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Ahmad AR, Ridgeway S, Shibl AA, Idaghdour Y, Jha AR. Falcon gut microbiota is shaped by diet and enriched in Salmonella. PLoS One 2024; 19:e0293895. [PMID: 38289900 PMCID: PMC10826950 DOI: 10.1371/journal.pone.0293895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 10/20/2023] [Indexed: 02/01/2024] Open
Abstract
The gut microbiome is increasingly being appreciated as a master regulator of animal health. However, avian gut microbiome studies commonly focus on birds of economic importance and the gut microbiomes of raptors remain underexplored. Here we examine the gut microbiota of 29 captive falcons-raptors of historic importance-in the context of avian evolution by sequencing the V4 region of the 16S rRNA gene. Our results reveal that evolutionary histories and diet are significantly associated with avian gut microbiota in general, whereas diet plays a major role in shaping the falcon gut microbiota. Multiple analyses revealed that gut microbial diversity, composition, and relative abundance of key diet-discriminating bacterial genera in the falcon gut closely resemble those of carnivorous raptors rather than those of their closest phylogenetic relatives. Furthermore, the falcon microbiota is dominated by Firmicutes and contains Salmonella at appreciable levels. Salmonella presence was associated with altered functional capacity of the falcon gut microbiota as its abundance is associated with depletion of multiple predicted metabolic pathways involved in protein mass buildup, muscle maintenance, and enrichment of antimicrobial compound degradation, thus increasing the pathogenic potential of the falcon gut. Our results point to the necessity of screening for Salmonella and other human pathogens in captive birds to safeguard both the health of falcons and individuals who come in contact with these birds.
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Affiliation(s)
- Anique R. Ahmad
- Genetic Heritage Group, Program in Biology, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Samuel Ridgeway
- Program in Biology, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Ahmed A. Shibl
- Genetic Heritage Group, Program in Biology, New York University Abu Dhabi, Abu Dhabi, UAE
| | | | - Aashish R. Jha
- Genetic Heritage Group, Program in Biology, New York University Abu Dhabi, Abu Dhabi, UAE
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Guan Y, Bao L, Zhou L, Dai C, Li Z, Zhang S, Shang Y, Niu W, Zhang Y, Wang H. Comparative analysis of the fecal microbiota of healthy and injured common kestrel ( Falco tinnunculus) from the Beijing Raptor Rescue Center. PeerJ 2023; 11:e15789. [PMID: 37637157 PMCID: PMC10452619 DOI: 10.7717/peerj.15789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 07/04/2023] [Indexed: 08/29/2023] Open
Abstract
The gut microbiota is a complex ecosystem that interacts with many other factors to affect the health and disease states of the host. The common kestrel (Falco tinnunculus) is protected at the national level in China. However, the available sequencing data of the gut microbiota from the feces of wild common kestrels, especially for being rescued individuals by professional organization, remains limited. In the present study, we characterized the fecal bacterial communities of healthy and injured common kestrels, and compared the structure of their fecal microbiota by analyzing the V3-V4 region of the 16S rRNA gene using high-throughput sequencing technology with the Illumina MiSeq platform. We found that Firmicutes, Proteobacteria and Actinobacteria were the most predominant phyla in common kestrels. Further, the beta diversity analysis showed that changes in gut microbes were associated with injuries to the common kestrel. The Bacteroides/Firmicutes ratio was significantly lower in the injured group. At the genus level, Glutamicibacter showed significant difference in the two groups. The aim of our current study was to characterize the basic bacterial composition and community structure in the feces of healthy common kestrels, and then compare the differences in the fecal microbiota between healthy and injured individuals. Patescibacteria, Spirochaetes, and Glutamicibacter may be studied as potential biomarkers for certain diseases in raptors. The results could provide the basic data for additional research on the fecal microbiota of common kestrels and contribute to the rescue of wild raptors in the future.
