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Lecoeur A, Blanc F, Gourichon D, Bruneau N, Burlot T, Pinard-van der Laan MH, Calenge F. Host genetics drives differences in cecal microbiota composition and immune traits of laying hens raised in the same environment. Poult Sci 2024; 103:103609. [PMID: 38547541 PMCID: PMC11000118 DOI: 10.1016/j.psj.2024.103609] [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: 12/14/2023] [Revised: 02/12/2024] [Accepted: 02/28/2024] [Indexed: 04/11/2024] Open
Abstract
Vaccination is one of the most effective strategies for preventing infectious diseases but individual vaccine responses are highly heterogeneous. Host genetics and gut microbiota composition are 2 likely drivers of this heterogeneity. We studied 94 animals belonging to 4 lines of laying hens: a White Leghorn experimental line genetically selected for a high antibody response against the Newcastle Disease Virus (NDV) vaccine (ND3) and its unselected control line (CTR), and 2 commercial lines (White Leghorn [LEG] and Rhode Island Red [RIR]). Animals were reared in the same conditions from hatching to 42 d of age, and animals from different genetic lines were mixed. Animals were vaccinated at 22 d of age and their humoral vaccine response against NDV was assessed by hemagglutination inhibition assay and ELISA from blood samples collected at 15, 19, and 21 d after vaccination. The immune parameters studied were the 3 immunoglobulins subtypes A, M, and Y and the blood cell composition was assessed by flow cytometry. The composition of the cecal microbiota was assessed at the end of the experiment by analyzing amplified 16S rRNA gene sequences to obtain amplicon sequence variants (ASV). The 4 lines showed significantly different levels of NDV vaccine response at the 3 measured points, with, logically, a higher response of the genetically selected ND3 line, and intermediate and low responses for the unselected CTR control line and for the 2 commercial lines, respectively. The ND3 line displayed also a higher proportion of immunoglobulins (IgA, IgM, and IgY). The RIR line showed the most different blood cell composition. The 4 lines showed significantly different microbiota characteristics: composition, abundances at all taxonomic levels, and correlations between genera and vaccine response. The tested genetic lines differ for immune parameters and gut microbiota composition and functions. These phenotypic differences can be attributed to genetic differences between lines. Causal relationships between both types of parameters are discussed and will be investigated in further studies.
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Affiliation(s)
- Alexandre Lecoeur
- Université Paris-Saclay, INRAE, AgroParisTech, Jouy-en-Josas 78350, France.
| | - Fany Blanc
- Université Paris-Saclay, INRAE, AgroParisTech, Jouy-en-Josas 78350, France
| | | | - Nicolas Bruneau
- Université Paris-Saclay, INRAE, AgroParisTech, Jouy-en-Josas 78350, France
| | | | | | - Fanny Calenge
- Université Paris-Saclay, INRAE, AgroParisTech, Jouy-en-Josas 78350, France
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2
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Lorenzo-Rebenaque L, Casto-Rebollo C, Diretto G, Frusciante S, Rodríguez JC, Ventero MP, Molina-Pardines C, Vega S, Marin C, Marco-Jiménez F. Modulation of Caecal Microbiota and Metabolome Profile in Salmonella-Infected Broilers by Phage Therapy. Int J Mol Sci 2023; 24:15201. [PMID: 37894882 PMCID: PMC10607084 DOI: 10.3390/ijms242015201] [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: 09/20/2023] [Revised: 10/11/2023] [Accepted: 10/12/2023] [Indexed: 10/29/2023] Open
Abstract
Bacteriophage therapy is considered one of the most promising tools to control zoonotic bacteria, such as Salmonella, in broiler production. Phages exhibit high specificity for their targeted bacterial hosts, causing minimal disruption to the niche microbiota. However, data on the gut environment's response to phage therapy in poultry are limited. This study investigated the influence of Salmonella phage on host physiology through caecal microbiota and metabolome modulation using high-throughput 16S rRNA gene sequencing and an untargeted metabolomics approach. We employed 24 caecum content samples and 24 blood serum samples from 4-, 5- and 6-week-old broilers from a previous study where Salmonella phages were administered via feed in Salmonella-infected broilers, which were individually weighed weekly. Phage therapy did not affect the alpha or beta diversity of the microbiota. Specifically, we observed changes in the relative abundance of 14 out of the 110 genera using the PLS-DA and Bayes approaches. On the other hand, we noted changes in the caecal metabolites (63 up-accumulated and 37 down-accumulated out of the 1113 caecal metabolites). Nevertheless, the minimal changes in blood serum suggest a non-significant physiological response. The application of Salmonella phages under production conditions modulates the caecal microbiome and metabolome profiles in broilers without impacting the host physiology in terms of growth performance.
