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Vaasjo E, Stothart MR, Black SR, Poissant J, Whiteside DP. The impact of management on the fecal microbiome of endangered greater sage-grouse ( Centrocercus urophasianus) in a zoo-based conservation program. CONSERVATION PHYSIOLOGY 2024; 12:coae052. [PMID: 39113731 PMCID: PMC11304599 DOI: 10.1093/conphys/coae052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 07/09/2024] [Accepted: 07/18/2024] [Indexed: 08/10/2024]
Abstract
Greater sage-grouse (Centrocercus urophasianus) are a critically endangered species in Canada with fewer than 140 individuals remaining on native habitats in southern Alberta and Saskatchewan. In 2014, the Wilder Institute/Calgary Zoo initiated North America's only zoo-based conservation breeding program for this species to bolster declining wild populations through conservation reintroductions. Within the managed population of sage-grouse, morbidity and mortality have primarily been associated with intestinal bacterial infections. As a preliminary study to assess the gastrointestinal health of this species in managed care, the fecal bacterial microbiome of adult and juvenile captive sage-grouse was characterized with 16S rRNA sequencing. The composition of the microbiome at the phylum level in greater sage-grouse is consistent with previous studies of the avian microbiome, with Bacillota as the most abundant phyla, and Actinomycetota, Bacteroidota and Pseudomonadota also being highly abundant. Antibiotic use and sex did not have a significant impact on the diversity or composition of the microbiome, but the management of juvenile sage-grouse did influence the development of the microbiome. Juveniles that were raised outdoors under maternal care developed a microbiome much more similar to adults when compared to chicks that were incubated and hand-raised. The local environment and parental care appear to be important factors influencing the diversity and composition of the gastrointestinal microbiome in this species.
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Affiliation(s)
- Emma Vaasjo
- Faculty of Veterinary Medicine, University of Calgary, 3280 Hospital Dr NW, Calgary, AB T2N 4Z6, Canada
- Animal Health Department, Wilder Institute/Calgary Zoo, 1300 Zoo Rd NE, Calgary, AB T2E 7V6, Canada
| | - Mason R Stothart
- Faculty of Veterinary Medicine, University of Calgary, 3280 Hospital Dr NW, Calgary, AB T2N 4Z6, Canada
| | - Sandra R Black
- Animal Health Department, Wilder Institute/Calgary Zoo, 1300 Zoo Rd NE, Calgary, AB T2E 7V6, Canada
| | - Jocelyn Poissant
- Faculty of Veterinary Medicine, University of Calgary, 3280 Hospital Dr NW, Calgary, AB T2N 4Z6, Canada
| | - Douglas P Whiteside
- Faculty of Veterinary Medicine, University of Calgary, 3280 Hospital Dr NW, Calgary, AB T2N 4Z6, Canada
- Animal Health Department, Wilder Institute/Calgary Zoo, 1300 Zoo Rd NE, Calgary, AB T2E 7V6, Canada
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2
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Dunbar A, Drigo B, Djordjevic SP, Donner E, Hoye BJ. Impacts of coprophagic foraging behaviour on the avian gut microbiome. Biol Rev Camb Philos Soc 2024; 99:582-597. [PMID: 38062990 DOI: 10.1111/brv.13036] [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: 08/14/2023] [Revised: 11/24/2023] [Accepted: 11/27/2023] [Indexed: 03/06/2024]
Abstract
Avian gut microbial communities are complex and play a fundamental role in regulating biological functions within an individual. Although it is well established that diet can influence the structure and composition of the gut microbiota, foraging behaviour may also play a critical, yet unexplored role in shaping the composition, dynamics, and adaptive potential of avian gut microbiota. In this review, we examine the potential influence of coprophagic foraging behaviour on the establishment and adaptability of wild avian gut microbiomes. Coprophagy involves the ingestion of faeces, sourced from either self (autocoprophagy), conspecific animals (allocoprophagy), or heterospecific animals. Much like faecal transplant therapy, coprophagy may (i) support the establishment of the gut microbiota of young precocial species, (ii) directly and indirectly provide nutritional and energetic requirements, and (iii) represent a mechanism by which birds can rapidly adapt the microbiota to changing environments and diets. However, in certain contexts, coprophagy may also pose risks to wild birds, and their microbiomes, through increased exposure to chemical pollutants, pathogenic microbes, and antibiotic-resistant microbes, with deleterious effects on host health and performance. Given the potentially far-reaching consequences of coprophagy for avian microbiomes, and the dearth of literature directly investigating these links, we have developed a predictive framework for directing future research to understand better when and why wild birds engage in distinct types of coprophagy, and the consequences of this foraging behaviour. There is a need for comprehensive investigation into the influence of coprophagy on avian gut microbiotas and its effects on host health and performance throughout ontogeny and across a range of environmental perturbations. Future behavioural studies combined with metagenomic approaches are needed to provide insights into the function of this poorly understood behaviour.
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Affiliation(s)
- Alice Dunbar
- Future Industries Institute (FII), University of South Australia, Mawson Lakes Campus, GPO Box 2471 5095, Adelaide, South Australia, Australia
| | - Barbara Drigo
- Future Industries Institute (FII), University of South Australia, Mawson Lakes Campus, GPO Box 2471 5095, Adelaide, South Australia, Australia
- UniSA STEM, University of South Australia, GPO Box 2471, Adelaide, South Australia, 5001, Australia
| | - Steven P Djordjevic
- Australian Institute for Microbiology and Infection, University of Technology Sydney, PO Box 123, Ultimo, New South Wales, 2007, Australia
- Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, PO Box 123, Ultimo, New South Wales, 2007, Australia
| | - Erica Donner
- Future Industries Institute (FII), University of South Australia, Mawson Lakes Campus, GPO Box 2471 5095, Adelaide, South Australia, Australia
- Cooperative Research Centre for Solving Antimicrobial Resistance in Agribusiness, Food, and Environments (CRC SAAFE), University of South Australia, GPO Box 2471 5095, Adelaide, South Australia, Australia
| | - Bethany J Hoye
- School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, New South Wales, 2522, Australia
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Rudzki EN, Antonson ND, Jones TM, Schelsky WM, Trevelline BK, Hauber ME, Kohl KD. Host avian species and environmental conditions influence the microbial ecology of brood parasitic brown-headed cowbird nestlings: What rules the roost? Mol Ecol 2024; 33:e17289. [PMID: 38327124 DOI: 10.1111/mec.17289] [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: 09/29/2023] [Revised: 01/17/2024] [Accepted: 01/23/2024] [Indexed: 02/09/2024]
Abstract
The role of species interactions, as well as genetic and environmental factors, all likely contribute to the composition and structure of the gut microbiome; however, disentangling these independent factors under field conditions represents a challenge for a functional understanding of gut microbial ecology. Avian brood parasites provide unique opportunities to investigate these questions, as brood parasitism results in parasite and host nestlings being raised in the same nest, by the same parents. Here we utilized obligate brood parasite brown-headed cowbird nestlings (BHCO; Molothrus ater) raised by several different host passerine species to better understand, via 16S rRNA sequencing, the microbial ecology of brood parasitism. First, we compared faecal microbial communities of prothonotary warbler nestlings (PROW; Protonotaria citrea) that were either parasitized or non-parasitized by BHCO and communities among BHCO nestlings from PROW nests. We found that parasitism by BHCO significantly altered both the community membership and community structure of the PROW nestling microbiota, perhaps due to the stressful nest environment generated by brood parasitism. In a second dataset, we compared faecal microbiotas from BHCO nestlings raised by six different host passerine species. Here, we found that the microbiota of BHCO nestlings was significantly influenced by the parental host species and the presence of an inter-specific nestmate. Thus, early rearing environment is important in determining the microbiota of brood parasite nestlings and their companion nestlings. Future work may aim to understand the functional effects of this microbiota variability on nestling performance and fitness.
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Affiliation(s)
- Elizabeth N Rudzki
- Department of Biological Sciences, Dietrich School of Arts and Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Nicholas D Antonson
- Department of Evolution, Ecology, and Behavior, School of Integrative Biology, College of Liberal Arts & Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Todd M Jones
- Department of Natural Resources and Environmental Sciences, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, Champaign, Illinois, USA
| | - Wendy M Schelsky
- Department of Evolution, Ecology, and Behavior, School of Integrative Biology, College of Liberal Arts & Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Natural Resources and Environmental Sciences, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Prairie Research Institute, Illinois Natural History Survey, University of Illinois, Champaign, Illinois, USA
| | - Brian K Trevelline
- Cornell Lab of Ornithology, Cornell University, Ithaca, New York, USA
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | - Mark E Hauber
- Department of Evolution, Ecology, and Behavior, School of Integrative Biology, College of Liberal Arts & Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, Champaign, Illinois, USA
- Advanced Science Research Center and Program in Psychology, Graduate Center, City University of New York, New York, New York, USA
| | - Kevin D Kohl
- Department of Biological Sciences, Dietrich School of Arts and Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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Hajra D, Kirthivasan N, Chakravortty D. Symbiotic Synergy from Sponges to Humans: Microflora-Host Harmony Is Crucial for Ensuring Survival and Shielding against Invading Pathogens. ACS Infect Dis 2024; 10:317-336. [PMID: 38170903 DOI: 10.1021/acsinfecdis.3c00554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Gut microbiota plays several roles in the host organism's metabolism and physiology. This phenomenon holds across different species from different kingdoms and classes. Different species across various classes engage in continuous crosstalk via various mechanisms with their gut microbiota, ensuring homeostasis of the host. In this Review, the diversity of the microflora, the development of the microflora in the host, its regulations by the host, and its functional implications on the host, especially in the context of dysbiosis, are discussed across different organisms from sponges to humans. Overall, our review aims to address the indispensable nature of the microbiome in the host's survival, fitness, and protection against invading pathogens.
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Affiliation(s)
- Dipasree Hajra
- Department of Microbiology & Cell Biology, Indian Institute of Science, Bangalore, Karnataka-560012, India
| | - Nikhita Kirthivasan
- Undergraduate Programme, Indian Institute of Science, Bangalore, Karnataka-560012, India
| | - Dipshikha Chakravortty
- Department of Microbiology & Cell Biology, Indian Institute of Science, Bangalore, Karnataka-560012, India
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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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Huang T, Han J, Liu Y, Fei M, Du X, He K, Zhao A. Dynamic distribution of gut microbiota in posthatching chicks and its relationship with average daily gain. Poult Sci 2023; 102:103008. [PMID: 37598556 PMCID: PMC10462888 DOI: 10.1016/j.psj.2023.103008] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 07/30/2023] [Accepted: 08/02/2023] [Indexed: 08/22/2023] Open
Abstract
The colonization and development of gut microbiota are essential for the health and growth of chicks after hatching. However, the colonization and prevalence of gut microbiota have not been well characterized, and knowledge of which microbes and their relationship with average daily gain in chicks is still limited. This study characterized the dynamic succession of microbiota in the intestinal tract of chicks and investigated its relationship with daily weight gain. A total of 121 fecal samples across 7 time points from d 0 to 10 posthatching were collected from 19 chicks randomly selected from 1,950 chicks. Using 16S rRNA gene sequencing examined microbial composition of fecal samples. The observed species index of alpha diversity increased with age, gradually achieving stability at 3 d of age. The microbiota of chicks after hatching was primarily Clostridium_sensu_stricto_1 (34.49%), and its relative abundance diminishes with age. In contrast, Lactobacillus had a low relative abundance in the first 2 d after hatching and gradually increased with age. Predicted functional capacities found that the microbiota of early-stage posthatching (d 0 and 1 after hatching) was involved in metabolism, including amino acid metabolism, metabolism of cofactors and vitamins, and nitrogen metabolism. However, at the later stage posthatching (from d 3-10 after hatching), the intestinal microbial function was involved in carbohydrate metabolism, amino acid metabolism, cell growth and death, and methane metabolism. It was identified that 47 operational taxonomic units were associated with average daily gain of chicks, 12 of which were annotated with Lactobacillus and significantly positive associated with average daily gain. In addition, Clostridium_sensu_stricto_1 was significantly negatively associated with average daily gain. Taken together, we characterized the dynamic successions of intestinal microbiota in hatching chicks. The intestinal microbiota of chicks has an impact on the host average daily gain. Our findings should be instrumental in improving local chick production.
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Affiliation(s)
- Tao Huang
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang A&F University, Hangzhou, 311300, China
| | - Jie Han
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang A&F University, Hangzhou, 311300, China
| | - Yongqi Liu
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang A&F University, Hangzhou, 311300, China
| | - Meina Fei
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang A&F University, Hangzhou, 311300, China
| | - Xue Du
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang A&F University, Hangzhou, 311300, China
| | - Ke He
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang A&F University, Hangzhou, 311300, China
| | - Ayong Zhao
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang A&F University, Hangzhou, 311300, China.