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Affiliation(s)
- Yu Guan
- Beijing Normal University, Beijing, China
| | - Lei Bao
- Beijing Normal University, Beijing, China
| | - Lei Zhou
- International Fund for Animal Welfare, Beijing Raptor Rescuer Center, Beijing, China
| | - Chang Dai
- International Fund for Animal Welfare, Beijing Raptor Rescuer Center, Beijing, China
| | - Zhisai Li
- International Fund for Animal Welfare, Beijing Raptor Rescuer Center, Beijing, China
| | - Shuai Zhang
- International Fund for Animal Welfare, Beijing Raptor Rescuer Center, Beijing, China
| | - Yugang Shang
- International Fund for Animal Welfare, Beijing Raptor Rescuer Center, Beijing, China
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Alba C, Sansano-Maestre J, Cid Vázquez MD, Martínez-Herrero MDC, Garijo-Toledo MM, Azami-Conesa I, Moraleda Fernández V, Gómez-Muñoz MT, Rodríguez JM. Captive Breeding and Trichomonas gallinae Alter the Oral Microbiome of Bonelli's Eagle Chicks. MICROBIAL ECOLOGY 2023; 85:1541-1551. [PMID: 35385973 PMCID: PMC10167124 DOI: 10.1007/s00248-022-02002-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 03/18/2022] [Indexed: 05/10/2023]
Abstract
Bonelli's eagle (Aquila fasciata) is an endangered raptor species in Europe, and trichomonosis is one of the menaces affecting chicks at nest. In this paper, we attempt to describe the oral microbiome of Bonelli's eagle nestlings and evaluate the influence of several factors, such as captivity breeding, Trichomonas gallinae infection, and the presence of lesions at the oropharynx. The core oral microbiome of Bonelli's eagle is composed of Firmicutes, Bacteroidota, Fusobacteria and Proteobacteria as the most abundant phyla, and Megamonas and Bacteroides as the most abundant genera. None of the factors analysed showed a significant influence on alfa diversity, but beta diversity was affected for some of them. Captivity breeding exerted a high influence on the composition of the oral microbiome, with significant differences in the four most abundant phyla, with a relative increase of Proteobacteria and a decrease of the other three phyla in comparison with chicks bred at nest. Some genera were more abundant in captivity bred chicks, such as Escherichia-Shigella, Enterococcus, Lactobacillus, Corynebacterium, Clostridium and Staphylococcus, while Bacteroides, Oceanivirga, Peptostreptococcus, Gemella, Veillonella, Mycoplasma, Suttonella, Alloscardovia, Varibaculum and Campylobacter were more abundant in nest raised chicks. T. gallinae infection slightly influenced the composition of the microbiome, but chicks displaying trichomonosis lesions had a higher relative abundance of Bacteroides and Gemella, being the last one an opportunistic pathogen of abscess complications in humans. Raptor's microbiomes are scarcely studied. This is the first study on the factors that influence the oral microbiome of Bonelli's eagle.
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Affiliation(s)
- Claudio Alba
- Department of Nutrition and Food Science, Faculty of Veterinary Sciences, University Complutense of Madrid, Madrid, Spain
| | - José Sansano-Maestre
- Department of Animal Production and Public Health, Faculty of Veterinary and Experimental Sciences, Catholic University of Valencia, Valencia, Spain
| | - María Dolores Cid Vázquez
- Department of Animal Health, Faculty of Veterinary Sciences, University Complutense of Madrid, Madrid, Spain
| | - María Del Carmen Martínez-Herrero
- Department of Animal Production and Health, Public Veterinary Health and Food Science and Technology, Faculty of Veterinary Medicine, Universidad Cardenal Herrera-CEU, CEU Universities, Valencia, Spain
| | - María Magdalena Garijo-Toledo
- Department of Animal Production and Health, Public Veterinary Health and Food Science and Technology, Faculty of Veterinary Medicine, Universidad Cardenal Herrera-CEU, CEU Universities, Valencia, Spain
| | - Iris Azami-Conesa
- Department of Animal Health, Faculty of Veterinary Sciences, University Complutense of Madrid, Madrid, Spain
| | | | - María Teresa Gómez-Muñoz
- Department of Animal Health, Faculty of Veterinary Sciences, University Complutense of Madrid, Madrid, Spain.
