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Storm MB, Arfaoui EMR, Simelane P, Denlinger J, Dias CA, da Conceição AG, Monadjem A, Bohmann K, Poulsen M, Bodawatta KH. Diet components associated with specific bacterial taxa shape overall gut community compositions in omnivorous African viverrids. Ecol Evol 2024; 14:e11486. [PMID: 39005885 PMCID: PMC11239323 DOI: 10.1002/ece3.11486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 05/14/2024] [Accepted: 05/15/2024] [Indexed: 07/16/2024] Open
Abstract
Gut bacterial communities provide flexibility to hosts during dietary changes. Despite the increasing number of studies exploring the associations between broader dietary guilds of mammalian hosts and their gut bacteria, it is generally unclear how diversity and variability in consumed diets link to gut bacterial taxa in wild non-primate mammals, particularly in omnivores. Here, we contribute to filling this gap by exploring consumed diets and gut bacterial community compositions with metabarcoding of faecal samples for two African mammals, Civettictis civetta and Genetta spp., from the family Viverridae. For each individual sample, we characterised bacterial communities and identified dietary taxa by sequencing vertebrate, invertebrate and plant markers. This led us to establish diet compositions that diverged from what has previously been found from visual identification methods. Specifically, while the two genera have been categorised into the same dietary guild, we detected more animal dietary items than plant items in C. civetta, while in Genetta spp., we observed the opposite. We further found that individuals with similar diets have similar gut bacterial communities within both genera. This association tended to be driven by specific links between dietary items and gut bacterial genera, rather than communities as a whole, implying diet-driven selection for specific gut microbes in individual wild hosts. Our findings underline the importance of molecular tools for improving characterisations of omnivorous mammalian diets and highlight the opportunities for simultaneously disentangling links between diets and gut symbionts. Such insights can inform robustness and flexibility in host-microbe symbioses to dietary change associated with seasonal and habitat changes.
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Affiliation(s)
- Malou B. Storm
- Section for Ecology and Evolution, Department of BiologyUniversity of CopenhagenCopenhagenDenmark
- Section for Molecular Ecology and EvolutionGlobe Institute, University of CopenhagenCopenhagenDenmark
| | - Emilia M. R. Arfaoui
- Section for Ecology and Evolution, Department of BiologyUniversity of CopenhagenCopenhagenDenmark
- Section for Molecular Ecology and EvolutionGlobe Institute, University of CopenhagenCopenhagenDenmark
| | - Phumlile Simelane
- Department of Biological SciencesUniversity of EswatiniKwaluseniEswatini
| | | | | | | | - Ara Monadjem
- Department of Biological SciencesUniversity of EswatiniKwaluseniEswatini
- Mammal Research Institute, Department of Zoology and EntomologyUniversity of PretoriaHatfield, PretoriaSouth Africa
| | - Kristine Bohmann
- Section for Molecular Ecology and EvolutionGlobe Institute, University of CopenhagenCopenhagenDenmark
| | - Michael Poulsen
- Section for Ecology and Evolution, Department of BiologyUniversity of CopenhagenCopenhagenDenmark
| | - Kasun H. Bodawatta
- Section for Molecular Ecology and EvolutionGlobe Institute, University of CopenhagenCopenhagenDenmark
- Natural History Museum of DenmarkUniversity of CopenhagenCopenhagenDenmark
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2
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Grimwood RM, Reyes EMR, Cooper J, Welch J, Taylor G, Makan T, Lim L, Dubrulle J, McInnes K, Holmes EC, Geoghegan JL. From islands to infectomes: host-specific viral diversity among birds across remote islands. BMC Ecol Evol 2024; 24:84. [PMID: 38926829 PMCID: PMC11209962 DOI: 10.1186/s12862-024-02277-4] [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: 02/28/2024] [Accepted: 06/23/2024] [Indexed: 06/28/2024] Open
Abstract
BACKGROUND Accelerating biodiversity loss necessitates monitoring the potential pathogens of vulnerable species. With a third of New Zealand's avifauna considered at risk of extinction, a greater understanding of the factors that influence microbial transmission in this island ecosystem is needed. We used metatranscriptomics to determine the viruses, as well as other microbial organisms (i.e. the infectomes), of seven bird species, including the once critically endangered black robin (Petroica traversi), on two islands in the remote Chatham Islands archipelago, New Zealand. RESULTS We identified 19 likely novel avian viruses across nine viral families. Black robins harboured viruses from the Flaviviridae, Herpesviridae, and Picornaviridae, while introduced starlings (Sturnus vulgaris) and migratory seabirds (Procellariiformes) carried viruses from six additional viral families. Potential cross-species virus transmission of a novel passerivirus (family: Picornaviridae) between native (black robins and grey-backed storm petrels) and introduced (starlings) birds was also observed. Additionally, we identified bacterial genera, apicomplexan parasites, as well as a novel megrivirus linked to disease outbreaks in other native New Zealand birds. Notably, island effects were outweighed by host taxonomy as a significant driver of viral composition, even among sedentary birds. CONCLUSIONS These findings underscore the value of surveillance of avian populations to identify and minimise escalating threats of disease emergence and spread in these island ecosystems. Importantly, they contribute to our understanding of the potential role of introduced and migratory birds in the transmission of microbes and associated diseases, which could impact vulnerable island-endemic species.
