China
| | - Fang Wang
- Chinese Academy of Sciences, Northwest Institute of Plateau Biology, Xi'ning, 810008, China
| | - Yingbao Liu
- College of Life Science, Yangtze University, Jingzhou, 434025, China
| | - Yuhui Zhang
- College of Eco-Environmental Engineering, Qinghai University, Xi'ning, 810016, China
| | - Kirill Sharshov
- Research Institute of Experimental and Clinical Medicine, Novosibirsk, 630117, Russia
| | - Linsheng Gui
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xi'ning, 810016, China. .,College of Agriculture and Animal Husbandry, Qinghai University, Xi'ning, 810016, China.
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Dennison SE, Paul-Murphy JR, Yandell BS, Adams WM. Effect of anesthesia, positioning, time, and feeding on the proventriculus: keel ratio of clinically healthy parrots. Vet Radiol Ultrasound 2010; 51:141-4. [PMID: 20402397 DOI: 10.1111/j.1740-8261.2009.01638.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Healthy, adult Hispaniolan Amazon parrots (Amazona ventralis) were imaged on three occasions to determine the effects of anesthesia, patient rotation, feeding, and short/long-term temporal factors on the proventriculus:keel ratio. Increasing rotation up to 15 degrees from right lateral resulted in increased inability to measure the proventriculus in up to 44% of birds, meaning that the proventriculus:keel ratio could not be calculated from those radiographs. There was a significant difference between the proventriculus:keel ratio for individual parrots when quantified 3 weeks apart. Despite this difference, all ratios remained within normal limits. No significant effect was identified due to anesthesia, feeding, fasting, or repeated imaging through an 8-h period. Interobserver agreement for measurability and correlation for the proventriculus:keel ratio values was high. It is recommended that the proventriculus:keel ratio be calculated from anesthetized parrots to attain images in true lateral recumbency. Ratio fluctuations within the normal range between radiographs obtained on different dates may be observed in normal parrots.
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Affiliation(s)
- Sophie E Dennison
- Department of Surgical Sciences, School of Veterinary Medicine, University of Wisconsin, 100 University Avenue, Madison, WI 53706, USA.
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