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Affiliation(s)
- Laura Lorenzo-Rebenaque
- Department of Animal Production and Health, Veterinary Public Health and Food Science and Technology, Biomedical Research Institute, Faculty of Veterinary Medicine, Cardenal Herrera-CEU University, CEU Universities, Calle Santiago Ramón y Cajal 20, Alfara del Patriarca, 45115 Valencia, Spain; (L.L.-R.); (S.V.); (C.M.)
| | - Cristina Casto-Rebollo
- Institute for Animal Science and Technology, Universitat Politècnica de València, 46022 Valencia, Spain;
| | - Gianfranco Diretto
- Italian Agency for New Technologies, Energy and Sustainable Development (ENEA), Biotechnology Laboratory, Centro Ricerche Casaccia, Via Anguillarese, 301, Santa Maria di Galeria, 00123 Rome, Italy; (G.D.); (S.F.)
| | - Sarah Frusciante
- Italian Agency for New Technologies, Energy and Sustainable Development (ENEA), Biotechnology Laboratory, Centro Ricerche Casaccia, Via Anguillarese, 301, Santa Maria di Galeria, 00123 Rome, Italy; (G.D.); (S.F.)
| | - Juan Carlos Rodríguez
- Microbiology Department, Dr. Balmis University General Hospital, Microbiology Division, Miguel Hernández University, ISABIAL, 03010 Alicante, Spain;
| | - María-Paz Ventero
- Microbiology Department, Dr. Balmis University General Hospital, ISABIAL, 03010 Alicante, Spain; (M.-P.V.); (C.M.-P.)
| | - Carmen Molina-Pardines
- Microbiology Department, Dr. Balmis University General Hospital, ISABIAL, 03010 Alicante, Spain; (M.-P.V.); (C.M.-P.)
| | - Santiago Vega
- Department of Animal Production and Health, Veterinary Public Health and Food Science and Technology, Biomedical Research Institute, Faculty of Veterinary Medicine, Cardenal Herrera-CEU University, CEU Universities, Calle Santiago Ramón y Cajal 20, Alfara del Patriarca, 45115 Valencia, Spain; (L.L.-R.); (S.V.); (C.M.)
| | - Clara Marin
- Department of Animal Production and Health, Veterinary Public Health and Food Science and Technology, Biomedical Research Institute, Faculty of Veterinary Medicine, Cardenal Herrera-CEU University, CEU Universities, Calle Santiago Ramón y Cajal 20, Alfara del Patriarca, 45115 Valencia, Spain; (L.L.-R.); (S.V.); (C.M.)