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7
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He Y, Zhang M, Dai C, Yu L. Comparison of the Gut Microbial Communities of Domestic and Wild Mallards ( Anas platyrhynchos) Based on High-Throughput Sequencing Technology. Animals (Basel) 2023; 13:2956. [PMID: 37760356 PMCID: PMC10525502 DOI: 10.3390/ani13182956] [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: 08/07/2023] [Revised: 09/12/2023] [Accepted: 09/15/2023] [Indexed: 09/29/2023] Open
Abstract
Mallards (Anas platyrhynchos) are currently one of the most popular species in rare bird breeding in several southern provinces of China, but there have been no studies comparing the gut microbial communities of domestic and wild mallards. In this study, 16S rRNA gene high-throughput sequencing technology was used to compare the composition and diversity of gut microbial communities in domestic and wild mallards. Alpha diversity analysis showed significant differences in gut microbial communities between the two groups of mallards, and the diversity and richness of gut microbial communities were significantly higher in wild mallards than in domestic mallards. Beta diversity analysis showed that the two groups of stool samples were mostly separated on the principal coordinate analysis (PCoA) plot. In domestic mallards, Firmicutes (68.0% ± 26.5%) was the most abundant bacterial phylum, followed by Proteobacteria (24.5% ± 22.9%), Bacteroidetes (3.1% ± 3.2%), Fusobacteria (2.2% ± 5.9%), and Actinobacteria (1.1% ± 1.8%). The dominant bacterial phyla in wild mallards were Firmicutes (79.0% ± 10.2%), Proteobacteria (12.9% ± 9.5%), Fusobacteria (3.4% ± 2.5%), and Bacteroidetes (2.8% ± 2.4%). At the genus level, a total of 10 dominant genera (Streptococcus, Enterococcus, Clostridium, Lactobacillus, Soilbacillus, Bacillus, Acinetobacter, Comamonas, Shigella, and Cetobacterium) with an average relative abundance greater than 1% were detected in the fecal samples of both groups. The average relative abundance of five potential pathogenic genera (Streptococcus, Enterococcus, Acinetobacter, Comamonas, and Shigella) was higher in domestic mallards than in wild mallards. The enrichment of pathogenic bacteria in the intestinal tract of domestic mallards should be of sufficient concern.
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Affiliation(s)
- Yaoyin He
- Animal Science and Technology College, Guangxi University, Nanning 530004, China; (Y.H.); (M.Z.)
| | - Minghui Zhang
- Animal Science and Technology College, Guangxi University, Nanning 530004, China; (Y.H.); (M.Z.)
| | - Chuanyin Dai
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin 541006, China;
| | - Lijiang Yu
- Animal Science and Technology College, Guangxi University, Nanning 530004, China; (Y.H.); (M.Z.)
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Prüter H, Gillingham MAF, Krietsch J, Kuhn S, Kempenaers B. Sexual transmission may drive pair similarity of the cloacal microbiome in a polyandrous species. J Anim Ecol 2023. [PMID: 37230950 DOI: 10.1111/1365-2656.13961] [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: 10/24/2022] [Accepted: 05/05/2023] [Indexed: 05/27/2023]
Abstract
All animals host a microbial community within and on their reproductive organs, known as the reproductive microbiome. In free-living birds, studies on the sexual transmission of bacteria have typically focused on a few pathogens instead of the bacterial community as a whole, despite a potential link to reproductive function. Theory predicts higher sexual transmission of the reproductive microbiome in females via the males' ejaculates and higher rates of transmission in promiscuous systems. We studied the cloacal microbiome of breeding individuals of a socially polyandrous, sex-role-reversed shorebird, the red phalarope (Phalaropus fulicarius). We expected (i) higher microbial diversity in females compared to males; (ii) low compositional differentiation between sexes; (iii) lower variation in composition between individuals (i.e. microbiome dispersion) in females than in males; (iv) convergence in composition as the breeding season progresses as a consequence of sexual transmission and/or shared habitat use; and (v) higher similarity in microbial composition between social pair members than between two random opposite-sex individuals. We found no or small between-sex differences in cloacal microbiome diversity/richness and composition. Dispersion of predicted functional pathways was lower in females than in males. As predicted, microbiome dispersion decreased with sampling date relative to clutch initiation of the social pair. Microbiome composition was significantly more similar among social pair members than among two random opposite-sex individuals. Pair membership explained 21.5% of the variation in taxonomic composition and 10.1% of functional profiles, whereas temporal and sex effects explained only 0.6%-1.6%. Consistent with evidence of functional convergence of reproductive microbiomes within pairs, some select taxa and predicted functional pathways were less variable between social pair members than between random opposite-sex individuals. As predicted if sexual transmission of the reproductive microbiome is high, sex differences in microbiome composition were weak in a socially polyandrous system with frequent copulations. Moreover, high within-pair similarity in microbiome composition, particularly for a few taxa spanning the spectrum of the beneficial-pathogenic axis, demonstrates the link between mating behaviour and the reproductive microbiome. Our study is consistent with the hypothesis that sexual transmission plays an important role in driving reproductive microbiome ecology and evolution.
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Affiliation(s)
- Hanna Prüter
- Department of Behavioural Ecology and Evolutionary Genetics, Max Planck Institute for Biological Intelligence, Seewiesen, Germany
| | - Mark A F Gillingham
- Department of Behavioural Ecology and Evolutionary Genetics, Max Planck Institute for Biological Intelligence, Seewiesen, Germany
- Biodiversity Research Institute (CSIC, Oviedo University, Principality of Asturias), University of Oviedo, Mieres, Spain
| | - Johannes Krietsch
- Department of Behavioural Ecology and Evolutionary Genetics, Max Planck Institute for Biological Intelligence, Seewiesen, Germany
| | - Sylvia Kuhn
- Department of Behavioural Ecology and Evolutionary Genetics, Max Planck Institute for Biological Intelligence, Seewiesen, Germany
| | - Bart Kempenaers
- Department of Behavioural Ecology and Evolutionary Genetics, Max Planck Institute for Biological Intelligence, Seewiesen, Germany
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9
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Diez-Méndez D, Bodawatta KH, Freiberga I, Klečková I, Jønsson KA, Poulsen M, Sam K. Indirect maternal effects via nest microbiome composition drive gut colonization in altricial chicks. Mol Ecol 2023. [PMID: 37096441 DOI: 10.1111/mec.16959] [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: 02/26/2022] [Revised: 04/07/2023] [Accepted: 04/12/2023] [Indexed: 04/26/2023]
Abstract
Gut microbial communities are complex and heterogeneous and play critical roles for animal hosts. Early-life disruptions to microbiome establishment can negatively impact host fitness and development. However, the consequences of such early-life disruptions remain unknown in wild birds. To help fill this gap, we investigated the effect of continuous early-life gut microbiome disruptions on the establishment and development of gut communities in wild Great tit (Parus major) and Blue tit (Cyanistes caeruleus) nestlings by applying antibiotics and probiotics. Treatment neither affected nestling growth nor their gut microbiome composition. Independent of treatment, nestling gut microbiomes of both species grouped by brood, which shared the highest numbers of bacterial taxa with both nest environment and their mother. Although fathers showed different gut communities than their nestlings and nests, they still contributed to structuring chick microbiomes. Lastly, we observed that the distance between nests increased inter-brood microbiome dissimilarity, but only in Great tits, indicating that species-specific foraging behaviour and/or microhabitat influence gut microbiomes. Overall, the strong maternal effect, driven by continuous recolonization from the nest environment and vertical transfer of microbes during feeding, appears to provide resilience towards early-life disruptions in nestling gut microbiomes.
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Affiliation(s)
- David Diez-Méndez
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, České Budějovice, Czech Republic
| | - Kasun H Bodawatta
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
- Molecular Ecology and Evolution, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Inga Freiberga
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, České Budějovice, Czech Republic
| | - Irena Klečková
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, České Budějovice, Czech Republic
| | - Knud A Jønsson
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Michael Poulsen
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Katerina Sam
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
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10
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Liukkonen M, Hukkanen M, Cossin-Sevrin N, Stier A, Vesterinen E, Grond K, Ruuskanen S. No evidence for associations between brood size, gut microbiome diversity and survival in great tit (Parus major) nestlings. Anim Microbiome 2023; 5:19. [PMID: 36949549 PMCID: PMC10031902 DOI: 10.1186/s42523-023-00241-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 03/13/2023] [Indexed: 03/24/2023] Open
Abstract
BACKGROUND The gut microbiome forms at an early stage, yet data on the environmental factors influencing the development of wild avian microbiomes is limited. As the gut microbiome is a vital part of organismal health, it is important to understand how it may connect to host performance. The early studies with wild gut microbiome have shown that the rearing environment may be of importance in gut microbiome formation, yet the results vary across taxa, and the effects of specific environmental factors have not been characterized. Here, wild great tit (Parus major) broods were manipulated to either reduce or enlarge the original brood soon after hatching. We investigated if brood size was associated with nestling bacterial gut microbiome, and whether gut microbiome diversity predicted survival. Fecal samples were collected at mid-nestling stage and sequenced with the 16S rRNA gene amplicon sequencing, and nestling growth and survival were measured. RESULTS Gut microbiome diversity showed high variation between individuals, but this variation was not significantly explained by brood size or body mass. Additionally, we did not find a significant effect of brood size on body mass or gut microbiome composition. We also demonstrated that early handling had no impact on nestling performance or gut microbiome. Furthermore, we found no significant association between gut microbiome diversity and short-term (survival to fledging) or mid-term (apparent juvenile) survival. CONCLUSIONS We found no clear association between early-life environment, offspring condition and gut microbiome. This suggests that brood size is not a significantly contributing factor to great tit nestling condition, and that other environmental and genetic factors may be more strongly linked to offspring condition and gut microbiome. Future studies should expand into other early-life environmental factors e.g., diet composition and quality, and parental influences.
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Affiliation(s)
- Martta Liukkonen
- Department of Biological and Environmental Science, University of Jyväskylä, Jyvaskyla, Finland.
| | - Mikaela Hukkanen
- Department of Biology, University of Turku, Turku, Finland
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | | | - Antoine Stier
- Department of Biology, University of Turku, Turku, Finland
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023 LEHNA, 69622, Lyon, France
- Institut Pluridisciplinaire Hubert Curien, UMR7178, Université de Strasbourg, CNRS, Strasbourg, France
| | | | - Kirsten Grond
- Department of Biological Sciences, University of Alaska Anchorage, Anchorage, AK, 99508, USA
| | - Suvi Ruuskanen
- Department of Biological and Environmental Science, University of Jyväskylä, Jyvaskyla, Finland
- Department of Biology, University of Turku, Turku, Finland
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11
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Functional and Compositional Changes in the Fecal Microbiome of a Shorebird during Migratory Stopover. mSystems 2023; 8:e0112822. [PMID: 36786579 PMCID: PMC10134852 DOI: 10.1128/msystems.01128-22] [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: 02/15/2023] Open
Abstract
Shorebirds migrate long distances twice annually, which requires intense physiological and morphological adaptations, including the ability to rapidly gain weight via fat deposition at stopover locations. The role of the microbiome in weight gain in avian hosts is unresolved, but there is substantial evidence to support the hypothesis that the microbiome is involved with host weight from mammalian microbiome literature. Here, we collected 100 fecal samples of Ruddy Turnstones to investigate microbiome composition and function during stopover weight gain in Delaware Bay, USA. Using 16S rRNA sequencing on 90 of these samples and metatranscriptomic sequencing on 22, we show that taxonomic composition of the microbiome shifts during weight gain, as do functional aspects of the metatranscriptome. We identified 10 genes that are associated with weight class, and polyunsaturated fatty acid biosynthesis in the microbiota is significantly increasing as birds gain weight. Our results support that the microbiome is a dynamic feature of host biology that interacts with both the host and the environment and may be involved in the rapid weight gain of shorebirds. IMPORTANCE Many animals migrate long distances annually, and these journeys require intense physiological and morphological adaptations. One such adaptation in shorebirds is the ability to rapidly gain weight at stopover locations in the middle of their migrations. The role of the microbiome in weight gain in birds is unresolved but is likely to play a role. Here, we collected 100 fecal samples from Ruddy Turnstones to investigate microbiome composition (who is there) and function (what they are doing) during stopover weight gain in Delaware Bay, USA. Using multiple molecular methods, we show that both taxonomic composition and function of the microbiome shifts during weight gain. We identified 10 genes that are associated with weight class, and polyunsaturated fatty acid biosynthesis in the microbiota is significantly increasing as birds gain weight. Our results support that the microbiome is a dynamic feature of host biology that interacts with both the host and the environment and may be involved in the rapid weight gain of shorebirds.