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Affiliation(s)
- Rebecca M Grimwood
- Department of Microbiology and Immunology, University of Otago, Dunedin, 9016, New Zealand
| | - Enzo M R Reyes
- Department of Conservation/Te Papa Atawhai, Nelson, New Zealand
| | - Jamie Cooper
- Department of Conservation/Te Papa Atawhai, Nelson, New Zealand
| | - Jemma Welch
- Department of Conservation/Te Papa Atawhai, Nelson, New Zealand
| | - Graeme Taylor
- Department of Conservation/Te Papa Atawhai, Nelson, New Zealand
| | - Troy Makan
- Department of Conservation/Te Papa Atawhai, Nelson, New Zealand
| | - Lauren Lim
- School of Medical Sciences, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Jérémy Dubrulle
- Department of Microbiology and Immunology, University of Otago, Dunedin, 9016, New Zealand
| | - Kate McInnes
- Department of Conservation/Te Papa Atawhai, Nelson, New Zealand
| | - Edward C Holmes
- School of Medical Sciences, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Jemma L Geoghegan
- Department of Microbiology and Immunology, University of Otago, Dunedin, 9016, New Zealand.
- Institute of Environmental Science and Research, Wellington, 5018, New Zealand.
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3
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Włodarczyk R, Drzewińska-Chańko J, Kamiński M, Meissner W, Rapczyński J, Janik-Superson K, Krawczyk D, Strapagiel D, Ożarowska A, Stępniewska K, Minias P. Stopover habitat selection drives variation in the gut microbiome composition and pathogen acquisition by migrating shorebirds. FEMS Microbiol Ecol 2024; 100:fiae040. [PMID: 38515294 PMCID: PMC11008731 DOI: 10.1093/femsec/fiae040] [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] [Received: 07/21/2023] [Revised: 02/28/2024] [Accepted: 03/20/2024] [Indexed: 03/23/2024] Open
Abstract
Long-distance host movements play a major regulatory role in shaping microbial communities of their digestive tract. Here, we studied gut microbiota composition during seasonal migration in five shorebird species (Charadrii) that use different migratory (stopover) habitats. Our analyses revealed significant interspecific variation in both composition and diversity of gut microbiome, but the effect of host identity was weak. A strong variation in gut microbiota was observed between coastal and inland (dam reservoir and river valley) stopover habitats within species. Comparisons between host age classes provided support for an increasing alpha diversity of gut microbiota during ontogeny and an age-related remodeling of microbiome composition. There was, however, no correlation between microbiome and diet composition across study species. Finally, we detected high prevalence of avian pathogens, which may cause zoonotic diseases in humans (e.g. Vibrio cholerae) and we identified stopover habitat as one of the major axes of variation in the bacterial pathogen exposure risk in shorebirds. Our study not only sheds new light on ecological processes that shape avian gut microbiota, but also has implications for our better understanding of host-pathogen interface and the role of birds in long-distance transmission of pathogens.