| | - Francisco Marco-Jiménez
- Institute for Animal Science and Technology, Universitat Politècnica de València, 46022 Valencia, Spain;
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3
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Kogut MH, Fernandez Miyakawa ME. Phenotype Alterations in the Cecal Ecosystem Involved in the Asymptomatic Intestinal Persistence of Paratyphoid Salmonella in Chickens. Animals (Basel) 2023; 13:2824. [PMID: 37760224 PMCID: PMC10525526 DOI: 10.3390/ani13182824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 08/28/2023] [Accepted: 09/04/2023] [Indexed: 09/29/2023] Open
Abstract
The gastrointestinal ecosystem involves interactions between the host, gut microbiota, and external environment. To colonize the gut of poultry, Salmonella must surmount barriers levied by the intestine including mucosal innate immune responses and microbiota-mediated niche restrictions. Accordingly, comprehending Salmonella intestinal colonization in poultry requires an understanding of how the pathogen interacts with the intestinal ecosystem. In chickens, the paratyphoid Salmonella have evolved the capacity to survive the initial immune response and persist in the avian ceca for months without triggering clinical signs. The persistence of a Salmonella infection in the avian host involves both host defenses and tolerogenic defense strategies. The initial phase of the Salmonella-gut ecosystem interaction is characteristically an innate pro-inflammatory response that controls bacterial invasion. The second phase is initiated by an expansion of the T regulatory cell population in the cecum of Salmonella-infected chickens accompanied by well-defined shifts in the enteric neuro-immunometabolic pathways that changes the local phenotype from pro-inflammatory to an anti-inflammatory environment. Thus, paratyphoid Salmonella in chickens have evolved a unique survival strategy that minimizes the inflammatory response (disease resistance) during the initial infection and then induces an immunometabolic reprogramming in the cecum that alters the host defense to disease tolerance that provides an environment conducive to drive asymptomatic carriage of the bacterial pathogen.
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Affiliation(s)
- Michael H. Kogut
- Southern Plains Agricultural Research Center, USDA-ARS, College Station, TX 77845, USA
| | - Mariano Enrique Fernandez Miyakawa
- Instituto de Patobiología, Instituto Nacional de Tecnología, Nicolas Repetto y Los Reseros S/N, Hurlingham 1686, Buenos Aires, Argentina;
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Jan TR, Lin CS, Wang SY, Yang WY. Cytokines and cecal microbiome modulations conferred by a dual vaccine in Salmonella-infected layers. Poult Sci 2022; 102:102373. [PMID: 36527813 PMCID: PMC9792558 DOI: 10.1016/j.psj.2022.102373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 11/14/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022] Open
Abstract
Zoonotic Salmonella infection is a critical and challenging issue for public health. Since human infections are mainly associated with consuming contaminated chicken products, strategies to reduce Salmonella carriage and shedding are essential. Here we investigate the mechanisms of the live attenuated Salmonella vaccine (AviPro Salmonella Duo) against Salmonella Enteritidis (SE) infection. We focused on inflammatory-related cytokine expressions and cecal microbiota modulations in specific-pathogen-free (SPF) and field layers. Forty-eight 2-day-old SPF layers were randomly allotted into S.SEvc, S.SEc, S.Vc, and S.Ct groups in trial 1. The equal number of filed layers at 25 wk were allocated into SEvc, SEc, Vc, and Ct groups in trial 2. Each group contained 12 layers. Groups were further assigned for vaccination (S.Vc and Vc groups), SE challenge (S.SEc and SEc groups), vaccination and the following SE challenge (S.SEvc and SEvc groups), or the placebo treatment (S.Ct and Ct groups). Cecal tissues and contents of layers on day 14 post-SE-challenges were collected for cytokine mRNA expression and 16S rRNA metagenomic analyses. We found that SE challenges significantly upregulated expressions of IFNγ, IL-1β, IL-12β, and NFκB1A in SPF layers. The vaccine notably counteracted the levels of IFNα, IFNγ, and NFκB1A activated by SE attacks. The vaccination, SE challenge, and their combination did not significantly affect alpha diversities but promoted dissimilarities in microbial communities between groups. Eubacterium_coprostanoligenes and Faecalibacterium_prausnitzii were identified as contributory taxa in the cecal microbiota of SE-challenged and vaccinated SPF layers. A significantly higher abundance of Faecalibacterium_prausnitzii in the ceca further correlated with the vaccination conferred protection against SE infection. In contrast, Oscillibacter_valericigenes and Mediterraneibacter_glycyrrhizinilyticus were featured taxa in Salmonella-infected field layers. Megamonas_hypermegale and Megamonas_rupellensis were identified as featured taxa in vaccinated field layers compared to SE-infected layers. To conclude, applying a dual Salmonella vaccine in this study modulated expressions of inflammatory-related cytokines and the cecal microbiome in layers, contributing to protection against SE infection. The feature microbes are promising for developing predictive indices and as antibiotic alternatives added to feed to reduce the risk of Salmonella shedding and contamination.