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Florkowski MR, Yorzinski JL. Gut microbiome diversity and composition is associated with exploratory behavior in a wild-caught songbird. Anim Microbiome 2023; 5:8. [PMID: 36739424 PMCID: PMC9899379 DOI: 10.1186/s42523-023-00227-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 01/16/2023] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The gut microbiome influences its host in a myriad of ways, from immune system development to nutrient utilization. However, our understanding of the relationship between the gut microbiome and behavior, especially in wild species, is still poor. One behavior that potentially interacts with the gut microbiome is exploratory behavior, which animals use to acquire new information from the environment. We hypothesized that diversity of the gut microbiome will be correlated with exploratory behavior in a wild-caught bird species. To test this hypothesis, we captured wild house sparrows (Passer domesticus) and collected fecal samples to measure the diversity of their gut microbiomes. We then introduced individuals to a novel environment and measured their exploratory behavior. RESULTS We found that birds with higher alpha diversity of the gut microbiome exhibited higher exploratory behavior. These results suggest that high exploratory birds encounter more types of environmental microbes that contribute to their diverse gut microbiome compared with less exploratory birds. Alternatively, increased gut microbiome diversity may contribute to increased exploratory behavior. We also found differences in beta diversity when comparing high and low exploring birds, indicating differences in microbiome community structure. When comparing predicted functional pathways of the birds' microbiomes, we found that the microbiomes of high explorers contained more pathways involved in biofilm formation and xenobiotic degradation than those of low explorers. CONCLUSIONS Overall, we found that the alpha and beta diversity of the gut microbiome is correlated with exploratory behavior of house sparrows. The predicted functions of the gut microbiome from high explorers differs from that of low explorers. Our study highlights the importance of considering the gut microbiome when investigating animal behavior.
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Affiliation(s)
- Melanie R. Florkowski
- grid.264756.40000 0004 4687 2082Ecology and Evolutionary Biology Program, Texas A&M University, 534 John Kimbrough Blvd, College Station, TX 77843 USA
| | - Jessica L. Yorzinski
- grid.264756.40000 0004 4687 2082Ecology and Evolutionary Biology Program, Texas A&M University, 534 John Kimbrough Blvd, College Station, TX 77843 USA ,grid.264756.40000 0004 4687 2082Department of Ecology and Conservation Biology, Texas A&M University, College Station, TX USA
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West AG, Digby A, Taylor MW. The mycobiota of faeces from the critically endangered kākāpō and associated nest litter. NEW ZEALAND JOURNAL OF ZOOLOGY 2023. [DOI: 10.1080/03014223.2023.2170428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Annie G. West
- Te Kura Mātauranga Koiora School of Biological Sciences, Waipapa Taumata Rau University of Auckland, Auckland, New Zealand
| | - Andrew Digby
- Te Papa Atawhai Department of Conservation, Kākāpō Recovery Programme, Invercargill, New Zealand
| | - Michael W. Taylor
- Te Kura Mātauranga Koiora School of Biological Sciences, Waipapa Taumata Rau University of Auckland, Auckland, New Zealand
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Effect of diet on gut microbiota diversity in mandarin ducks (Aix galericulata) revealed by Illumina high-throughput sequencing. Arch Microbiol 2022; 204:725. [DOI: 10.1007/s00203-022-03333-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 11/03/2022] [Accepted: 11/10/2022] [Indexed: 11/27/2022]
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Maraci Ö, Antonatou-Papaioannou A, Jünemann S, Engel K, Castillo-Gutiérrez O, Busche T, Kalinowski J, Caspers BA. Timing matters: age-dependent impacts of the social environment and host selection on the avian gut microbiota. MICROBIOME 2022; 10:202. [PMID: 36434663 PMCID: PMC9700942 DOI: 10.1186/s40168-022-01401-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 10/25/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND The establishment of the gut microbiota in early life is a critical process that influences the development and fitness of vertebrates. However, the relative influence of transmission from the early social environment and host selection throughout host ontogeny remains understudied, particularly in avian species. We conducted conspecific and heterospecific cross-fostering experiments in zebra finches (Taeniopygia guttata) and Bengalese finches (Lonchura striata domestica) under controlled conditions and repeatedly sampled the faecal microbiota of these birds over the first 3 months of life. We thus documented the development of the gut microbiota and characterised the relative impacts of the early social environment and host selection due to species-specific characteristics and individual genetic backgrounds across ontogeny by using 16S ribosomal RNA gene sequencing. RESULTS The taxonomic composition and community structure of the gut microbiota changed across ontogenetic stages; juvenile zebra finches exhibited higher alpha diversity than adults at the post-breeding stage. Furthermore, in early development, the microbial communities of juveniles raised by conspecific and heterospecific foster parents resembled those of their foster family, emphasising the importance of the social environment. In later stages, the social environment continued to influence the gut microbiota, but host selection increased in importance. CONCLUSIONS We provided a baseline description of the developmental succession of gut microbiota in zebra finches and Bengalese finches, which is a necessary first step for understanding the impact of the early gut microbiota on host fitness. Furthermore, for the first time in avian species, we showed that the relative strengths of the two forces that shape the establishment and maintenance of the gut microbiota (i.e. host selection and dispersal from the social environment) change during development, with host selection increasing in importance. This finding should be considered when experimentally manipulating the early-life gut microbiota. Our findings also provide new insights into the mechanisms of host selection. Video Abstract.
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Affiliation(s)
- Öncü Maraci
- Department of Behavioural Ecology, Bielefeld University, Bielefeld, Germany.
| | - Anna Antonatou-Papaioannou
- Evolutionary Biology, Bielefeld University, Bielefeld, Germany
- Institute of Biology-Zoology, Freie Universität Berlin, Berlin, Germany
| | - Sebastian Jünemann
- Institute for Bio- and Geosciences, Research Center Jülich, Jülich, Germany
- Faculty of Technology, Bielefeld University, Bielefeld, Germany
| | - Kathrin Engel
- Department of Behavioural Ecology, Bielefeld University, Bielefeld, Germany
| | - Omar Castillo-Gutiérrez
- Faculty of Technology, Bielefeld University, Bielefeld, Germany
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Tobias Busche
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Jörn Kalinowski
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Barbara A Caspers
- Department of Behavioural Ecology, Bielefeld University, Bielefeld, Germany
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Swanson MT, Henson MW, Handika H, Achmadi AS, Anita S, Rowe KC, Esselstyn JA. Mycoplasmataceae dominate microbial community differences between gut regions in mammals with a simple gut architecture. J Mammal 2022. [DOI: 10.1093/jmammal/gyac098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Faunivorous mammals with simple guts are thought to rely primarily on endogenously produced enzymes to digest food, in part because they lack fermentation chambers for facilitating mutualistic interactions with microbes. However, variation in microbial community composition along the length of the gastrointestinal tract has yet to be assessed in faunivorous species with simple guts. We tested for differences in bacterial taxon abundances and community compositions between the small intestines and colons of 26 individuals representing four species of shrew in the genus Crocidura. We sampled these hosts from a single locality on Sulawesi Island, Indonesia, to control for potential geographic and temporal variation. Bacterial community composition differed significantly between the two gut regions and members of the family Mycoplasmataceae contributed substantially to these differences. Three operational taxonomic units (OTUs) of an unclassified genus in this family were more abundant in the small intestine, whereas 1 OTU of genus Ureaplasma was more abundant in the colon. Species of Ureaplasma encode an enzyme that degrades urea, a metabolic byproduct of protein catabolism. Additionally, a Hafnia–Obesumbacterium OTU, a genus known to produce chitinase in bat gastrointestinal tracts, was also more abundant in the colon compared to the small intestine. The presence of putative chitinase- and urease-producing bacteria in shrew guts suggests mutualisms with microorganisms play a role in facilitating the protein-rich, faunivorous diets of simple gut mammals.
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Affiliation(s)
- Mark T Swanson
- Museum of Natural Science and Department of Biological Sciences, 119 Foster Hall, Louisiana State University , Baton Rouge, Louisiana 70803 , USA
| | - Michael W Henson
- Department of Geophysical Sciences, University of Chicago , Illinois 60616 , USA
| | - Heru Handika
- Museum of Natural Science and Department of Biological Sciences, 119 Foster Hall, Louisiana State University , Baton Rouge, Louisiana 70803 , USA
| | - Anang S Achmadi
- Museum Zoologicum Bogoriense, Research Center for Biosystematics and Evolution, Research Organization for Life Sciences and Environment, National Research and Innovation Agency (BRIN) , Cibinong 16912 , Indonesia
| | - Syahfitri Anita
- Museum Zoologicum Bogoriense, Research Center for Biosystematics and Evolution, Research Organization for Life Sciences and Environment, National Research and Innovation Agency (BRIN) , Cibinong 16912 , Indonesia
| | - Kevin C Rowe
- Sciences Department, Museums Victoria Research Institute , G.P.O. Box 666, Melbourne, Victoria 3001 , Australia
- School of Biosciences, University of Melbourne , Royal Parade, Parkville, Melbourne, Victoria 3052 , Australia
| | - Jacob A Esselstyn
- Museum of Natural Science and Department of Biological Sciences, 119 Foster Hall, Louisiana State University , Baton Rouge, Louisiana 70803 , USA
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West AG, Digby A, Lear G, Taylor MW, Bromley M, Buckley E, Chatterton J, Cox MP, Cramer RA, Crane J, Dearden PK, Eason D, Fisher MC, Gago S, Gartrell B, Gemmell NJ, Glare TR, Guhlin J, Howard J, Lacap-Bugler D, Le Lec M, Lin XX, Lofgren L, Mackay J, Meis J, Morelli KA, Perrott J, Petterson M, Quinones-Mateu M, Rhodes J, Roberts J, Stajich J, Taylor MW, Tebbutt SJ, Truter-Meyer A, Uddstrom L, Urban L, van Rhijn N, Vercoe D, Vesely E, Weir BS, West AG, Winter DJ, Yeung J, Taylor MW. Influence of management practice on the microbiota of a critically endangered species: a longitudinal study of kākāpō chick faeces and associated nest litter. Anim Microbiome 2022; 4:55. [PMID: 36175950 PMCID: PMC9523977 DOI: 10.1186/s42523-022-00204-w] [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: 03/28/2022] [Accepted: 08/29/2022] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND The critically endangered kākāpō is a flightless, nocturnal parrot endemic to Aotearoa New Zealand. Recent efforts to describe the gastrointestinal microbial community of this threatened herbivore revealed a low-diversity microbiota that is often dominated by Escherichia-Shigella bacteria. Given the importance of associated microbial communities to animal health, and increasing appreciation of their potential relevance to threatened species conservation, we sought to better understand the development of this unusual gut microbiota profile. To this end, we conducted a longitudinal analysis of faecal material collected from kākāpō chicks during the 2019 breeding season, in addition to associated nest litter material. RESULTS Using an experimental approach rarely seen in studies of threatened species microbiota, we evaluated the impact of a regular conservation practice on the developing kākāpō microbiota, namely the removal of faecal material from nests. Artificially removing chick faeces from nests had negligible impact on bacterial community diversity for either chicks or nests (p > 0.05). However, the gut microbiota did change significantly over time as chick age increased (p < 0.01), with an increasing relative abundance of Escherichia-Shigella coli over the study period and similar observations for the associated nest litter microbiota (p < 0.01). Supplementary feeding substantially altered gut bacterial diversity of kākāpō chicks (p < 0.01), characterised by a significant increase in Lactobacillus bacteria. CONCLUSIONS Overall, chick age and hand rearing conditions had the most marked impact on faecal bacterial communities. Similarly, the surrounding nest litter microbiota changed significantly over time since a kākāpō chick was first placed in the nest, though we found no evidence that removal of faecal material influenced the bacterial communities of either litter or faecal samples. Taken together, these observations will inform ongoing conservation and management of this most enigmatic of bird species.
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Affiliation(s)
- Annie G. West
- grid.9654.e0000 0004 0372 3343School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142 New Zealand
| | - Andrew Digby
- Department of Conservation, Kākāpō Recovery Team, PO Box 743, Invercargill, New Zealand
| | - Gavin Lear
- grid.9654.e0000 0004 0372 3343School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142 New Zealand
| | - Kākāpō Recovery Team
- Department of Conservation, Kākāpō Recovery Team, PO Box 743, Invercargill, New Zealand
| | | | - Michael W. Taylor
- grid.9654.e0000 0004 0372 3343School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142 New Zealand
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Sun F, Chen J, Liu K, Tang M, Yang Y. The avian gut microbiota: Diversity, influencing factors, and future directions. Front Microbiol 2022; 13:934272. [PMID: 35992664 PMCID: PMC9389168 DOI: 10.3389/fmicb.2022.934272] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 07/08/2022] [Indexed: 11/13/2022] Open
Abstract
The gut microbiota is viewed as the “second genome” of animals, sharing intricate relationships with their respective hosts. Because the gut microbial community and its diversity are affected by many intrinsic and extrinsic factors, studying intestinal microbes has become an important research topic. However, publications are dominated by studies on domestic or captive birds, while research on the composition and response mechanism of environmental changes in the gut microbiota of wild birds remains scarce. Therefore, it is important to understand the co-evolution of host and intestinal bacteria under natural conditions to elucidate the diversity, maintenance mechanisms, and functions of gut microbes in wild birds. Here, the existing knowledge of gut microbiota in captive and wild birds is summarized, along with previous studies on the composition and function, research methods employed, and factors influencing the avian gut microbial communities. Furthermore, research hotspots and directions were also discussed to identify the dynamics of the avian gut microbiota, aiming to contribute to studies of avian microbiology in the future.
