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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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Schmiedová L, Černá K, Li T, Těšický M, Kreisinger J, Vinkler M. Bacterial communities along parrot digestive and respiratory tracts: the effects of sample type, species and time. Int Microbiol 2024; 27:127-142. [PMID: 37222909 PMCID: PMC10830831 DOI: 10.1007/s10123-023-00372-y] [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: 01/04/2023] [Revised: 04/26/2023] [Accepted: 05/03/2023] [Indexed: 05/25/2023]
Abstract
Digestive and respiratory tracts are inhabited by rich bacterial communities that can vary between their different segments. In comparison with other bird taxa with developed caeca, parrots that lack caeca have relatively lower variability in intestinal morphology. Here, based on 16S rRNA metabarcoding, we describe variation in microbiota across different parts of parrot digestive and respiratory tracts both at interspecies and intraspecies levels. In domesticated budgerigar (Melopsittacus undulatus), we describe the bacterial variation across eight selected sections of respiratory and digestive tracts, and three non-destructively collected sample types (faeces, and cloacal and oral swabs). Our results show important microbiota divergence between the upper and lower digestive tract, but similarities between respiratory tract and crop, and also between different intestinal segments. Faecal samples appear to provide a better proxy for intestinal microbiota composition than the cloacal swabs. Oral swabs had a similar bacterial composition as the crop and trachea. For a subset of tissues, we confirmed the same pattern also in six different parrot species. Finally, using the faeces and oral swabs in budgerigars, we revealed high oral, but low faecal microbiota stability during a 3-week period mimicking pre-experiment acclimation. Our findings provide a basis essential for microbiota-related experimental planning and result generalisation in non-poultry birds.
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Affiliation(s)
- Lucie Schmiedová
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic.
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic.
| | - Kateřina Černá
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Tao Li
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Martin Těšický
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Jakub Kreisinger
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Michal Vinkler
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
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Wu Y, Xiong Y, Ji Y, Cheng Y, Zhu Q, Jiao X, Chang Y, Zhao N, Yang J, Lei F, Song G. Metabolic and microbial changes in light-vented bulbul during recent northward range expansion. Curr Zool 2024; 70:24-33. [PMID: 38476130 PMCID: PMC10926257 DOI: 10.1093/cz/zoad005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 02/10/2023] [Indexed: 03/14/2024] Open
Abstract
Endotherms recently expanding to cold environments generally exhibit strong physiological acclimation to sustain high body temperature. During this process, gut microbes likely play a considerable role in host physiological functions, including digestion and thermogenesis. The light-vented bulbul Pycnonotus sinensis represents one such species. It used to be restricted to the Oriental realm but expanded its distribution range north to the Palearctic areas during the past few decades. Here, we explored the seasonal dynamics of the resting metabolic rate (RMR) and microbiota for local and newly colonized populations of the species. Our results showed that the mass-adjusted RMR and body mass were positively correlated with latitude variations in both seasons. Consistently, the gut microbiota showed a corresponding variation to the northern cold environments. In the two northern populations, the alpha diversity decreased compared with those of the two southern populations. Significant differences were detected in dominant phyla, such as Firmicutes, Bacteroidetes, Proteobacteria, and Desulfobacterota in both seasons. The core microbiota showed geographic differences in the winter, including the elevated relative abundance of 5 species in northern populations. Finally, to explore the link between microbial communities and host metabolic thermogenesis, we conducted a correlation analysis between microbiota and mass-adjusted RMR. We found that more genera were significantly correlated with mass-adjusted RMR in the wintering season compared to the breeding season (71 vs. 23). These results suggest that microbiota of the lighted-vented bulbul linked with thermogenesis in diversity and abundance under northward expansion.