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Affiliation(s)
- Tong-Rong Jan
- Department of Veterinary Medicine, School of Veterinary Medicine, National Taiwan University, Taipei City 106, Taiwan
| | - Chen-Si Lin
- Department of Veterinary Medicine, School of Veterinary Medicine, National Taiwan University, Taipei City 106, Taiwan; Zoonoses Research Center and School of Veterinary Medicine, National Taiwan University, Taipei City, 106, Taiwan
| | - Sheng-Yao Wang
- Department of Animal Science and Technology, National Taiwan University, Taipei City, 106, Taiwan
| | - Wen-Yuan Yang
- Department of Veterinary Medicine, School of Veterinary Medicine, National Taiwan University, Taipei City 106, Taiwan; Zoonoses Research Center and School of Veterinary Medicine, National Taiwan University, Taipei City, 106, Taiwan.
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Super Shedding in Enteric Pathogens: A Review. Microorganisms 2022; 10:microorganisms10112101. [DOI: 10.3390/microorganisms10112101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/18/2022] [Accepted: 10/19/2022] [Indexed: 11/06/2022] Open
Abstract
Super shedding occurs when a small number of individuals from a given host population shed high levels of a pathogen. Beyond this general definition, various interpretations of the shedding patterns have been proposed to identify super shedders, leading to the description of the super shedding phenomenon in a wide range of pathogens, in particular enteric pathogens, which are of considerable interest. Several underlying mechanisms may explain this observation, including factors related to the environment, the gut microbiota, the pathogen itself (i.e., genetic polymorphism), and the host (including immune factors). Moreover, data suggest that the interplay of these parameters, in particular at the host–pathogen–gut microbiota interface, is of crucial importance for the determination of the super shedding phenotype in enteric pathogens. As a phenomenon playing an important role in the epidemics of enteric diseases, the evidence of super shedding has highlighted the need to develop various control strategies.
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Hankel J, Kittler S, Chuppava B, Galvez E, Strowig T, Becker A, von Köckritz-Blickwede M, Plötz M, Visscher C. Luminal and mucosa-associated caecal microbiota of chickens after experimental Campylobacter jejuni infection in the absence of Campylobacter-specific phages of group II and III. Microb Genom 2022; 8. [PMID: 36190827 DOI: 10.1099/mgen.0.000874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Campylobacteriosis is still the most commonly reported zoonosis in the European Union causing gastrointestinal disease in humans. One of the most common sources for these food-borne infections is broiler meat. Interactions between Campylobacter (C.) jejuni and the intestinal microbiota might influence Campylobacter colonization in chickens. The aim of the present study was to gain further knowledge about exclusive interactions of the host microbiota with C. jejuni in Campylobacter-specific phage-free chickens under standardized conditions and special biosafety precautions.Therefore, 12 artificially infected (C. jejuni inoculum with a challenge dose of 7.64 log10 c.f.u.) and 12 control chickens of the breed Ross 308 were kept under special biosafety measures in an animal facility. At day 42 of life, microbiota studies were performed on samples of caecal digesta and mucus. No Campylobacter-specific phages were detected by real-time PCR analysis of caecal digesta of control or artificially infected chickens. Amplification of the 16S rRNA gene was performed within the hypervariable region V4 and subsequently sequenced with Illumina MiSeq platform. R (version 4.0.2) was used to compare the microbiota between C. jejuni-negative and C. jejuni-positive chickens. The factor chickens' infection status contributed significantly to the differences in microbial composition of mucosal samples, explaining 10.6 % of the microbiota variation (P=0.007) and in digesta samples, explaining 9.69 % of the microbiota variation (P=0.015). The strongest difference between C. jejuni-non-infected and C. jejuni-infected birds was observed for the family Peptococcaceae whose presence in C. jejuni-infected birds could not be demonstrated. Further, several genera of the family Ruminococcaceae appeared to be depressed in its abundance due to Campylobacter infection. A negative correlation was found between Christensenellaceae R-7 group and Campylobacter in C. jejuni-colonised chickens, both genera potentially competing for substrate. This makes Christensenellaceae R-7 group highly interesting for further studies that aim to find control options for Campylobacter infections and assess the relevance of this finding for chicken health and Campylobacter colonization.