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Zauner S, Vogel M, Polzin J, Yuen B, Mußmann M, El-Hacen EHM, Petersen JM. Microbial communities in developmental stages of lucinid bivalves. ISME COMMUNICATIONS 2022; 2:56. [PMID: 37938693 PMCID: PMC9723593 DOI: 10.1038/s43705-022-00133-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 04/12/2022] [Accepted: 05/27/2022] [Indexed: 11/09/2023]
Abstract
Bivalves from the family Lucinidae host sulfur-oxidizing bacterial symbionts, which are housed inside specialized gill epithelial cells and are assumed to be acquired from the environment. However, little is known about the Lucinidae life cycle and symbiont acquisition in the wild. Some lucinid species broadcast their gametes into the surrounding water column, however, a few have been found to externally brood their offspring by the forming gelatinous egg masses. So far, symbiont transmission has only been investigated in one species that reproduces via broadcast spawning. Here, we show that the lucinid Loripes orbiculatus from the West African coast forms egg masses and these are dominated by diverse members of the Alphaproteobacteria, Clostridia, and Gammaproteobacteria. The microbial communities of the egg masses were distinct from those in the environments surrounding lucinids, indicating that larvae may shape their associated microbiomes. The gill symbiont of the adults was undetectable in the developmental stages, supporting horizontal transmission of the symbiont with environmental symbiont acquisition after hatching from the egg masses. These results demonstrate that L. orbiculatus acquires symbionts from the environment independent of the host's reproductive strategy (brooding or broadcast spawning) and reveal previously unknown associations with microbes during lucinid early development.
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Affiliation(s)
- Sarah Zauner
- Division of Microbial Ecology, Department for Microbiology and Ecosystem Science, University of Vienna, Centre for Microbiology and Environmental Systems Science, Djerassiplatz 1, 1030, Vienna, Austria.
- University of Vienna, Doctoral School in Microbiology and Environmental Science, Djerassiplatz 1, 1030, Vienna, Austria.
| | - Margaret Vogel
- Division of Microbial Ecology, Department for Microbiology and Ecosystem Science, University of Vienna, Centre for Microbiology and Environmental Systems Science, Djerassiplatz 1, 1030, Vienna, Austria
| | - Julia Polzin
- Division of Microbial Ecology, Department for Microbiology and Ecosystem Science, University of Vienna, Centre for Microbiology and Environmental Systems Science, Djerassiplatz 1, 1030, Vienna, Austria
| | - Benedict Yuen
- Division of Microbial Ecology, Department for Microbiology and Ecosystem Science, University of Vienna, Centre for Microbiology and Environmental Systems Science, Djerassiplatz 1, 1030, Vienna, Austria
| | - Marc Mußmann
- Division of Microbial Ecology, Department for Microbiology and Ecosystem Science, University of Vienna, Centre for Microbiology and Environmental Systems Science, Djerassiplatz 1, 1030, Vienna, Austria
| | - El-Hacen M El-Hacen
- Conservation Ecology Group, Groningen Institute for Evolutionary Life Sciences, University of Groningen, P.O. Box 11103, 9700CC, Groningen, The Netherlands
- Parc National du Banc d'Arguin (PNBA) Chami, B.P. 5355, Wilaya de Dakhlet Nouadhibou, Mauritania
| | - Jillian M Petersen
- Division of Microbial Ecology, Department for Microbiology and Ecosystem Science, University of Vienna, Centre for Microbiology and Environmental Systems Science, Djerassiplatz 1, 1030, Vienna, Austria.
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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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Carranco AS, Romo D, de Lourdes Torres M, Wilhelm K, Sommer S, Gillingham MAF. Egg microbiota is the starting point of hatchling gut microbiota in the endangered yellow-spotted Amazon river turtle. Mol Ecol 2022; 31:3917-3933. [PMID: 35621392 DOI: 10.1111/mec.16548] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 04/30/2022] [Accepted: 05/17/2022] [Indexed: 11/29/2022]
Abstract
Establishment and development of gut microbiota during vertebrates' early life are likely to be important predictors of health and fitness. Host-parental and host-environment interactions are essential to these processes. In oviparous reptiles whose nests represent a source of the parent's microbial inocula, the relative role of host-selection and stochastic environmental factors during gut microbial assemblage remains unknown. We sampled eggs incubated in artificial nests as well as hatchlings and juveniles (up to 30 days old) of the yellow-spotted Amazon river turtle (Podocnemis unifilis) developing in tubs filled with river water. We examined the relative role of the internal egg microbiota and the abiotic environment on hatchling and juvenile turtle's cloacal microbiota assemblages during the first 30 days of development. A mean of 71% of ASVs in hatched eggs could be traced to the nest environmental microbiota and in turn a mean of 77% of hatchlings' cloacal ASVs were traced to hatched eggs. Between day 5 and 20 of juvenile turtle's development, the river water environment plays a key role in the establishment of the gut microbiota (accounting for a mean of 13%-34.6% of cloacal ASVs) and strongly influences shifts in microbial diversity and abundance. After day 20, shifts in gut microbiota composition were mainly driven by host-selection processes. Therefore, colonization by environmental microbiota is key in the initial stages of establishing the host's gut microbiota which is subsequently shaped by host-selection processes. Our study provides a novel quantitative understanding of the host-environment interactions during gut microbial assemblage of oviparous reptiles.
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Affiliation(s)
- Ana Sofia Carranco
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany
| | - David Romo
- Tiputini Biodiversity Station, Universidad San Francisco de Quito, Cumbaya-, Quito, Ecuador
| | - Maria de Lourdes Torres
- Laboratorio de Biotecnología Vegetal, Universidad San Francisco de Quito, Cumbaya-, Quito, Ecuador
| | - Kerstin Wilhelm
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany
| | - Simone Sommer
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany
| | - Mark A F Gillingham
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany.,Biodiversity Research Institute (CSIC, Oviedo University, Principality of Asturias), Campus of Mieres, University of Oviedo, 33600, Mieres, Spain
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22
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Kuznetsova EV, Kosolapov DB, Krylov AV. Changes in Size-Morphological Structure of Bacterioplankton in Freshwater Environments of Svalbard. CONTEMP PROBL ECOL+ 2022. [DOI: 10.1134/s199542552202007x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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23
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Obrochta S, Savo Sardaro ML, Amato KR, Murray MH. Relationships Between Migration and Microbiome Composition and Diversity in Urban Canada Geese. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.742369] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Microbiome analysis presents an opportunity to understand how urban environments affect avian physiology. For example, habitat use can affect microbiome diversity and composition, and hosts with more diverse gut microbiota are thought to be more resistant to pathogens and have increased fitness. However, the microbiome is an understudied aspect of avian ecology, particularly in the context of migration and urbanization in wild birds. For this study, we hypothesized that, within urban birds, migrants would exhibit greater microbial diversity and inter-individual variation in microbiome composition than residents because they are exposed to more diverse habitats. We focused on Canada geese (Branta canadensis), one of many migratory species that exhibit increasingly more year-round residency in cities. We used 16S rRNA gene amplicon sequencing to quantify microbiome taxonomic composition in fecal samples from 32 GPS-tracked Canada geese, 22 of which were year-round residents of the Chicago area and 10 of which were migrants. Similar to recent studies on wild species feeding near human habitation, urban resident geese had higher gut microbial diversity than migrants. They also had increased inter-individual variation in microbiome composition and, on average, lower relative abundances of bacteria in the phylum Firmicutes, and the genera Terrisporobacter, Turicibacter, and Cellulosilyticum, which all have metabolic functions that may aid in goose digestion. Therefore, the gut microbiome of resident geese may provide fewer potential health benefits. These patterns may be a result of anthropogenic influences on aspects of resident goose ecology, such as diet, as well the influence of migration on migrant goose ecology and biology. Overall, our results suggest that reduced migration for urban-adapted wildlife species may have important consequences for physiology and health.
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Costantini MS, Medeiros MC, Crampton LH, Reed FA. Wild gut microbiomes reveal individuals, species, and location as drivers of variation in two critically endangered Hawaiian honeycreepers. PeerJ 2021; 9:e12291. [PMID: 34760361 PMCID: PMC8557688 DOI: 10.7717/peerj.12291] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 09/21/2021] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND The gut microbiome of animals is an important component that has strong influence on the health, fitness, and behavior of its host. Most research in the microbiome field has focused on human populations and commercially important species. However, researchers are now considering the link between endangered species conservation and the microbiome. In Hawai'i, several threats (e.g., avian malaria and habitat loss) have caused widespread population declines of Hawaiian honeycreepers (subfamily: Carduelinae). These threats can have a significant effect on the avian gut microbiome and may even lead to disruption of microbial function. However, the gut microbiome of honeycreeper in the wild has yet to be explored. METHODS We collected 13 and 42 fecal samples, respectively, from two critically endangered honeycreeper species, the 'akikiki (Oreomystis bairdi) and the 'akeke'e (Loxops caeruleirostris). The 16S rRNA gene was sequenced and processed though a MOTHUR-based bioinformatics pipeline. Bacterial ASVs were identified using the DADA2 program and bacterial community analyses, including alpha and beta diversity measures, were conducted using R packages Phyloseq and vegan. RESULTS A total of 8,958 bacterial ASVs were identified from the fecal samples. Intraspecific differences in the gut microbiome among individual birds explained most of the variation present in the dataset, however differences between species did exist. Both species had distinct microbiomes with minimal overlap in beta diversity. 'Akikiki had a more diverse microbiome compared to 'akeke'e. Additionally, small but stastically significant differences in beta diversity also exist between sampling location and sexes in 'akikiki. CONCLUSION 'Akikiki and 'akeke'e are currently the focus of captive breeding efforts and plans to translocate the two species to other islands are underway. This baseline knowledge will help inform management decisions for these honeycreeper species in their native habitats, on other islands, and in captivity.
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Affiliation(s)
- Maria S. Costantini
- School of Life Sciences, University of Hawaiʻi at Mānoa, Honolulu, Hawaiʻi, United States
| | - Matthew C.I. Medeiros
- School of Life Sciences, University of Hawaiʻi at Mānoa, Honolulu, Hawaiʻi, United States
- Pacific Biosciences Research Center, University of Hawaiʻi at Mānoa, Honolulu, Hawaií, United States
| | - Lisa H. Crampton
- Hawaiʻi Division of Forestry and Wildlife, Hanapepe, Hawaiʻi, United States
- Pacific Cooperative Studies Unit, University of Hawaiʻi, Honolulu, Hawaiʻi, United States
| | - Floyd A. Reed
- School of Life Sciences, University of Hawaiʻi at Mānoa, Honolulu, Hawaiʻi, United States
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Skeen HR, Cooper NW, Hackett SJ, Bates JM, Marra PP. Repeated sampling of individuals reveals impact of tropical and temperate habitats on microbiota of a migratory bird. Mol Ecol 2021; 30:5900-5916. [PMID: 34580952 DOI: 10.1111/mec.16170] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 08/26/2021] [Accepted: 09/02/2021] [Indexed: 01/04/2023]
Abstract
Migratory animals experiencing substantial change in diet and habitat across the annual cycle may have corresponding shifts in host-associated microbial diversity. Using automated telemetry and radio tags to recapture birds, we examined gut microbiota structure in the same population and often same individual of Kirtland's Warblers (Setophaga kirtlandii) initially sampled on their wintering grounds in The Bahamas and subsequently resampled within their breeding territories in Michigan, USA. Initial sampling occurred in March and April and resampling occurred in May, June and early July. The composition of the most abundant phyla and classes of the warblers' microbiota is similar to that of other migratory birds. However, we detected notable variation in abundance and diversity of numerous bacterial taxa, including a decrease in microbial richness and significant differences in microbial communities when comparing the microbiota of birds first captured in The Bahamas to that of birds recaptured in Michigan. This is observed at the individual and population level. Furthermore, we found that 22 bacterial genera exhibit heightened abundance within specific sampling periods and are probably associated with diet and environmental change. Finally, we described a small, species-specific shared microbial profile that spans multiple time periods and environments within the migratory cycle. Our research highlights that the avian gut microbiota is dynamic over time, most significantly impacted by changing environments associated with migration. These results support the need for full annual cycle monitoring of migratory bird microbiota to improve understanding of seasonal host movement ecologies and response to recurrent physiological stressors.