| | - Juan Miguel Rodríguez
- Department of Nutrition and Food Science, Faculty of Veterinary Sciences, University Complutense of Madrid, Madrid, Spain
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Ma X, Li J, Chen B, Li X, Ling Z, Feng S, Cao S, Zuo Z, Deng J, Huang X, Cai D, Wen Y, Zhao Q, Wang Y, Zhong Z, Peng G, Jiang Y, Gu Y. Analysis of microbial diversity in the feces of Arborophila rufipectus. Front Microbiol 2023; 13:1075041. [PMID: 36817108 PMCID: PMC9932278 DOI: 10.3389/fmicb.2022.1075041] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 12/31/2022] [Indexed: 02/05/2023] Open
Abstract
Introduction Intestinal microbiota composition plays a crucial role in modulating the health of the host. This evaluation indicator is very sensitive and profoundly impacts the protection of endangered species. Currently, information on the gut microbiota of wild birds remains scarce. Therefore, this study aimed to describe the gut microbial community structure and potentially, the pathogen composition of wild Arborophila rufipectus. Methods To guarantee comprehensive data analysis, we collected fecal samples from wild A. rufipectus and Lophura nycthemera in their habitats for two quarters. The 16S rRNA gene was then sequenced using high-throughput sequencing technology to examine the intestinal core microbiota, microbial diversity, and potential pathogens with the aim of determining if the composition of the intestinal microflora varies seasonally. Results and Discussion The gut microbiota of A. rufipectus and L. nycthemera primarily comprised four phyla: Proteobacteria (45.98%), Firmicutes (35.65%), Bacteroidetes (11.77%), and Actinobacteria (3.48%), which accounted for 96.88% of the total microbial composition in all samples. At the genus level, core microorganisms were found, including Shigella (10.38%), Clostridium (6.16%), Pseudomonas (3.03%), and Rickettsiella (1.99%). In these genera, certain microbial species have been shown to be pathogenic. This study provides important indicators for analyzing the health status of A. rufipectus and formulating protective measures.
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Affiliation(s)
- Xiaoping Ma
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Junshu Li
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Benping Chen
- Authority of Administration, Sichuan Laojunshan National Nature Reserve, Yibin, China
| | - Xinni Li
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Zhenwen Ling
- Authority of Administration, Sichuan Laojunshan National Nature Reserve, Yibin, China
| | - Shenglin Feng
- Authority of Administration, Sichuan Laojunshan National Nature Reserve, Yibin, China
| | - Sanjie Cao
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Zhicai Zuo
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Junliang Deng
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Xiaobo Huang
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Dongjie Cai
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Yiping Wen
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Qin Zhao
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Ya Wang
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Zhijun Zhong
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Guangneng Peng
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Yaozhang Jiang
- Department of Bioengineering, Sichuan Water Conservancy Vocational College, Chengdu, China,*Correspondence: Yaozhang Jiang, ; Yu Gu,
| | - Yu Gu
- College of Life Sciences, Sichuan Agricultural University, Chengdu, China,*Correspondence: Yaozhang Jiang, ; Yu Gu,
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Costanzo A, Ambrosini R, Franzetti A, Romano A, Cecere JG, Morganti M, Rubolini D, Gandolfi I. The cloacal microbiome of a cavity-nesting raptor, the lesser kestrel ( Falco naumanni). PeerJ 2022; 10:e13927. [PMID: 36221261 PMCID: PMC9548316 DOI: 10.7717/peerj.13927] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 07/30/2022] [Indexed: 01/19/2023] Open
Abstract
Background Microbial communities are found on any part of animal bodies exposed to the environment, and are particularly prominent in the gut, where they play such a major role in the host metabolism and physiology to be considered a "second genome". These communities, collectively known as "microbiome", are well studied in humans and model species, while studies on wild animals have lagged behind. This is unfortunate, as different studies suggested the central role of the gut microbiome in shaping the evolutionary trajectories of species and their population dynamics. Among bird species, only few descriptions of raptor gut microbiomes are available, and mainly carried out on captive individuals. Objectives In this study, we aimed at improving the knowledge of raptor microbiomes by providing the first description of the gut microbiome of the lesser kestrel (Falco naumanni), a cavity-nesting raptor. Results The gut microbiome of the lesser kestrel was dominated by Actinobacteria (83.9%), Proteobacteria (8.6%) and Firmicutes (4.3%). We detected no differences in microbiome composition between males and females. Furthermore, the general composition of the microbiome appears similar to that of phylogenetically distant cavity-nesting species. Conclusions Our results broaden the knowledge of raptor gut microbial communities and let us hypothesize that the distinct nest environment in terms of microclimate and presence of organic material from previous breeding attempts, to which cavity-nesting species that reuse the nest are exposed, might be an important driver shaping microbiomes.