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Affiliation(s)
- Julia Hankel
- Institute for Animal Nutrition, University of Veterinary Medicine Hannover, Foundation, Bischofsholer Damm 15, D 30173 Hannover, Germany
| | - Sophie Kittler
- Institute for Food Quality and Food Safety, University of Veterinary Medicine Hannover, Foundation, Bischofsholer Damm 15, D 30173 Hannover, Germany
| | - Bussarakam Chuppava
- Institute for Animal Nutrition, University of Veterinary Medicine Hannover, Foundation, Bischofsholer Damm 15, D 30173 Hannover, Germany
| | - Eric Galvez
- Helmholtz Center for Infection Research, Inhoffenstraße 7, D 38124 Braunschweig, Germany.,Hannover Medical School, Carl-Neuberg-Straße 1, D 30625 Hannover, Germany
| | - Till Strowig
- Helmholtz Center for Infection Research, Inhoffenstraße 7, D 38124 Braunschweig, Germany.,Hannover Medical School, Carl-Neuberg-Straße 1, D 30625 Hannover, Germany
| | - André Becker
- Institute for Food Quality and Food Safety, University of Veterinary Medicine Hannover, Foundation, Bischofsholer Damm 15, D 30173 Hannover, Germany
| | - Maren von Köckritz-Blickwede
- Research Center for Emerging Infections and Zoonoses, University of Veterinary Medicine Hannover, Foundation, Bünteweg 17, D 30559 Hannover, Germany
| | - Madeleine Plötz
- Institute for Food Quality and Food Safety, University of Veterinary Medicine Hannover, Foundation, Bischofsholer Damm 15, D 30173 Hannover, Germany
| | - Christian Visscher
- Institute for Animal Nutrition, University of Veterinary Medicine Hannover, Foundation, Bischofsholer Damm 15, D 30173 Hannover, Germany
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Cazals A, Rau A, Estellé J, Bruneau N, Coville JL, Menanteau P, Rossignol MN, Jardet D, Bevilacqua C, Bed’Hom B, Velge P, Calenge F. Comparative analysis of the caecal tonsil transcriptome in two chicken lines experimentally infected with Salmonella Enteritidis. PLoS One 2022; 17:e0270012. [PMID: 35976909 PMCID: PMC9384989 DOI: 10.1371/journal.pone.0270012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 08/03/2022] [Indexed: 11/18/2022] Open
Abstract
Managing Salmonella enterica Enteritidis (SE) carriage in chicken is necessary to ensure human food safety and enhance the economic, social and environmental sustainability of chicken breeding. Salmonella can contaminate poultry products, causing human foodborne disease and economic losses for farmers. Both genetic selection for a decreased carriage and gut microbiota modulation strategies could reduce Salmonella propagation in farms. Two-hundred and twenty animals from the White Leghorn inbred lines N and 61 were raised together on floor, infected by SE at 7 days of age, transferred into isolators to prevent oro-fecal recontamination and euthanized at 12 days post-infection. Caecal content DNA was used to measure individual Salmonella counts (ISC) by droplet digital PCR. A RNA sequencing approach was used to measure gene expression levels in caecal tonsils after infection of 48 chicks with low or high ISC. The analysis between lines identified 7516 differentially expressed genes (DEGs) corresponding to 62 enriched Gene Ontology (GO) Biological Processes (BP) terms. A comparison between low and high carriers allowed us to identify 97 DEGs and 23 enriched GO BP terms within line 61, and 1034 DEGs and 288 enriched GO BP terms within line N. Among these genes, we identified several candidate genes based on their putative functions, including FUT2 or MUC4, which could be involved in the control of SE infection, maybe through interactions with commensal bacteria. Altogether, we were able to identify several genes and pathways associated with differences in SE carriage level. These results are discussed in relation to individual caecal microbiota compositions, obtained for the same animals in a previous study, which may interact with host gene expression levels for the control of the caecal SE load.