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Affiliation(s)
- Heather R Skeen
- Committee on Evolutionary Biology, University of Chicago, Chicago, Illinois, USA.,Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, Illinois, USA
| | - Nathan W Cooper
- Migratory Bird Center, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, District of Columbia, USA.,Department of Biology and McCourt School of Public Policy, Georgetown University, Washington, District of Columbia, USA
| | - Shannon J Hackett
- Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, Illinois, USA
| | - John M Bates
- Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, Illinois, USA
| | - Peter P Marra
- Department of Biology and McCourt School of Public Policy, Georgetown University, Washington, District of Columbia, USA
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Zhu Y, Li Y, Yang H, He K, Tang K. Establishment of Gut Microbiome During Early Life and Its Relationship With Growth in Endangered Crested Ibis ( Nipponia nippon). Front Microbiol 2021; 12:723682. [PMID: 34434183 PMCID: PMC8382091 DOI: 10.3389/fmicb.2021.723682] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 07/20/2021] [Indexed: 12/13/2022] Open
Abstract
Gut microbiota during early life could influence host fitness in vertebrates. Studies on how gut microbiota colonize the gut in birds using frequent sampling during early developmental stages and how shifts in microbiota diversity influence host growth are lacking. Here, we examine the microbiome profiles of 151 fecal samples from 14 young crested ibis (Nipponia nippon), an endangered bird species, collected longitudinally across 13 time points during the early stages of development and investigated their correlation with host growth. Gut diversity showed a non-linear change during development, which involved multiple colonization and extinction events, mainly associated with Proteobacteria and Firmicutes. Gut microbiota in young crested ibis became more similar with increasing age. In addition, gut microbiota exhibited a strong temporal structure and two specific developmental stages; the beginning of the latter stage coincided with the introduction of fresh loach, with a considerable increase in the relative abundance of Fusobacteria and several Firmicutes, which may be involved in lipid metabolism. Crested ibis chick growth rate was negatively correlated with gut microbiota diversity and negatively associated with the abundance of Halomonadaceae, Streptococci, Corynebacteriaceae, and Dietziaceae. Our findings highlight the importance of frequent sampling when studying microbiome development during early stages of development of vertebrates. The role of microbial diversity in host growth during the early stages of development of birds warrants further investigations.
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Affiliation(s)
- Ying Zhu
- Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, China
| | - Yudong Li
- Sichuan Province Laboratory for Natural Resources Protection and Sustainable Utilization, Sichuan Provincial Academy of Natural Resource Sciences, Chengdu, China
| | - Haiqiong Yang
- Emei Breeding Center for Crested Ibis, Emei, Chengdu, China
| | - Ke He
- College of Animal Sciences and Technology, Zhejiang A&F University, Hangzhou, China
| | - Keyi Tang
- College of Life Sciences, Sichuan Normal University, Chengdu, China
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27
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Li C, Liu Y, Gong M, Zheng C, Zhang C, Li H, Wen W, Wang Y, Liu G. Diet-induced microbiome shifts of sympatric overwintering birds. Appl Microbiol Biotechnol 2021; 105:5993-6005. [PMID: 34272578 DOI: 10.1007/s00253-021-11448-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 06/21/2021] [Accepted: 06/27/2021] [Indexed: 11/29/2022]
Abstract
Gut microbiota have a significant impact on host physiology and health, and host genetics and diet are considered as two important factors, but it is difficult to discriminate the influence of each single factor (host or diet) on gut microbiota under natural conditions. Moreover, current studies of avian microbiota mainly focus on domestic or captive birds, and it is still uncertain how host and diet take part in changing avian gut microbiota composition, diversity, and function in the wild. Here, high-throughput sequencing of 16S rRNA was used to identify the gut microbiota communities for sympatric wintering Great Bustards and Common Cranes at different diets. The results showed that 8.87% operational taxonomic units (OTUs) were shared among all sampling birds; in contrast, 39.43% of Kyoto Encyclopedia of Genes and Genomes (KEGG) functional pathways were common among all individuals, indicating the existence of gut microbiota conservatism both in microbiota structure and function. Microbiota abundance and diversity differed between Great Bustards and Common Cranes in a specific wintering site, and microbiota variation was detected for the same host species under two different sites, suggesting that the change of gut microbiota was induced by both host and diet. Furthermore, we found that changes of both microbial communities and functional pathways were larger between hosts than those between diets, which revealed that host might be the dominant factor determining microbiota characteristics and function, while diet further drove the divergence of gut microbiota. Gut microbiota functions appeared to be more conserved than bacterial community structure, indicating that different bacteria may function in a similar way, while microbiota OTU diversity might not be necessarily associated with functional diversity. With diet shifting, gut microbiota changed both in terms of microbial communities and functional pathways for the sympatric birds, which implies that avian habitats and their physiological microbiota would be influenced by different farmland management regimes. KEY POINTS: • Gut microbiota can be shaped by both diets and hosts in sympatric species. • Host was the dominant factor shaping the gut microbiota communities and functional pathways. • Gut microbiota were conservative both in structure and in function, but more conservative in function.
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Affiliation(s)
- Chao Li
- Beijing Key Laboratory of Wetland Services and Restoration, Institute of Wetland Research, Chinese Academy of Forestry, Beijing, 100091, China
| | - Yan Liu
- Beijing Key Laboratory of Captive Wildlife Technologies, Beijing Zoo, Beijing, 100044, China
| | - Minghao Gong
- Beijing Key Laboratory of Wetland Services and Restoration, Institute of Wetland Research, Chinese Academy of Forestry, Beijing, 100091, China
| | - Changming Zheng
- Beijing Key Laboratory of Captive Wildlife Technologies, Beijing Zoo, Beijing, 100044, China
| | - Chenglin Zhang
- Beijing Key Laboratory of Captive Wildlife Technologies, Beijing Zoo, Beijing, 100044, China
| | - Huixin Li
- Beijing Key Laboratory of Wetland Services and Restoration, Institute of Wetland Research, Chinese Academy of Forestry, Beijing, 100091, China
| | - Wanyu Wen
- Beijing Key Laboratory of Wetland Services and Restoration, Institute of Wetland Research, Chinese Academy of Forestry, Beijing, 100091, China
| | - Yuhang Wang
- Beijing Key Laboratory of Wetland Services and Restoration, Institute of Wetland Research, Chinese Academy of Forestry, Beijing, 100091, China
| | - Gang Liu
- Beijing Key Laboratory of Wetland Services and Restoration, Institute of Wetland Research, Chinese Academy of Forestry, Beijing, 100091, China.
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Ran J, Wan QH, Fang SG. Gut microbiota of endangered crested ibis: Establishment, diversity, and association with reproductive output. PLoS One 2021; 16:e0250075. [PMID: 33891612 PMCID: PMC8064547 DOI: 10.1371/journal.pone.0250075] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 03/30/2021] [Indexed: 12/26/2022] Open
Abstract
Gut microbiota is known to influence the host’s health; an imbalance of the gut microbial community leads to various intestinal and non-intestinal diseases. Research on gut microbes of endangered birds is vital for their conservation. However, a thorough understanding of the gut microbiome composition present in crested ibises at different ages and its correlation with crested ibis reproductive capacity has remained elusive. Here, we used 16S rRNA gene sequencing to explore the fecal microbial structure of nestlings and adult birds, and the difference in gut microbiota between healthy and sterile crested ibises. We observed that (1) bacterial microbiota, alpha and beta diversity of one-day-old nestlings significantly distinguished from other nestlings; abundance of Proteobacteria decreased, while that of Fusobacteria increased with an increase in the age of the nestlings; (2) there was no significant difference in community composition among adult crested ibises aged one, two, three, and five years; (3) the abundance of Proteobacteria and alpha diversity indices were higher in sterile crested ibises than in healthy crested ibises; thus, Proteobacteria can act as a diagnostic biomarker of reproductive dysfunction in crested ibises. This study significantly contributes to the field of ecology and conservation, as it provides a platform for assessing the reproductive capacity of endangered crested ibises, based on the gut microbiota composition. Further studies may unravel additional factors influencing crested ibises’ reproductive health, which will further help the management and control of the crested ibis population.
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Affiliation(s)
- Jian Ran
- MOE Key Laboratory of Biosystems Homeostasis & Protection, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, P. R. China
| | - Qiu-Hong Wan
- MOE Key Laboratory of Biosystems Homeostasis & Protection, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, P. R. China
| | - Sheng-Guo Fang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, P. R. China
- * E-mail:
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29
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Zhou L, Huo X, Liu B, Wu H, Feng J. Comparative Analysis of the Gut Microbial Communities of the Eurasian Kestrel ( Falco tinnunculus) at Different Developmental Stages. Front Microbiol 2020; 11:592539. [PMID: 33391209 PMCID: PMC7775371 DOI: 10.3389/fmicb.2020.592539] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 11/18/2020] [Indexed: 12/21/2022] Open
Abstract
The gut microflora play a very important role in the life of animals. Although an increasing number of studies have investigated the gut microbiota of birds in recent years, there is a lack of research work on the gut microbiota of wild birds, especially carnivorous raptors, which are thought to be pathogen vectors. There are also a lack of studies focused on the dynamics of the gut microbiota during development in raptors. In this study, 16S rRNA gene amplicon high-throughput sequencing was used to analyze the gut microbiota community composition of a medium-sized raptor, the Eurasian Kestrel (Falco tinnunculus), and to reveal stage-specific signatures in the gut microbiota of nestlings during the pre-fledging period. Moreover, differences in the gut microbiota between adults and nestlings in the same habitat were explored. The results indicated that the Eurasian Kestrel hosts a diverse assemblage of gut microbiota. Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes were the primary phyla shared within the guts of adults and chicks. However, adults harbored higher abundances of Proteobacteria while nestlings exhibited higher abundances of Firmicutes and Actinobacteria, and consequently the majority of dominant genera observed in chicks differed from those in adults. Although no significant differences in diversity were observed across the age groups during nestling ontogeny, chicks from all growth stages harbored richer and more diverse bacterial communities than adults. In contrast, the differences in gut microbial communities between adults and younger nestlings were more pronounced. The gut microbes of the nestlings in the last growth stage were converged with those of the adults. This study provides basic reference data for investigations of the gut microbiota community structure of wild birds and deepens our understanding of the dynamics of the gut microflora during raptor development.
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Affiliation(s)
- Lei Zhou
- College of Animal Science and Technology, College of Veterinary Medicine, Jilin Agricultural University, Changchun, China
| | - Xiaona Huo
- School of Life Sciences, Jilin Agricultural University, Changchun, China
| | - Boyu Liu
- College of Animal Science and Technology, College of Veterinary Medicine, Jilin Agricultural University, Changchun, China
| | - Hui Wu
- School of Life Sciences, Jilin Agricultural University, Changchun, China
| | - Jiang Feng
- School of Life Sciences, Jilin Agricultural University, Changchun, China
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30
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Chen CY, Chen CK, Chen YY, Fang A, Shaw GTW, Hung CM, Wang D. Maternal gut microbes shape the early-life assembly of gut microbiota in passerine chicks via nests. MICROBIOME 2020; 8:129. [PMID: 32917256 PMCID: PMC7488855 DOI: 10.1186/s40168-020-00896-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 07/21/2020] [Indexed: 05/28/2023]
Abstract
BACKGROUND Knowledge is growing on how gut microbiota are established, but the effects of maternal symbiotic microbes throughout early microbial successions in birds remain elusive. In this study, we examined the contributions and transmission modes of maternal microbes into the neonatal microbiota of a passerine, the zebra finch (Taeniopygia guttata), based on fostering experiments. RESULTS Using 16S rRNA amplicon sequencing, we found that zebra finch chicks raised by their biological or foster parents (the society finch Lonchura striata domestica) had gut microbial communities converging with those of the parents that reared them. Moreover, source-tracking models revealed high contribution of zebra finches' oral cavity/crop microbiota to their chicks' early gut microbiota, which were largely replaced by the parental gut microbiota at later stages. The results suggest that oral feeding only affects the early stage of hatchling gut microbial development. CONCLUSIONS Our study indicates that passerine chicks mainly acquire symbionts through indirect maternal transmission-passive environmental uptake from nests that were smeared with the intestinal and cloacal microbes of parents that raised them. Gut microbial diversity was low in hand-reared chicks, emphasizing the importance of parental care in shaping the gut microbiota. In addition, several probiotics were found in chicks fostered by society finches, which are excellent foster parents for other finches in bird farms and hosts of brood parasitism by zebra finches in aviaries; this finding implies that avian species that can transfer probiotics to chicks may become selectively preferred hosts of brood parasitism in nature. Video Abstract.