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Affiliation(s)
- Yun Wu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ying Xiong
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Department of Zoology, College of Life science, Sichuan Agricultural University, Ya’an 625099, Sichuan, China
| | - Yanzhu Ji
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yalin Cheng
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qianghui Zhu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaolu Jiao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yongbin Chang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Henan Engineering Research Center of Bird-Related Outage, Zhengzhou Normal University, Zhengzhou 450044, China
| | - Na Zhao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- School of Ecology and Environment, Anhui Normal University, Wuhu 241002, Anhui, China
| | - Jing Yang
- School of Environmental Science and Engineering, Shaanxi University of Science and Technology, Xian 710021, China
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
| | - Gang Song
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
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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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Zhang S, Shen Y, Wang S, Lin Z, Su R, Jin F, Zhang Y. Responses of the gut microbiota to environmental heavy metal pollution in tree sparrow (Passer montanus) nestlings. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 264:115480. [PMID: 37716068 DOI: 10.1016/j.ecoenv.2023.115480] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 08/22/2023] [Accepted: 09/12/2023] [Indexed: 09/18/2023]
Abstract
Gut microbiota plays a critical role in regulating the health and adaptation of wildlife. However, our understanding of how exposure to environmental heavy metals influences the gut microbiota of wild birds, particularly during the vulnerable and sensitive nestling stage, remains limited. In order to investigate the relationship between heavy metals and the gut microbiota, we analyzed the characteristics of gut microbiota and heavy metals levels in tree sparrow nestlings at different ages (6, 9 and 12-day-old). The study was conducted in two distinct areas: Baiyin (BY), which is heavily contaminated with heavy metals, and Liujiaxia (LJX), a relatively unpolluted area. Our result reveled a decrease in gut microbiota diversity and increased inter-individual variation among nestlings in BY. However, we also observed an increase in the abundance of bacterial groups and an up-regulation of bacterial metabolic functions associated with resistance to heavy metals toxicity in BY. Furthermore, we identified a metal-associated shift in the relative abundance of microbial taxa in 12-day-old tree sparrow nestlings in BY, particularly involving Aeromonadaceae, Ruminococcaceae and Pseudomonadaceae. Moreover, a significant positive correlation was found between the body condition of tree sparrow nestlings and the abundance of Bifidobacteriaceae in BY. Collectively, our findings indicate that the gut microbiota of tree sparrow nestlings is susceptible to heavy metals during early development. However, the results also highlight the presence of adaptive responses that enable them to effectively cope with environmental heavy metal pollution.
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Affiliation(s)
- Sheng Zhang
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Yue Shen
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Shengnan Wang
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Zhaocun Lin
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Rui Su
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Fei Jin
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Yingmei Zhang
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, School of Life Sciences, Lanzhou University, Lanzhou 730000, China.
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Schmiedová L, Kreisinger J, Kubovčiak J, Těšický M, Martin JF, Tomášek O, Kauzálová T, Sedláček O, Albrecht T. Gut microbiota variation between climatic zones and due to migration strategy in passerine birds. Front Microbiol 2023; 14:1080017. [PMID: 36819027 PMCID: PMC9928719 DOI: 10.3389/fmicb.2023.1080017] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 01/09/2023] [Indexed: 02/05/2023] Open
Abstract
Introduction Decreasing biotic diversity with increasing latitude is an almost universal macroecological pattern documented for a broad range of taxa, however, there have been few studies focused on changes in gut microbiota (GM) across climatic zones. Methods Using 16S rRNA amplicon profiling, we analyzed GM variation between temperate (Czechia) and tropical (Cameroon) populations of 99 passerine bird species and assessed GM similarity of temperate species migrating to tropical regions with that of residents/short-distance migrants and tropical residents. Our study also considered the possible influence of diet on GM. Results We observed no consistent GM diversity differences between tropical and temperate species. In the tropics, GM composition varied substantially between dry and rainy seasons and only a few taxa exhibited consistent differential abundance between tropical and temperate zones, irrespective of migration behavior and seasonal GM changes. During the breeding season, trans-Saharan migrant GM diverged little from species not overwintering in the tropics and did not show higher similarity to tropical passerines than temperate residents/short-distance migrants. Interestingly, GM of two temperate-breeding trans-Saharan migrants sampled in the tropical zone matched that of tropical residents and converged with other temperate species during the breeding season. Diet had a slight effect on GM composition of tropical species, but no effect on GM of temperate hosts. Discussion Consequently, our results demonstrate extensive passerine GM plasticity, the dominant role of environmental factors in its composition and limited effect of diet.