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Affiliation(s)
- Anaïs Cazals
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
- Mouse Genetics Laboratory, Department of Genomes and Genetics, Institut Pasteur, Paris, France
| | - Andrea Rau
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
- BioEcoAgro Joint Research Unit, INRAE, Université de Liège, Université de Lille, Université de Picardie Jules Verne, Peronne, France
| | - Jordi Estellé
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
| | - Nicolas Bruneau
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
| | - Jean-Luc Coville
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
| | | | | | - Deborah Jardet
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
| | - Claudia Bevilacqua
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
| | - Bertrand Bed’Hom
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
| | - Philippe Velge
- UMR ISP, INRAE, Université F. Rabelais, Nouzilly, France
| | - Fanny Calenge
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
- * E-mail:
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Goossens E, Boonyarittichaikij R, Dekeukeleire D, Hertzog L, Van Praet S, Pasmans F, Bonte D, Verheyen K, Lens L, Martel A, Verbrugghe E. Tree Species Diversity and Forest Edge Density Jointly Shape the Gut Microbiota Composition in Juvenile Great Tits (Parus major). Front Microbiol 2022; 13:790189. [PMID: 35356520 PMCID: PMC8959704 DOI: 10.3389/fmicb.2022.790189] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 02/10/2022] [Indexed: 01/19/2023] Open
Abstract
Despite the microbiome’s key role in health and fitness, little is known about the environmental factors shaping the gut microbiome of wild birds. With habitat fragmentation being recognised as a major threat to biological diversity, we here determined how forest structure influences the bacterial species richness and diversity of wild great tit nestlings (Parus major). Using an Illumina metabarcoding approach which amplifies the 16S bacterial ribosomal RNA gene, we measured gut microbiota diversity and composition from 49 great tit nestlings, originating from 23 different nests that were located in 22 different study plots across a gradient of forest fragmentation and tree species diversity. Per nest, an average microbiome was determined on which the influence of tree species (composition and richness) and forest fragmentation (fragment area and edge density) was examined and whether this was linked to host characteristics (body condition and fledging success). We found an interaction effect of edge density with tree species richness or composition on both the microbial richness (alpha diversity: Chao1 and Shannon) and community structure (beta diversity: weighted and unweighted UniFrac). No significant short-term impact was observed of the overall faecal microbiome on host characteristics, but rather an adverse effect of specific bacterial genera on fledging success. These results highlight the influence of environmental factors on the microbial richness as well as the phylogenetic diversity during a life stage where the birds’ microbiota is shaped, which could lead to long-term consequences for host fitness.
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Affiliation(s)
- Evy Goossens
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Roschong Boonyarittichaikij
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
- Department of Clinical Sciences and Public Health, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom, Thailand
| | - Daan Dekeukeleire
- Terrestrial Ecology Unit, Department of Biology, Ghent University, Ghent, Belgium
| | - Lionel Hertzog
- Terrestrial Ecology Unit, Department of Biology, Ghent University, Ghent, Belgium
| | - Sarah Van Praet
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Frank Pasmans
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Dries Bonte
- Terrestrial Ecology Unit, Department of Biology, Ghent University, Ghent, Belgium
| | - Kris Verheyen
- Forest & Nature Lab, Department of Environment, Ghent University, Ghent, Belgium
| | - Luc Lens
- Terrestrial Ecology Unit, Department of Biology, Ghent University, Ghent, Belgium
| | - An Martel
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Elin Verbrugghe
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
- *Correspondence: Elin Verbrugghe,
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