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Affiliation(s)
- Cheng-Yu Chen
- Biodiversity Research Center, Academia Sinica, Taipei, 115201 Taiwan
| | - Chih-Kuan Chen
- Biodiversity Research Center, Academia Sinica, Taipei, 115201 Taiwan
- Department of Pathology, University of Southern California, Los Angeles, CA 90033 USA
- The IEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung, 402204 Taiwan
| | - Yi-Ying Chen
- Biodiversity Research Center, Academia Sinica, Taipei, 115201 Taiwan
| | - Andrew Fang
- Department of Molecular Biology and Human Genetics, Tzu Chi University, Hualien, 970301 Taiwan
| | | | - Chih-Ming Hung
- Biodiversity Research Center, Academia Sinica, Taipei, 115201 Taiwan
| | - Daryi Wang
- Biodiversity Research Center, Academia Sinica, Taipei, 115201 Taiwan
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Schmiedová L, Kreisinger J, Požgayová M, Honza M, Martin JF, Procházka P. Gut microbiota in a host-brood parasite system: insights from common cuckoos raised by two warbler species. FEMS Microbiol Ecol 2020; 96:5872480. [PMID: 32672792 DOI: 10.1093/femsec/fiaa143] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 07/15/2020] [Indexed: 11/13/2022] Open
Abstract
An animal's gut microbiota (GM) is shaped by a range of environmental factors affecting the bacterial sources invading the host. At the same time, animal hosts are equipped with intrinsic mechanisms enabling regulation of GM. However, there is limited knowledge on the relative importance of these forces. To assess the significance of host-intrinsic vs environmental factors, we studied GM in nestlings of an obligate brood parasite, the common cuckoo (Cuculus canorus), raised by two foster species, great reed warblers (Acrocephalus arundinaceus) and Eurasian reed warblers (A. scirpaceus), and compared these with GM of the fosterers' own nestlings. We show that fecal GM varied between cuckoo and warbler nestlings when accounting for the effect of foster/parent species, highlighting the importance of host-intrinsic regulatory mechanisms. In addition to feces, cuckoos also expel a deterrent secretion, which provides protection against olfactory predators. We observed an increased abundance of bacterial genera capable of producing repulsive volatile molecules in the deterrent secretion. Consequently, our results support the hypothesis that microbiota play a role in this antipredator mechanism. Interestingly, fosterer/parent identity affected only cuckoo deterrent secretion and warbler feces microbiota, but not that of cuckoo feces, suggesting a strong selection of bacterial strains in the GM by cuckoo nestlings.
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Affiliation(s)
- Lucie Schmiedová
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, CZ-12800 Prague, Czech Republic
| | - Jakub Kreisinger
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, CZ-12800 Prague, Czech Republic
| | - Milica Požgayová
- Institute of Vertebrate Biology, Czech Academy of Sciences, Květná 8, CZ-60365 Brno, Czech Republic
| | - Marcel Honza
- Institute of Vertebrate Biology, Czech Academy of Sciences, Květná 8, CZ-60365 Brno, Czech Republic
| | | | - Petr Procházka
- Institute of Vertebrate Biology, Czech Academy of Sciences, Květná 8, CZ-60365 Brno, Czech Republic
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Campos-Cerda F, Bohannan BJM. The Nidobiome: A Framework for Understanding Microbiome Assembly in Neonates. Trends Ecol Evol 2020; 35:573-582. [PMID: 32360079 DOI: 10.1016/j.tree.2020.03.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 03/08/2020] [Accepted: 03/16/2020] [Indexed: 02/07/2023]
Abstract
The importance of microbial associations to animals' development, physiology, and fitness is widely recognized. In most animals, these microbial associations must be developed anew with every generation, making microbiome assembly a critical ecological and evolutionary process. To fully understand neonate microbial colonization, we need to study the interacting effects of neonate, parents, nest, and external environment. We propose an integrative approach based on the concept of the 'nidobiome', a new unit of microbiome-host interactions, which brings together these key elements. We discuss the contribution of each element on microbial colonization at different stages of host development, and we provide a framework based on key developmental events to compare microbiome assembly across animal species.
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Affiliation(s)
- Felipe Campos-Cerda
- Institute of Ecology and Evolution, Biology Department, University of Oregon, Eugene, OR 97405, USA.
| | - Brendan J M Bohannan
- Institute of Ecology and Evolution, Biology Department, University of Oregon, Eugene, OR 97405, USA
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Zou S, Gong L, Khan TA, Pan L, Yan L, Li D, Cao L, Li Y, Ding X, Yi G, Sun Y, Hu S, Xia L. Comparative analysis and gut bacterial community assemblages of grass carp and crucian carp in new lineages from the Dongting Lake area. Microbiologyopen 2020; 9:e996. [PMID: 32175674 PMCID: PMC7221430 DOI: 10.1002/mbo3.996] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 12/31/2019] [Accepted: 12/31/2019] [Indexed: 12/17/2022] Open
Abstract
Gut microbiota are known to play an important role in health and nutrition of the host and have been attracting an increasing attention. Farming of new lineages of grass carp and crucian carp has been developed rapidly as these species were found to outperform indigenous ones in terms of growth rate and susceptibility to diseases. Despite this rapid development, no studies have addressed the characteristics of their gut microbiota as a potential factor responsible for the improved characteristics. To reveal whether microbiomes of the new lineages are different from indigenous ones, and therefore could be responsible for improved growth features, intestinal microbiota from the new lineages were subjected to high-throughput sequencing. While the phyla Firmicutes, Fusobacteria and Proteobacteria were representing the core bacterial communities that comprised more than 75% in all fish intestinal samples, significant differences were found in the microbial community composition of the new linages versus indigenous fish populations, suggesting the possibility that results in the advantages of enhanced disease resistance and rapid growth for the new fish lineages. Bacterial composition was similar between herbivorous and omnivorous fish. The relative abundance of Bacteroidetes and Actinobacteria was significantly higher in omnivores compared to that of herbivores, whereas Cetobacterium_sp. was abundant in herbivores. We also found that the gut microbiota of freshwater fish in the Dongting lake area was distinct from those of other areas. Network graphs showed the reduced overall connectivity of gut bacteria in indigenous fish, whereas the bacteria of the new fish lineage groups showed hubs with more node degree. A phylogenetic investigation of communities by reconstruction of unobserved states inferred function profile showed several metabolic processes were more active in the new lineages compared to indigenous fish. Our findings suggest that differences in gut bacterial community composition may be an important factor contributing to the rapid growth and high disease resistance of the new fish lineages.
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Affiliation(s)
- Sheng Zou
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular BiologyCollege of Life ScienceHunan Normal UniversityChangshaChina
| | - Liang Gong
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular BiologyCollege of Life ScienceHunan Normal UniversityChangshaChina
| | - Tahir Ali Khan
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular BiologyCollege of Life ScienceHunan Normal UniversityChangshaChina
| | - Lifei Pan
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular BiologyCollege of Life ScienceHunan Normal UniversityChangshaChina
| | - Liang Yan
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular BiologyCollege of Life ScienceHunan Normal UniversityChangshaChina
| | - Dongjie Li
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular BiologyCollege of Life ScienceHunan Normal UniversityChangshaChina
| | - Lina Cao
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular BiologyCollege of Life ScienceHunan Normal UniversityChangshaChina
| | - Yanping Li
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular BiologyCollege of Life ScienceHunan Normal UniversityChangshaChina
| | - Xuezhi Ding
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular BiologyCollege of Life ScienceHunan Normal UniversityChangshaChina
| | - Ganfeng Yi
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular BiologyCollege of Life ScienceHunan Normal UniversityChangshaChina
| | - Yunjun Sun
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular BiologyCollege of Life ScienceHunan Normal UniversityChangshaChina
| | - Shengbiao Hu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular BiologyCollege of Life ScienceHunan Normal UniversityChangshaChina
| | - Liqiu Xia
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular BiologyCollege of Life ScienceHunan Normal UniversityChangshaChina
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Dai D, Wu SG, Zhang HJ, Qi GH, Wang J. Dynamic alterations in early intestinal development, microbiota and metabolome induced by in ovo feeding of L-arginine in a layer chick model. J Anim Sci Biotechnol 2020; 11:19. [PMID: 32175081 PMCID: PMC7063725 DOI: 10.1186/s40104-020-0427-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 01/13/2020] [Indexed: 12/11/2022] Open
Abstract
Background Prenatal nutrition is crucial for embryonic development and neonatal growth, and has the potential to be a main determinant of life-long health. In the present study, we used a layer chick model to investigate the effects of in ovo feeding (IOF) of L-arginine (Arg) on growth, intestinal development, intestinal microbiota and metabolism. The treatments included the non-injected control, saline-injected control, and saline containing 2, 6, or 10 mg Arg groups. Results IOF Arg increased early intestinal index and villus height, and enhanced uptake of residual yolk lipid, contributing to subsequent improvement in the early growth performance of chicks. Prenatal Arg supplementation also increased the early microbial α-diversity, the relative abundance of Lactobacillales and Clostridiales, and decreased the relative abundance of Proteobacteria of cecum in chicks. Furthermore, the shift of cecal microbiota composition and the colonization of potential probiotics were accelerated by IOF of Arg. Simultaneously, metabolomics showed that metabolisms of galactose, taurine-conjugated bile acids and lipids were modulated to direct more energy and nutrients towards rapid growth of intestine at the beginning of post-hatch when embryos received IOF of Arg. Conclusions Prenatal Arg supplementation showed beneficial effects on the early intestinal development, cecal microbiota and host metabolism of layer chicks, contributing to subsequent improvement in the early growth performance. These findings provide new insight into the role of IOF of Arg in the establishment of the gut microbiota of newly-hatched layer chicks, and can expand our fundamental knowledge about prenatal nutrition, early bacterial colonization and intestinal development in neonate.
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Affiliation(s)
- Dong Dai
- Laboratory of Quality & Safety Risk Assessment for Animal Products on Feed Hazards (Beijing) of the Ministry of Agriculture & Rural Affairs, and National Engineering Research Center of Biological Feed, Feed Research Institute, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South St., Haidian District, Beijing, 100081 China
| | - Shu-Geng Wu
- Laboratory of Quality & Safety Risk Assessment for Animal Products on Feed Hazards (Beijing) of the Ministry of Agriculture & Rural Affairs, and National Engineering Research Center of Biological Feed, Feed Research Institute, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South St., Haidian District, Beijing, 100081 China
| | - Hai-Jun Zhang
- Laboratory of Quality & Safety Risk Assessment for Animal Products on Feed Hazards (Beijing) of the Ministry of Agriculture & Rural Affairs, and National Engineering Research Center of Biological Feed, Feed Research Institute, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South St., Haidian District, Beijing, 100081 China
| | - Guang-Hai Qi
- Laboratory of Quality & Safety Risk Assessment for Animal Products on Feed Hazards (Beijing) of the Ministry of Agriculture & Rural Affairs, and National Engineering Research Center of Biological Feed, Feed Research Institute, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South St., Haidian District, Beijing, 100081 China
| | - Jing Wang
- Laboratory of Quality & Safety Risk Assessment for Animal Products on Feed Hazards (Beijing) of the Ministry of Agriculture & Rural Affairs, and National Engineering Research Center of Biological Feed, Feed Research Institute, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South St., Haidian District, Beijing, 100081 China
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Capunitan DC, Johnson O, Terrill RS, Hird SM. Evolutionary signal in the gut microbiomes of 74 bird species from Equatorial Guinea. Mol Ecol 2020; 29:829-847. [PMID: 31943484 DOI: 10.1111/mec.15354] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 01/06/2020] [Accepted: 01/08/2020] [Indexed: 12/26/2022]
Abstract
How the microbiome interacts with hosts across evolutionary time is poorly understood. Data sets including many host species are required to conduct comparative analyses. Here, we analyzed 142 intestinal microbiome samples from 92 birds belonging to 74 species from Equatorial Guinea, using the 16S rRNA gene. Using four definitions for microbial taxonomic units (97%OTU, 99%OTU, 99%OTU with singletons removed, ASV), we conducted alpha and beta diversity analyses. We found that raw abundances and diversity varied between the data sets but relative patterns were largely consistent across data sets. Host taxonomy, diet and locality were significantly associated with microbiomes, at generally similar levels using three distance metrics. Phylogenetic comparative methods assessed the evolutionary relationship between the microbiome as a trait of a host species and the underlying bird phylogeny. Using multiple ways of defining "microbiome traits", we found that a neutral Brownian motion model did not explain variation in microbiomes. Instead, we found a White Noise model (indicating little phylogenetic signal), was most likely. There was some support for the Ornstein-Uhlenbeck model (that invokes selection), but the level of support was similar to that of a White Noise simulation, further supporting the White Noise model as the best explanation for the evolution of the microbiome as a trait of avian hosts. Our study demonstrated that both environment and evolution play a role in the gut microbiome and the relationship does not follow a neutral model; these biological results are qualitatively robust to analytical choices.