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Affiliation(s)
- Radosław Włodarczyk
- University of Lodz, Faculty of Biology and Environmental Protection, Department of Biodiversity Studies and Bioeducation,, Banacha 1/3, 90-237 Łódź, Poland
| | - Joanna Drzewińska-Chańko
- University of Lodz, Faculty of Biology and Environmental Protection, Department of Biodiversity Studies and Bioeducation,, Banacha 1/3, 90-237 Łódź, Poland
| | - Maciej Kamiński
- University of Lodz, Faculty of Biology and Environmental Protection, Department of Biodiversity Studies and Bioeducation,, Banacha 1/3, 90-237 Łódź, Poland
| | - Włodzimierz Meissner
- Ornithology Unit, Department of Vertebrate Ecology and Zoology, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland
| | - Jan Rapczyński
- Forestry Student Scientific Association, Ornithological Section, Warsaw University of Life Sciences, Nowoursynowska 166, 02-787 Warszawa, Poland
| | - Katarzyna Janik-Superson
- University of Lodz, Faculty of Biology and Environmental Protection, Biobank Lab, Department of Oncobiology and Epigenetics, Pomorska 139, 90-235 Łódź, Poland
| | - Dawid Krawczyk
- University of Lodz, Faculty of Biology and Environmental Protection, Department of Invertebrate Zoology and Hydrobiology, Banacha 12/16, 90-237 Łódź, Poland
| | - Dominik Strapagiel
- University of Lodz, Faculty of Biology and Environmental Protection, Biobank Lab, Department of Oncobiology and Epigenetics, Pomorska 139, 90-235 Łódź, Poland
| | - Agnieszka Ożarowska
- Ornithology Unit, Department of Vertebrate Ecology and Zoology, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland
| | - Katarzyna Stępniewska
- Ornithology Unit, Department of Vertebrate Ecology and Zoology, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland
| | - Piotr Minias
- University of Lodz, Faculty of Biology and Environmental Protection, Department of Biodiversity Studies and Bioeducation,, Banacha 1/3, 90-237 Łódź, Poland
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4
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Ahmad AR, Ridgeway S, Shibl AA, Idaghdour Y, Jha AR. Falcon gut microbiota is shaped by diet and enriched in Salmonella. PLoS One 2024; 19:e0293895. [PMID: 38289900 PMCID: PMC10826950 DOI: 10.1371/journal.pone.0293895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 10/20/2023] [Indexed: 02/01/2024] Open
Abstract
The gut microbiome is increasingly being appreciated as a master regulator of animal health. However, avian gut microbiome studies commonly focus on birds of economic importance and the gut microbiomes of raptors remain underexplored. Here we examine the gut microbiota of 29 captive falcons-raptors of historic importance-in the context of avian evolution by sequencing the V4 region of the 16S rRNA gene. Our results reveal that evolutionary histories and diet are significantly associated with avian gut microbiota in general, whereas diet plays a major role in shaping the falcon gut microbiota. Multiple analyses revealed that gut microbial diversity, composition, and relative abundance of key diet-discriminating bacterial genera in the falcon gut closely resemble those of carnivorous raptors rather than those of their closest phylogenetic relatives. Furthermore, the falcon microbiota is dominated by Firmicutes and contains Salmonella at appreciable levels. Salmonella presence was associated with altered functional capacity of the falcon gut microbiota as its abundance is associated with depletion of multiple predicted metabolic pathways involved in protein mass buildup, muscle maintenance, and enrichment of antimicrobial compound degradation, thus increasing the pathogenic potential of the falcon gut. Our results point to the necessity of screening for Salmonella and other human pathogens in captive birds to safeguard both the health of falcons and individuals who come in contact with these birds.
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Affiliation(s)
- Anique R. Ahmad
- Genetic Heritage Group, Program in Biology, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Samuel Ridgeway
- Program in Biology, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Ahmed A. Shibl
- Genetic Heritage Group, Program in Biology, New York University Abu Dhabi, Abu Dhabi, UAE
| | | | - Aashish R. Jha
- Genetic Heritage Group, Program in Biology, New York University Abu Dhabi, Abu Dhabi, UAE
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5
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Jones I, Marsh K, Handby TM, Hopkins K, Slezacek J, Bearhop S, Harrison XA. The influence of diet on gut microbiome and body mass dynamics in a capital-breeding migratory bird. PeerJ 2023; 11:e16682. [PMID: 38130921 PMCID: PMC10734429 DOI: 10.7717/peerj.16682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 11/24/2023] [Indexed: 12/23/2023] Open
Abstract
Gut-associated microbial communities are known to play a vital role in the health and fitness of their hosts. Though studies investigating the factors associated with among-individual variation in microbiome structure in wild animal species are increasing, knowledge of this variation at the individual level is scarce, despite the clear link between microbiome and nutritional status uncovered in humans and model organisms. Here, we combine detailed observational data on life history and foraging preference with 16S rRNA profiling of the faecal microbiome to investigate the relationship between diet, microbiome stability and rates of body mass gain in a migratory capital-breeding bird, the light-bellied Brent goose (Branta bernicla hrota). Our findings suggest that generalist feeders have microbiomes that are intermediate in diversity and composition between two foraging specialisms, and also show higher within-individual plasticity. We also suggest a link between foraging phenotype and the rates of mass gain during the spring staging of a capital breeder. This study offers rare insight into individual-level temporal dynamics of the gut microbiome of a wild host. Further work is needed to uncover the functional link between individual dietary choices, gut microbiome structure and stability, and the implications this has for the reproductive success of this capital breeder.