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Affiliation(s)
- Alessandra Costanzo
- Department of Environmental Sciences and Policy, University of Milan, Milan, Italy
| | - Roberto Ambrosini
- Department of Environmental Sciences and Policy, University of Milan, Milan, Italy
| | - Andrea Franzetti
- Department of Earth and Environmental Sciences, University of Milan—Bicocca, Milan, Italy
| | - Andrea Romano
- Department of Environmental Sciences and Policy, University of Milan, Milan, Italy
| | - Jacopo G. Cecere
- Area Avifauna Migratrice, Istituto Superiore per La Protezione e La Ricerca Ambientale (ISPRA), Ozzano Emilia, (BO), Italy
| | - Michelangelo Morganti
- IRSA-CNR, Water Research Institute-National Research Council of Italy, Brugherio, Italy
| | - Diego Rubolini
- Department of Environmental Sciences and Policy, University of Milan, Milan, Italy
- IRSA-CNR, Water Research Institute-National Research Council of Italy, Brugherio, Italy
| | - Isabella Gandolfi
- Department of Earth and Environmental Sciences, University of Milan—Bicocca, Milan, Italy
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Zhang K, Wang X, Gong X, Sui J. Gut Microbiome Differences in Rescued Common Kestrels (Falco tinnunculus) Before and After Captivity. Front Microbiol 2022; 13:858592. [PMID: 35794924 PMCID: PMC9251364 DOI: 10.3389/fmicb.2022.858592] [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: 01/20/2022] [Accepted: 05/19/2022] [Indexed: 11/13/2022] Open
Abstract
Gut microbes significantly impact animal health, yet research on the gut microbiota of most birds, especially raptors, is lacking. This study investigated the effects of dietary and environmental changes on the composition and abundance of gut microbiota in 17 rescued common kestrels (Falco tinnunculus) through 16S rRNA gene high-throughput sequencing of microorganisms in the feces of the birds. Firmicutes (relative abundance, 43.63%), Proteobacteria (37.26%), Actinobacteria (7.31%), and Bacteroidetes (5.48%) were the dominant phyla in the gut microbiota of the common kestrels. A comparison of the gut microbiota before and after captivity revealed that community composition and abundance of the common kestrel gut microbiota differed among different living conditions including diet and environment. At the phylum level, the abundance of Firmicutes was higher (P < 0.05), and that of Proteobacteria was lower (P < 0.05), after captivity (54.62 and 27.16%, respectively) compared with before captivity (33.67 and 46.41%, respectively), but no significant differences were found among other phyla. At the genus level, the abundance of Lactobacillus was higher (P < 0.05) after captivity (15.77%) compared with the abundance before captivity (5.02%). Hierarchical clustering and principal component analyses showed that common kestrels in different living conditions exhibited differences (P < 0.05) in gut microbiota at phylum and genus levels. Functional prediction of gene sequences using PICRUSt2 further revealed that pathways related to glucose metabolism and amino acid metabolism were enhanced (P < 0.05) after captivity. Collectively, the findings from this study demonstrated that the relative abundance of specific microbes in the gut of the rescued common kestrels either increased or decreased, and that dietary and environment changes might be the predominant factors affecting the gut microbiota of these birds during rescue or captivity.
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Lu Z, Li S, Li H, Wang Z, Meng D, Liu J. The gut microbiota of wild wintering great bustard ( Otis tarda dybowskii): survey data from two consecutive years. PeerJ 2021; 9:e12562. [PMID: 34909281 PMCID: PMC8641483 DOI: 10.7717/peerj.12562] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 11/07/2021] [Indexed: 01/08/2023] Open
Abstract
Background The composition of the intestinal microbiota plays a significant role in modulating host health. It serves as a sensitive evaluation indicator and has substantial implications in protecting endangered species. Great Bustards are typical farmland-dependent wintering birds that are highly susceptible to the interference of human activities. However, information regarding their gut microbiota remains scarce. Methods To ensure a comprehensive analysis of this crucial data, we collected fecal samples from wild Great Bustards at their wintering habitat for two consecutive years. High-throughput sequencing of the 16S rRNA gene was subsequently applied to characterize their core gut microbiota and determine whether the gut microbial composition was similar or varied interannually. Results The gut microbiota of the Great Bustard was primarily comprised of four phyla: Firmicutes (82.87%), Bacteroidetes (7.98%), Proteobacteria (4.49%), and Actinobacteria (3.67%), accounting for 99.01% of the microbial community in all samples. Further analysis revealed 22 genera of core microbes and several pathogens. Notably, there were no significant differences in the alpha-diversity and beta-diversity between the two sample groups from different years. Conclusions This study provides essential information for assessing the health and developing targeted protective measures of this threatened species.
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Affiliation(s)
- Zhiyuan Lu
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China.,College of Life Sciences, Cangzhou Normal University, Cangzhou, China
| | - Sisi Li
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China.,Hebei Key Laboratory of Wetland Ecology and Conservation, Hengshui, China
| | - Hongxia Li
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Zhucheng Wang
- College of Life Sciences, Cangzhou Normal University, Cangzhou, China
| | - Derong Meng
- College of Life Sciences, Cangzhou Normal University, Cangzhou, China
| | - Jingze Liu
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
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