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Affiliation(s)
- Lucie Schmiedová
- Department of Zoology, Faculty of Science, Charles University, Prague, Czechia,Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czechia
| | - Jakub Kreisinger
- Department of Zoology, Faculty of Science, Charles University, Prague, Czechia,*Correspondence: Jakub Kreisinger,
| | - Jan Kubovčiak
- Department of Zoology, Faculty of Science, Charles University, Prague, Czechia
| | - Martin Těšický
- Department of Zoology, Faculty of Science, Charles University, Prague, Czechia
| | | | - Oldřich Tomášek
- Department of Zoology, Faculty of Science, Charles University, Prague, Czechia,Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czechia
| | - Tereza Kauzálová
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czechia
| | - Ondřej Sedláček
- Department of Ecology, Faculty of Science, Charles University, Prague, Czechia
| | - Tomáš Albrecht
- Department of Zoology, Faculty of Science, Charles University, Prague, Czechia,Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czechia
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Joakim RL, Irham M, Haryoko T, Rowe KMC, Dalimunthe Y, Anita S, Achmadi AS, McGuire JA, Perkins S, Bowie RCK. Geography and elevation as drivers of cloacal microbiome assemblages of a passerine bird distributed across Sulawesi, Indonesia. Anim Microbiome 2023; 5:4. [PMID: 36647179 PMCID: PMC9841722 DOI: 10.1186/s42523-022-00219-3] [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: 02/04/2022] [Accepted: 12/13/2022] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Empirical field studies allow us to view how ecological and environmental processes shape the biodiversity of our planet, but collecting samples in situ creates inherent challenges. The majority of empirical vertebrate gut microbiome research compares multiple host species against abiotic and biotic factors, increasing the potential for confounding environmental variables. To minimize these confounding factors, we focus on a single species of passerine bird found throughout the geologically complex island of Sulawesi, Indonesia. We assessed the effects of two environmental factors, geographic Areas of Endemism (AOEs) and elevation, as well as host sex on the gut microbiota assemblages of the Sulawesi Babbler, Pellorneum celebense, from three different mountains across the island. Using cloacal swabs, high-throughput-amplicon sequencing, and multiple statistical models, we identified the core microbiome and determined the signal of these three factors on microbial composition. RESULTS The five most prevalent bacterial phyla within the gut microbiome of P. celebense were Proteobacteria (32.6%), Actinobacteria (25.2%), Firmicutes (22.1%), Bacteroidetes (8.7%), and Plantomycetes (2.6%). These results are similar to those identified in prior studies of passeriform microbiomes. Overall, microbiota diversity decreased as elevation increased, irrespective of sex or AOE. A single ASV of Clostridium was enriched in higher elevation samples, while lower elevation samples were enriched with the genera Perlucidibaca (Family Moraxellaceae), Lachnoclostridium (Family Lachnospiraceae), and an unidentified species in the Family Pseudonocardiaceae. CONCLUSIONS While the core microbiota families recovered here are consistent with other passerine studies, the decreases in diversity as elevation increases has only been seen in non-avian hosts. Additionally, the increased abundance of Clostridium at high elevations suggests a potential microbial response to lower oxygen levels. This study emphasizes the importance of incorporating multiple statistical models and abiotic factors such as elevation in empirical microbiome research, and is the first to describe an avian gut microbiome from the island of Sulawesi.