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Affiliation(s)
- Isabelle Jones
- Centre for Ecology and Conservation, University of Exeter, Penryn, United Kingdom
| | - Kirsty Marsh
- Centre for Ecology and Conservation, University of Exeter, Penryn, United Kingdom
| | - Tess M. Handby
- Centre for Ecology and Conservation, University of Exeter, Penryn, United Kingdom
| | - Kevin Hopkins
- Institute of Zoology, Zoological Socety of London, London, United Kingdom
| | - Julia Slezacek
- Konrad Lorenz Institute of Ethology, University of Veterinary Medicine, Vienna, Austria
| | - Stuart Bearhop
- Centre for Ecology and Conservation, University of Exeter, Penryn, United Kingdom
| | - Xavier A. Harrison
- Centre for Ecology and Conservation, University of Exeter, Penryn, United Kingdom
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6
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Brunetti AE, Lyra ML, Monteiro JPC, Zurano JP, Baldo D, Haddad CFB, Moeller AH. Convergence of gut microbiota in myrmecophagous amphibians. Proc Biol Sci 2023; 290:20232223. [PMID: 37964521 PMCID: PMC10646458 DOI: 10.1098/rspb.2023.2223] [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: 09/30/2023] [Accepted: 10/20/2023] [Indexed: 11/16/2023] Open
Abstract
The gut microbiome composition of terrestrial vertebrates is known to converge in response to common specialized dietary strategies, like leaf-eating (folivory) or ant- and termite-eating (myrmecophagy). To date, such convergence has been studied in mammals and birds, but has been neglected in amphibians. Here, we analysed 15 anuran species (frogs and toads) representing five Neotropical families and demonstrated the compositional convergence of the gut microbiomes of distantly related myrmecophagous species. Specifically, we found that the gut microbial communities of bufonids and microhylids, which have independently evolved myrmecophagy, were significantly more similar than expected based on their hosts' evolutionary divergence. Conversely, we found that gut microbiome composition was significantly associated with host evolutionary history in some cases. For instance, the microbiome composition of Xenohyla truncata, one of the few known amphibians that eat fruits, was not different from those of closely related tree frogs with an arthropod generalist diet. Bacterial taxa overrepresented in myrmecophagous species relative to other host families include Paludibacter, Treponema, and Rikenellaceae, suggesting diet-mediated selection and prey-to-predator transmission likely driving the observed compositional convergence. This study provides a basis for examining the roles of the gut microbiome in host tolerance and sequestration of toxic alkaloids from ants and termites.