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Affiliation(s)
- Darien C Capunitan
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Oscar Johnson
- Museum of Natural Science, Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Ryan S Terrill
- Museum of Natural Science, Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA.,Moore Laboratory of Zoology, Occidental College, Los Angeles, CA, USA
| | - Sarah M Hird
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA.,Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
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Prenatal Transfer of Gut Bacteria in Rock Pigeon. Microorganisms 2019; 8:microorganisms8010061. [PMID: 31905837 PMCID: PMC7022786 DOI: 10.3390/microorganisms8010061] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 12/27/2019] [Indexed: 02/07/2023] Open
Abstract
Vertebrates evolved in concert with bacteria and have developed essential mutualistic relationships. Gut bacteria are vital for the postnatal development of most organs and the immune and metabolic systems and may likewise play a role during prenatal development. Prenatal transfer of gut bacteria is shown in four mammalian species, including humans. For the 92% of the vertebrates that are oviparous, prenatal transfer is debated, but it has been demonstrated in domestic chicken. We hypothesize that also non-domestic birds can prenatally transmit gut bacteria. We investigated this in medium-sized Rock pigeon (Columba livia), ensuring neonates producing fair-sized first faeces. The first faeces of 21 neonate rock pigeons hatched in an incubator, contained a microbiome (bacterial community) the composition of which resembled the cloacal microbiome of females sampled from the same population (N = 5) as indicated by multiple shared phyla, orders, families, and genera. Neonates and females shared 16.1% of the total number of OTUs present (2881), and neonates shared 45.5% of their core microbiome with females. In contrast, the five females shared only 0.3% of the 1030 female OTUs present. These findings suggest that prenatal gut bacterial transfer may occur in birds. Our results support the hypothesis that gut bacteria may be important for prenatal development and present a heritability pathway of gut bacteria in vertebrates.
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37
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KOBAYASHI A, TSUCHIDA S, UEDA A, YAMADA T, MURATA K, NAKAMURA H, USHIDA K. Role of coprophagy in the cecal microbiome development of an herbivorous bird Japanese rock ptarmigan. J Vet Med Sci 2019; 81:1389-1399. [PMID: 31406033 PMCID: PMC6785603 DOI: 10.1292/jvms.19-0014] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 07/15/2019] [Indexed: 01/01/2023] Open
Abstract
The transgenerational maintenance of symbiotic microbes that benefit host nutrition and health is evolutionarily advantageous. In some vertebrate lineages, coprophagy is used as a strategy for effectively transmitting microbes across generations. However, this strategy has still not been studied in birds. Accordingly, the aim of the present study was to evaluate the role of maternal cecal feces consumption by Japanese rock ptarmigan (Lagopus muta japonica) chicks as a strategy for acquiring essential gut microbes. Both the duration of coprophagy behavior by the chicks and the development process of the chick cecal microbiome (n=20 one- to three-week-old chicks, from three broods) were investigated. In all three broods, coprophagy behavior was only observed from 3 to 18 days of age. Furthermore, there was no significant difference in the number of bacterial operational taxonomic units (OTUs) in 1-week-old chicks (n=651) and adults (n=609), and most of the main OTUs observed in the adults were already present in the 1-week-old chicks. These results indicate that, in this precocial bird species, coprophagy may contribute to the early establishment of cecal bacteria that are essential for food digestion and, thus, chick survival. In fact, Japanese rock ptarmigan chicks consume the same food as their hens from the time of hatching. This behavior may have applications to ex-situ conservation.
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Affiliation(s)
| | - Sayaka TSUCHIDA
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto 606-8522, Japan
- Chubu University, Academy of Emerging Sciences, Kasugai, Aichi 487-8501, Japan
| | - Atsushi UEDA
- Department of Life Science and Technology, School of Life Science and Technology, Tokyo Institute of Technology, Tokyo 152-8550, Japan
| | - Takuji YAMADA
- Department of Life Science and Technology, School of Life Science and Technology, Tokyo Institute of Technology, Tokyo 152-8550, Japan
| | - Koichi MURATA
- Faculty of Bioresource Sciences, Nihon University, Kanagawa 252-0800, Japan
| | - Hiroshi NAKAMURA
- General Foundation Hiroshi Nakamura International Institute for Ornithology, Nagano 380-0934, Japan
| | - Kazunari USHIDA
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto 606-8522, Japan
- Chubu University, Academy of Emerging Sciences, Kasugai, Aichi 487-8501, Japan
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38
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Grond K, Santo Domingo JW, Lanctot RB, Jumpponen A, Bentzen RL, Boldenow ML, Brown SC, Casler B, Cunningham JA, Doll AC, Freeman S, Hill BL, Kendall SJ, Kwon E, Liebezeit JR, Pirie-Dominix L, Rausch J, Sandercock BK. Composition and Drivers of Gut Microbial Communities in Arctic-Breeding Shorebirds. Front Microbiol 2019; 10:2258. [PMID: 31649627 PMCID: PMC6795060 DOI: 10.3389/fmicb.2019.02258] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 09/17/2019] [Indexed: 01/02/2023] Open
Abstract
Gut microbiota can have important effects on host health, but explanatory factors and pathways that determine gut microbial composition can differ among host lineages. In mammals, host phylogeny is one of the main drivers of gut microbiota, a result of vertical transfer of microbiota during birth. In birds, it is less clear what the drivers might be, but both phylogeny and environmental factors may play a role. We investigated host and environmental factors that underlie variation in gut microbiota composition in eight species of migratory shorebirds. We characterized bacterial communities from 375 fecal samples collected from adults of eight shorebird species captured at a network of nine breeding sites in the Arctic and sub-Arctic ecoregions of North America, by sequencing the V4 region of the bacterial 16S ribosomal RNA gene. Firmicutes (55.4%), Proteobacteria (13.8%), Fusobacteria (10.2%), and Bacteroidetes (8.1%) dominated the gut microbiota of adult shorebirds. Breeding location was the main driver of variation in gut microbiota of breeding shorebirds (R2 = 11.6%), followed by shorebird host species (R2 = 1.8%), and sampling year (R2 = 0.9%), but most variation remained unexplained. Site variation resulted from differences in the core bacterial taxa, whereas rare, low-abundance bacteria drove host species variation. Our study is the first to highlight a greater importance of local environment than phylogeny as a driver of gut microbiota composition in wild, migratory birds under natural conditions.
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Affiliation(s)
- Kirsten Grond
- Division of Biology, Kansas State University, Manhattan, KS, United States
| | | | - Richard B Lanctot
- Migratory Bird Management, U.S. Fish & Wildlife Service, Anchorage, AK, United States
| | - Ari Jumpponen
- Division of Biology, Kansas State University, Manhattan, KS, United States
| | | | - Megan L Boldenow
- Department of Biology and Wildlife, University of Alaska Fairbanks, Fairbanks, AK, United States
| | | | - Bruce Casler
- Independent Researcher, Nehalem, OR, United States
| | - Jenny A Cunningham
- Department of Fisheries and Wildlife Sciences, University of Missouri, Columbia, MO, United States
| | - Andrew C Doll
- Denver Museum of Nature & Science, Denver, CO, United States
| | - Scott Freeman
- Arctic National Wildlife Refuge, U.S. Fish & Wildlife Service, Fairbanks, AK, United States
| | - Brooke L Hill
- Department of Biology and Wildlife, University of Alaska Fairbanks, Fairbanks, AK, United States
| | - Steven J Kendall
- Arctic National Wildlife Refuge, U.S. Fish & Wildlife Service, Fairbanks, AK, United States
| | - Eunbi Kwon
- Department of Fish and Wildlife Conservation, Virginia Tech, Blacksburg, VA, United States
| | | | | | - Jennie Rausch
- Environment and Climate Change Canada, Yellowknife, NT, Canada
| | - Brett K Sandercock
- Department of Terrestrial Ecology, Norwegian Institute for Nature Research, Trondheim, Norway
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39
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Videvall E, Song SJ, Bensch HM, Strandh M, Engelbrecht A, Serfontein N, Hellgren O, Olivier A, Cloete S, Knight R, Cornwallis CK. Major shifts in gut microbiota during development and its relationship to growth in ostriches. Mol Ecol 2019; 28:2653-2667. [DOI: 10.1111/mec.15087] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 03/16/2019] [Accepted: 03/18/2019] [Indexed: 12/26/2022]
Affiliation(s)
| | - Se Jin Song
- Department of Pediatrics University of California San Diego San Diego California
| | | | | | - Anel Engelbrecht
- Directorate Animal Sciences Western Cape Department of Agriculture Elsenburg South Africa
| | | | | | - Adriaan Olivier
- Klein Karoo International, Research and Development Oudtshoorn South Africa
| | - Schalk Cloete
- Directorate Animal Sciences Western Cape Department of Agriculture Elsenburg South Africa
- Department of Animal Sciences Stellenbosch University Matieland South Africa
| | - Rob Knight
- Department of Pediatrics University of California San Diego San Diego California
- Department of Computer Science & Engineering University of California San Diego San Diego California
- Center for Microbiome Innovation University of California San Diego San Diego California
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40
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Kosek K, Luczkiewicz A, Kozioł K, Jankowska K, Ruman M, Polkowska Ż. Environmental characteristics of a tundra river system in Svalbard. Part 1: Bacterial abundance, community structure and nutrient levels. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 653:1571-1584. [PMID: 30545665 DOI: 10.1016/j.scitotenv.2018.11.378] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 11/24/2018] [Accepted: 11/25/2018] [Indexed: 06/09/2023]
Abstract
The Arctic hosts a set of unique ecosystems, characterised by extreme environmental conditions and undergoing a rapid change resulting from the average temperature rising. We present a study on an aquatic ecosystem of the Revelva catchment (Spitsbergen), based on samples collected from the lake, river and their tributaries, in the summer of 2016. The landscape variety of the study site and the seasonal change in the hydrological regime modify the availability of nutrients. In general, the upper part of the catchment consists of the mountain rocky slopes which are especially abundant in iron minerals, sulphides and phosphorus minerals. The lower part of the catchment is covered by plants - lichens, saxifrages and bryophytes, which are a different source of nutrients. In the analysed water samples, the maximum concentrations of nutrients such as iron, boron and phosphorus were 0.28 μg L-1, 4.52 μg L-1 and 1.91 μg L-1, respectively, in June, while in September, Fe and B reached the concentrations of 1.32 μg L-1 and 2.71 μg L-1, respectively. The concentration of P in September was below the detection limit of 1.00 μg L-1, which may be explained by the necessity of bacteria to consume it immediately on current needs. We noted also an increase in TOC concentration between the June and September samples, which could originate both from the biomass accumulation in the catchment and the permafrost melting contributing to the hydrological regime of the river. The bacterial community developed in this environment consisted mainly of Proteobacteria, Actinobacteria, Bacteroidetes and Firmicutes phylum, while the presence of Acidobacteria was less pronounced than in other tundra-related environments. The described catchment shows that despite the relatively small amount of bioavailable nutrients, the Revelva system is biodiverse and one of the most significant biogeochemical changes occurs there in response to seasonally switching water sources.
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Affiliation(s)
- Klaudia Kosek
- Department of Analytical Chemistry, Faculty of Chemistry, Gdansk University of Technology, 11/12 Narutowicza St., Gdansk 80-233, Poland
| | - Aneta Luczkiewicz
- Department of Water and Waste-Water Technology, Faculty of Civil and Environmental Engineering, Gdansk University of Technology, 11/12 Narutowicza St., Gdansk 80-233, Poland
| | - Krystyna Kozioł
- Institute of Geography, Faculty of Geography and Biology, Pedagogical University in Cracow, Podchorążych 2 St., Cracow 30-084, Poland; Institute of Geophysics, Polish Academy of Sciences, 64 Księcia Janusza St., Warsaw 01-452, Poland
| | - Katarzyna Jankowska
- Department of Water and Waste-Water Technology, Faculty of Civil and Environmental Engineering, Gdansk University of Technology, 11/12 Narutowicza St., Gdansk 80-233, Poland
| | - Marek Ruman
- Faculty of Earth Sciences, University of Silesia,60 Będzińska St., Sosnowiec 41-200, Poland
| | - Żaneta Polkowska
- Department of Analytical Chemistry, Faculty of Chemistry, Gdansk University of Technology, 11/12 Narutowicza St., Gdansk 80-233, Poland.