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Affiliation(s)
- Andrés E. Brunetti
- Laboratorio de Genética Evolutiva, Instituto de Biología Subtropical (IBS, UNaM-CONICET), Posadas, Misiones 3300, Argentina
- Department of Insect Symbiosis, Max Planck Institute for Chemical Ecology, Jena 07745, Germany
| | - Mariana L. Lyra
- New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, United Arab Emirates
| | - Juliane P. C. Monteiro
- Departamento de Biodiversidade e Centro de Aquicultura da UNESP (CAUNESP), Instituto de Biociências, UNESP-Universidade Estadual Paulista, Rio Claro, SP 13506-900, Brazil
| | - Juan P. Zurano
- Instituto de Biología Subtropical (IBS, UNaM-CONICET), Puerto Iguazú, Misiones 3370, Argentina
| | - Diego Baldo
- Laboratorio de Genética Evolutiva, Instituto de Biología Subtropical (IBS, UNaM-CONICET), Posadas, Misiones 3300, Argentina
| | - Celio F. B. Haddad
- Departamento de Biodiversidade e Centro de Aquicultura da UNESP (CAUNESP), Instituto de Biociências, UNESP-Universidade Estadual Paulista, Rio Claro, SP 13506-900, Brazil
| | - Andrew H. Moeller
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14850, USA
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7
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Ochoa-Sánchez M, Acuña Gomez EP, Moreno L, Moraga CA, Gaete K, Eguiarte LE, Souza V. Body site microbiota of Magellanic and king penguins inhabiting the Strait of Magellan follow species-specific patterns. PeerJ 2023; 11:e16290. [PMID: 37933257 PMCID: PMC10625763 DOI: 10.7717/peerj.16290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 09/22/2023] [Indexed: 11/08/2023] Open
Abstract
Animal hosts live in continuous interaction with bacterial partners, yet we still lack a clear understanding of the ecological drivers of animal-associated bacteria, particularly in seabirds. Here, we investigated the effect of body site in the structure and diversity of bacterial communities of two seabirds in the Strait of Magellan: the Magellanic penguin (Spheniscus magellanicus) and the king penguin (Aptenodytes patagonicus). We used 16S rRNA gene sequencing to profile bacterial communities associated with body sites (chest, back, foot) of both penguins and the nest soil of Magellanic penguin. Taxonomic composition showed that Moraxellaceae family (specifically Psychrobacter) had the highest relative abundance across body sites in both penguin species, whereas Micrococacceae had the highest relative abundance in nest soil. We were able to detect a bacterial core among 90% of all samples, which consisted of Clostridium sensu stricto and Micrococcacea taxa. Further, the king penguin had its own bacterial core across its body sites, where Psychrobacter and Corynebacterium were the most prevalent taxa. Microbial alpha diversity across penguin body sites was similar in most comparisons, yet we found subtle differences between foot and chest body sites of king penguins. Body site microbiota composition differed across king penguin body sites, whereas it remained similar across Magellanic penguin body sites. Interestingly, all Magellanic penguin body site microbiota composition differed from nest soil microbiota. Finally, bacterial abundance in penguin body sites fit well under a neutral community model, particularly in the king penguin, highlighting the role of stochastic process and ecological drift in microbiota assembly of penguin body sites. Our results represent the first report of body site bacterial communities in seabirds specialized in subaquatic foraging. Thus, we believe it represents useful baseline information that could serve for long-term comparisons that use marine host microbiota to survey ocean health.
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Affiliation(s)
- Manuel Ochoa-Sánchez
- Instituto de Ecología, Universidad Nacional Autónoma de México, CDMX, Mexico
- Centro de Estudios del Cuaternario de Fuego, Patagonia y Antártica (CEQUA), Punta Arenas, Chile
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Ciudad de México, México
| | | | - Lucila Moreno
- Departamento de Zoología, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile
| | - Claudio A. Moraga
- Centro de Estudios del Cuaternario de Fuego, Patagonia y Antártica (CEQUA), Punta Arenas, Chile
| | - Katherine Gaete
- Centro de Estudios del Cuaternario de Fuego, Patagonia y Antártica (CEQUA), Punta Arenas, Chile
| | - Luis E. Eguiarte
- Instituto de Ecología, Universidad Nacional Autónoma de México, CDMX, Mexico
| | - Valeria Souza
- Instituto de Ecología, Universidad Nacional Autónoma de México, CDMX, Mexico
- Centro de Estudios del Cuaternario de Fuego, Patagonia y Antártica (CEQUA), Punta Arenas, Chile
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8
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Herder EA, Skeen HR, Lutz HL, Hird SM. Body Size Poorly Predicts Host-Associated Microbial Diversity in Wild Birds. Microbiol Spectr 2023; 11:e0374922. [PMID: 37039681 PMCID: PMC10269867 DOI: 10.1128/spectrum.03749-22] [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: 09/14/2022] [Accepted: 03/12/2023] [Indexed: 04/12/2023] Open
Abstract
The composition and diversity of avian microbiota are shaped by many factors, including host ecologies and environmental variables. In this study, we examine microbial diversity across 214 bird species sampled in Malawi at five major body sites: blood, buccal cavity, gizzard, intestinal tract, and cloaca. Microbial community dissimilarity differed significantly across body sites. Ecological theory predicts that as area increases, so does diversity. We tested the hypothesis that avian microbiota diversity is correlated with body size, used as a proxy for area, using comparative phylogenetic methods. Using Pagel's lambda, we found that few microbial diversity metrics had significant phylogenetic signals. Phylogenetic generalized least squares identified a significant but weak negative correlation between host size and microbial diversity of the blood and a similarly significant but weakly positive correlation between the cloacal microbiota and host size among birds within the order Passeriformes. Phylosymbiosis, or a congruent branching pattern between host phylogeny and their associated microbiota similarity, was tested and found to be weak or not significant in four of the body sites with sufficient sample size (blood, buccal, cloaca, and intestines). Taken together, these results suggest that the avian microbiome is highly variable, with microbiota diversity demonstrating few clear associations with bird size. Finally, the blood microbiota have a unique relationship with host size. IMPORTANCE All animals coexist and interact with microorganisms, including bacteria, archaea, microscopic eukaryotes, and viruses. These microorganisms can have an enormous influence on the biology and health of macro-organisms. However, the general rules that govern these host-associated microbial communities are poorly described, especially in wild animals. In this paper, we investigate the microbial communities of over 200 species of birds from Malawi and characterize five body site bacterial microbiota in depth. Because the evolutionary relationships of the host underlie the relationship between any host-associated microbiota relationships, we use phylogenetic comparative methods to account for this relationship. We find that the size of a host (the bird) and the diversity and composition of the microbiota are largely uncorrelated. We also find that the general pattern of similarity between host phylogeny and microbiota similarity is weak. Together, we see that bird microbiota are not strongly tied to host size or evolutionary history.
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Affiliation(s)
- Elizabeth A. Herder
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Heather R. Skeen
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut, USA
- Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, Illinois, USA
| | - Holly L. Lutz
- Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, Illinois, USA
- Department of Pediatrics, UC San Diego School of Medicine, La Jolla, California, USA
| | - Sarah M. Hird
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
- Institute for Systems Genomics, University of Connecticut, Storrs, Connecticut, USA
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9
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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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10
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Zhou T, Liu S, Jiang A. Comparison of gut microbiota between immigrant and native populations of the Silver-eared Mesia ( Leiothrix argentauris) living in mining area. Front Microbiol 2023; 14:1076523. [PMID: 36760498 PMCID: PMC9904241 DOI: 10.3389/fmicb.2023.1076523] [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: 10/21/2022] [Accepted: 01/06/2023] [Indexed: 01/26/2023] Open
Abstract
The complex gut bacterial communities have a major impact on organismal health. However, knowledge of the effects of habitat change on the gut microbiota of wild birds is limited. In this study, we characterized the gut microbiota of two different subspecies of the Silver-eared Mesia (Leiothrix argentauris), the native subspecies (L. a. rubrogularis) and immigrant subspecies (L. a. vernayi), using 16S rRNA gene high-throughput sequencing. These two subspecies live in a trace metal-contaminated area, and L. a. vernayi was trafficked. They are an excellent system for studying how the gut microbiome of wild animal changes when they move to new habitats. We hypothesized that the immigrant subspecies would develop the same adaptations as the native subspecies in response to habitat changes. The results showed that there were no significant differences in the composition, diversity, or functional metabolism of gut microbiota between native and immigrant subspecies under the combined action of similar influencing factors (the p values of all analyses of variance >0.05). In addition, the composition and functional metabolism of gut microbiota in two subspecies showed adaptation against trace metal damage. Linear discriminant analysis effect size (LEfSe) analysis revealed that Massilia in the intestinal microbiota of immigrant subspecies was significantly higher than that of native subspecies, suggesting that immigrant subspecies suffered habitat change. Finally, we found that these two subspecies living in the mining area had an extremely high proportion of pathogenic bacteria in their gut microbiota (about 90%), much higher than in other species (about 50%) living in wild environment. Our results revealed the adaptation of intestinal microbiota of immigrant Silver-eared Mesias under heavy metals stress, which would provide guidance for biodiversity conservation and pollution management in mining area.