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Gillingham MAF, Béchet A, Cézilly F, Wilhelm K, Rendón-Martos M, Borghesi F, Nissardi S, Baccetti N, Azafzaf H, Menke S, Kayser Y, Sommer S. Offspring Microbiomes Differ Across Breeding Sites in a Panmictic Species. Front Microbiol 2019; 10:35. [PMID: 30787910 PMCID: PMC6372503 DOI: 10.3389/fmicb.2019.00035] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Accepted: 01/10/2019] [Indexed: 01/20/2023] Open
Abstract
High dispersal rates are known to homogenize host’s population genetic structure in panmictic species and to disrupt host local adaptation to the environment. Long-distance dispersal might also spread micro-organisms across large geographical areas. However, so far, to which extent selection mechanisms that shape host’s population genetics are mirrored in the population structure of the enteric microbiome remains unclear. High dispersal rates and horizontal parental transfer may homogenize bacterial communities between breeding sites (homogeneous hypothesis). Alternatively, strong selection from the local environment may differentiate bacterial communities between breeding sites (heterogeneous hypothesis). Furthermore, selection from age-specific environmental or physiological factors may differentiate the microbiome between juveniles and adults. Here, we analyzed the cloacal bacterial 16S rRNA gene of fledgling greater flamingos, Phoenicopterus roseus, across nine western Mediterranean breeding sites and four breeding seasons (n = 731) and adult birds (n = 27) from a single site. We found that fledgling cloacal microbiome, as measured by alpha diversity, beta diversity, the relative abundance of assigned sequence variants (ASVs) belonging to a phylum and genus composition within phylum, varied significantly between sampling sites and across time within site despite high adult dispersal rates. The spatio-temporal effects were stronger on individual ASV absence/presence than on ASV abundance (i.e., than on core microbiome composition). Spatial effects had a stronger effect than temporal effects, particularly on ASV abundance. Our study supports the heterogeneous hypothesis whereby local environmental conditions select and differentiate bacterial communities, thus countering the homogenizing effects of high-dispersing host species. In addition, differences in core microbiome between adult vs. fledgling samples suggests that differences in age-specific environmental and/or physiological factors result in differential selection pressure of core enteric microbiome between age classes, even within the same environment. In particular, the genus Corynebacterium, associated with both seasonal fat uptake and migration in previous studies, was much more abundant in high-dispersing fledglings than in more resident adults. To conclude, selection mechanisms that shape the host’s genetic structure cannot be extended to the genetic structure of the enteric microbiome, which has important implications regarding our understanding of both host local adaptation mechanisms and enteric microbiome population genetics.
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Affiliation(s)
| | - Arnaud Béchet
- Institut de Recherche de la Tour du Valat, Arles, France
| | - Frank Cézilly
- Université de Bourgogne, Equipe Ecologie Evolutive, UMR CNRS 6282 Biogéosciences, Dijon, France
| | - Kerstin Wilhelm
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany
| | - Manuel Rendón-Martos
- Consejería de Medio Ambiente y Ordenación del Territorio, R.N. Laguna de Fuente de Piedra, Fuente de Piedra, Spain
| | - Fabrizio Borghesi
- Department of Biological Sciences, Geological and Environmental, University of Bologna, Ravenna, Italy
| | | | - Nicola Baccetti
- Istituto Superiore per la Protezione e Ricerca Ambientale, Rome, Italy
| | - Hichem Azafzaf
- Association "Les Amis des Oiseaux" (AAO/BirdLife Tunisie), Ariana Center, Ariana, Tunisia
| | - Sebastian Menke
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany
| | - Yves Kayser
- Institut de Recherche de la Tour du Valat, Arles, France
| | - Simone Sommer
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany
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Knutie SA, Gotanda KM. A Non-invasive Method to Collect Fecal Samples from Wild Birds for Microbiome Studies. MICROBIAL ECOLOGY 2018; 76:851-855. [PMID: 29623358 DOI: 10.1007/s00248-018-1182-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 03/22/2018] [Indexed: 06/08/2023]
Abstract
Over the past few decades, studies have demonstrated that the gut microbiota strongly influences the physiology, behavior, and fitness of its host. Such studies have been conducted primarily in humans and model organisms under controlled laboratory conditions. More recently, researchers have realized the importance of placing host-associated microbiota studies into a more ecological context; however, few non-destructive methods have been established to collect fecal samples from wild birds. Here, we present an inexpensive and easy-to-use kit for the non-invasive collection of feces from small birds. The portability of the collection kit makes this method amenable to field studies, especially those in remote areas. The main components of the collection kit include a flat-bottomed paper bag, a large modified weigh boat (tray), vinyl-coated hardware cloth fencing (grate), a clothespin, and a 10% bleach solution (to sterilize the tray and grate). In the paper bag, a sterile tray is placed under a small grate, which prevents the birds from contacting the feces and reduces the risk of contamination. After capture, the bird is placed in the bag for 3-5 min until it defecates. After the bird is removed from the bag, the tray is extracted and the fecal sample is moved to a collection tube and frozen or preserved. We believe that our method is an affordable and easy option for researchers studying the gut microbiota of wild birds.
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Affiliation(s)
- Sarah A Knutie
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, 06269, USA.
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Hird SM, Ganz H, Eisen JA, Boyce WM. The Cloacal Microbiome of Five Wild Duck Species Varies by Species and Influenza A Virus Infection Status. mSphere 2018; 3:e00382-18. [PMID: 30355662 PMCID: PMC6200988 DOI: 10.1128/msphere.00382-18] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 09/26/2018] [Indexed: 02/08/2023] Open
Abstract
Waterfowl, especially ducks of the genus Anas, are natural reservoir species for influenza A virus (IAV). Duck populations contain nearly all the known diversity of IAVs, and the birds are asymptomatic to infection. Previous work established that IAV infection status is correlated with changes in the cloacal microbiome in juvenile mallards. Here, we analyze five Anas species to determine whether these duck species have similar IAV+ and IAV- cloacal microbiomes, or if the relationships among a host, influenza virus, and the microbiome are species specific. We assessed taxonomic composition of the microbiome, alpha diversity, and beta diversity and found very few patterns related to microbiome and infection status across species, while detecting strong differences within species. A host species-specific signal was stronger in IAV- ducks than IAV+ ducks, and the effect size of host species on the microbiome was three times higher in IAV- birds than IAV+ birds. The mallards and the northern shovelers, the species with highest sample sizes but also with differing feeding ecology, showed especially contrasting patterns in microbiome composition, alpha diversity, and beta diversity. Our results indicate that the microbiome may have a unique relationship with influenza virus infection at the species level.IMPORTANCE Waterfowl are natural reservoir species for influenza A virus (IAV). Thus, they maintain high levels of pathogen diversity, are asymptomatic to the infection, and also contribute to the risk of a global influenza pandemic. An individual's microbiome is a critical part in how a vertebrate manages pathogens and illness. Here, we describe the cloacal microbiome of 300 wild ducks, from five species (four with previously undescribed microbiomes), including both IAV-negative and IAV-positive individuals. We demonstrate that there is not one consistent "flu-like" microbiome or response to flu across species. Individual duck species appear to have unique relationships between their microbiomes and IAV, and IAV-negative birds have a stronger tie to host species than the IAV-positive birds. In a broad context, understanding the role of the microbiome in IAV reservoir species may have future implications for avian disease management.
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Affiliation(s)
- Sarah M Hird
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Holly Ganz
- AnimalBiome, Oakland, California, USA
- Genome Center, University of California, Davis, Davis, California, USA
| | - Jonathan A Eisen
- Genome Center, University of California, Davis, Davis, California, USA
| | - Walter M Boyce
- Pathology, Microbiology and Immunology, University of California, Davis, Davis, California, USA
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Teyssier A, Lens L, Matthysen E, White J. Dynamics of Gut Microbiota Diversity During the Early Development of an Avian Host: Evidence From a Cross-Foster Experiment. Front Microbiol 2018; 9:1524. [PMID: 30038608 PMCID: PMC6046450 DOI: 10.3389/fmicb.2018.01524] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 06/19/2018] [Indexed: 11/18/2022] Open
Abstract
Despite the increasing knowledge on the processes involved in the acquisition and development of the gut microbiota in model organisms, the factors influencing early microbiota successions in natural populations remain poorly understood. In particular, little is known on the role of the rearing environment in the establishment of the gut microbiota in wild birds. Here, we examined the influence of the nesting environment on the gut microbiota of Great tits (Parus major) by performing a partial cross-fostering experiment during the intermediate stage of nestling development. We found that the cloacal microbiota of great tit nestlings underwent substantial changes between 8 and 15 days of age, with a strong decrease in diversity, an increase in the relative abundance of Firmicutes and a shift in the functional features of the community. Second, the nesting environment significantly influenced community composition, with a divergence among separated true siblings and a convergence among foster siblings. Third, larger shifts in both microbiota diversity and composition correlated with lower nestling body condition. Our results shed new light on the dynamics of microbial diversity during the ontogeny of avian hosts, indicating that the nest environment continues to shape the gut microbiota during the later stages of nestling development and that the increase in gut diversity between hatching and adulthood may not be as linear as previously suspected. Lastly, the microbiota changes incurred during this period may have implications for nestling body condition which can lead to long-term consequences for host fitness.
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Affiliation(s)
- Aimeric Teyssier
- Terrestrial Ecology Unit, Department of Biology, Ghent University, Ghent, Belgium
- Evolutionary Ecology Group, Department of Biology, University of Antwerp, Antwerp, Belgium
- Laboratoire Evolution et Diversité Biologique, UMR 5174 Centre National de la Recherche Scientifique–Université Paul Sabatier–Institut de Recherche pour le Développement, Toulouse, France
| | - Luc Lens
- Terrestrial Ecology Unit, Department of Biology, Ghent University, Ghent, Belgium
| | - Erik Matthysen
- Evolutionary Ecology Group, Department of Biology, University of Antwerp, Antwerp, Belgium
| | - Joël White
- Laboratoire Evolution et Diversité Biologique, UMR 5174 Centre National de la Recherche Scientifique–Université Paul Sabatier–Institut de Recherche pour le Développement, Toulouse, France
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45
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Noguera JC, Aira M, Pérez-Losada M, Domínguez J, Velando A. Glucocorticoids modulate gastrointestinal microbiome in a wild bird. ROYAL SOCIETY OPEN SCIENCE 2018; 5:171743. [PMID: 29765642 PMCID: PMC5936907 DOI: 10.1098/rsos.171743] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 03/14/2018] [Indexed: 05/04/2023]
Abstract
It has recently been hypothesized that stress exposure (e.g. via glucocorticoid secretion) may dysregulate the bacterial gut microbiome, a crucial 'organ' in animal health. However, whether stress exposure (e.g. via glucocorticoid secretion) affects the bacterial gut microbiome of natural populations is unknown. We have experimentally altered the basal glucocorticoid level (corticosterone implants) in a wild avian species, the yellow-legged gull Larus michahellis, to assess its effects on the gastrointestinal microbiota. Our results suggest underrepresentation of several microbial taxa in the corticosterone-implanted birds. Importantly, such reduction included potentially pathogenic avian bacteria (e.g. Mycoplasma and Microvirga) and also some commensal taxa that may be beneficial for birds (e.g. Firmicutes). Our findings clearly demonstrate a close link between microbiome communities and glucocorticoid levels in natural populations. Furthermore, they suggest a beneficial effect of stress in reducing the risk of infection that should be explored in future studies.
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Affiliation(s)
- José C. Noguera
- Grupo de Ecología Animal, Universidade de Vigo, Torre CACTI, 36310, Vigo, Spain
- Author for correspondence: José C. Noguera e-mail:
| | - Manuel Aira
- Grupo de Ecología Animal, Universidade de Vigo, Torre CACTI, 36310, Vigo, Spain
| | - Marcos Pérez-Losada
- Computational Biology Institute, Milken Institute School of Public Health, George Washington University, Ashburn, VA, USA
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Portugal
| | - Jorge Domínguez
- Grupo de Ecología Animal, Universidade de Vigo, Torre CACTI, 36310, Vigo, Spain
| | - Alberto Velando
- Grupo de Ecología Animal, Universidade de Vigo, Torre CACTI, 36310, Vigo, Spain
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46
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Risely A, Waite DW, Ujvari B, Hoye BJ, Klaassen M. Active migration is associated with specific and consistent changes to gut microbiota in
Calidris
shorebirds. J Anim Ecol 2017; 87:428-437. [DOI: 10.1111/1365-2656.12784] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2017] [Accepted: 10/21/2017] [Indexed: 12/21/2022]
Affiliation(s)
- Alice Risely
- Centre for Integrative Ecology Deakin University Geelong Vic. Australia
| | - David W. Waite
- Australian Centre for Ecogenomics University of Queensland Brisbane Qld Australia
| | - Beata Ujvari
- Centre for Integrative Ecology Deakin University Geelong Vic. Australia
| | - Bethany J. Hoye
- Centre for Integrative Ecology Deakin University Geelong Vic. Australia
- School of Biological Sciences University of Wollongong Wollongong NSW Australia
| | - Marcel Klaassen
- Centre for Integrative Ecology Deakin University Geelong Vic. Australia
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