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Lu Z, Li S, Wang M, Wang C, Meng D, Liu J. Comparative Analysis of the Gut Microbiota of Three Sympatric Terrestrial Wild Bird Species Overwintering in Farmland Habitats. Front Microbiol 2022; 13:905668. [PMID: 35928156 PMCID: PMC9343720 DOI: 10.3389/fmicb.2022.905668] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Accepted: 06/16/2022] [Indexed: 11/13/2022] Open
Abstract
The gut microbiota of wild birds are affected by complex factors, and cross-species transmission may pose challenges for the host to maintain stable gut symbionts. Farmland habitats are environments strongly manipulated by humans, and the environmental characteristics within a large area are highly consistent. These features provide the ideal natural conditions for conducting cross-species comparative studies on gut microbiota among wild birds. This study aimed to investigate and compare the gut microbiota of three common farmland-dependent bird species, Great Bustard (Otis tarda dybowskii), Common Crane (Grus grus), and Common Coot (Fulica atra), in a homogeneous habitat during the wintering period. The results indicated that under the combined action of similar influencing factors, the gut microbiota of different host species did not undergo adaptive convergence, maintained relatively independent structures, and exhibited host-driven signals. In addition, we also detected various pathogenic genera that may cause outbreaks of periodic infections among sympatric migratory birds. We conclude that phylosymbiosis may occur between some wild birds and their gut microbiota. Usage of non-invasive methods to monitor the changes in the gut microbiota of wild bird fecal samples has important implications for the conservation of endangered species.
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Affiliation(s)
- Zhiyuan Lu
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
- College of Life Sciences, Cangzhou Normal University, Cangzhou, China
| | - Sisi Li
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Min Wang
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Can Wang
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Derong Meng
- College of Life Sciences, Cangzhou Normal University, Cangzhou, China
| | - Jingze Liu
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
- *Correspondence: Jingze Liu,
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Kubovčiak J, Schmiedová L, Albrecht T, Těšický M, Tomášek O, Kauzálová T, Kreisinger J. Within-community variation of interspecific divergence patterns in passerine gut microbiota. Ecol Evol 2022; 12:e9071. [PMID: 35813907 PMCID: PMC9251858 DOI: 10.1002/ece3.9071] [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: 02/01/2022] [Revised: 05/31/2022] [Accepted: 06/07/2022] [Indexed: 12/11/2022] Open
Abstract
Gut microbiota (GM) often exhibit variation between different host species and co-divergence with hosts' phylogeny. Identifying these patterns is a key for understanding the mechanisms that shaped symbiosis between GM and its hosts. Therefore, both GM-host species specificity and GM-host co-divergence have been investigated by numerous studies. However, most of them neglected a possibility that different groups of bacteria within GM can vary in the tightness of their association with the host. Consequently, unlike most of these studies, we aimed to directly address how the strength of GM-host species specificity and GM-host co-divergence vary across different GM clades. We decomposed GM communities of 52 passerine species (394 individuals), characterized by 16S rRNA amplicon sequence variant (ASV) profiles, into monophyletic Binned Taxonomic units (BTUs). Subsequently, we analyzed strength of host species specificity and correlation with host phylogeny separately for resulting BTUs. We found that most BTUs exhibited significant host-species specificity in their composition. Notably, BTUs exhibiting high host-species specificity comprised bacterial taxa known to impact host's physiology and immune system. However, BTUs rarely displayed significant co-divergence with host phylogeny, suggesting that passerine GM evolution is not shaped primarily through a shared evolutionary history between the host and its gut microbes.
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Affiliation(s)
- Jan Kubovčiak
- Department of Zoology, Faculty of ScienceCharles UniversityPragueCzech Republic
| | - Lucie Schmiedová
- Department of Zoology, Faculty of ScienceCharles UniversityPragueCzech Republic
| | - Tomáš Albrecht
- Department of Zoology, Faculty of ScienceCharles UniversityPragueCzech Republic
- Institute of Vertebrate BiologyCzech Academy of SciencesBrnoCzech Republic
| | - Martin Těšický
- Department of Zoology, Faculty of ScienceCharles UniversityPragueCzech Republic
| | - Oldřich Tomášek
- Institute of Vertebrate BiologyCzech Academy of SciencesBrnoCzech Republic
| | - Tereza Kauzálová
- Institute of Vertebrate BiologyCzech Academy of SciencesBrnoCzech Republic
| | - Jakub Kreisinger
- Department of Zoology, Faculty of ScienceCharles UniversityPragueCzech Republic
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