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Affiliation(s)
- Rachael L. Joakim
- grid.254250.40000 0001 2264 7145Department of Biology, The City College of New York, 160 Convent Avenue, New York, NY 10031 USA ,grid.253482.a0000 0001 0170 7903The Graduate Center of The City University of New York, Biology Program, 365 5Th Ave, New York, NY 10016 USA ,grid.241963.b0000 0001 2152 1081Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY 10024 USA ,grid.241963.b0000 0001 2152 1081The Richard Gilder Graduate School, American Museum of Natural History, New York, NY 10024 USA
| | - Mohammad Irham
- Museum Zoologicum Bogoriense, Research Centre for Biology, National Research and Innovation Agency, Jl. Raya Jakarta - Bogor Km 46, Cibinong, 16911 Indonesia
| | - Tri Haryoko
- Museum Zoologicum Bogoriense, Research Centre for Biology, National Research and Innovation Agency, Jl. Raya Jakarta - Bogor Km 46, Cibinong, 16911 Indonesia
| | - Karen M. C. Rowe
- grid.436717.00000 0004 0500 6540Sciences Department, Museums Victoria, Carlton, VIC Australia ,grid.1008.90000 0001 2179 088XBioSciences Department, University of Melbourne, Parkville, VIC Australia
| | - Yohanna Dalimunthe
- Museum Zoologicum Bogoriense, Research Centre for Biology, National Research and Innovation Agency, Jl. Raya Jakarta - Bogor Km 46, Cibinong, 16911 Indonesia
| | - Syahfitri Anita
- Museum Zoologicum Bogoriense, Research Centre for Biology, National Research and Innovation Agency, Jl. Raya Jakarta - Bogor Km 46, Cibinong, 16911 Indonesia
| | - Anang S. Achmadi
- Museum Zoologicum Bogoriense, Research Centre for Biology, National Research and Innovation Agency, Jl. Raya Jakarta - Bogor Km 46, Cibinong, 16911 Indonesia
| | - Jimmy A. McGuire
- grid.47840.3f0000 0001 2181 7878Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA 94720 USA
| | - Susan Perkins
- grid.254250.40000 0001 2264 7145Department of Biology, The City College of New York, 160 Convent Avenue, New York, NY 10031 USA ,grid.253482.a0000 0001 0170 7903The Graduate Center of The City University of New York, Biology Program, 365 5Th Ave, New York, NY 10016 USA
| | - Rauri C. K. Bowie
- grid.47840.3f0000 0001 2181 7878Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA 94720 USA
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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: 20] [Impact Index Per Article: 10.0] [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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Schmiedová L, Tomášek O, Pinkasová H, Albrecht T, Kreisinger J. Variation in diet composition and its relation to gut microbiota in a passerine bird. Sci Rep 2022; 12:3787. [PMID: 35260644 PMCID: PMC8904835 DOI: 10.1038/s41598-022-07672-9] [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: 10/09/2021] [Accepted: 02/17/2022] [Indexed: 12/04/2022] Open
Abstract
Quality and quantity of food items consumed has a crucial effect on phenotypes. In addition to direct effects mediated by nutrient resources, an individual’s diet can also affect the phenotype indirectly by altering its gut microbiota, a potent modulator of physiological, immunity and cognitive functions. However, most of our knowledge of diet-microbiota interactions is based on mammalian species, whereas little is still known about these effects in other vertebrates. We developed a metabarcoding procedure based on cytochrome c oxidase I high-throughput amplicon sequencing and applied it to describe diet composition in breeding colonies of an insectivorous bird, the barn swallow (Hirundo rustica). To identify putative diet-microbiota associations, we integrated the resulting diet profiles with an existing dataset for faecal microbiota in the same individual. Consistent with previous studies based on macroscopic analysis of diet composition, we found that Diptera, Hemiptera, Coleoptera and Hymenoptera were the dominant dietary components in our population. We revealed pronounced variation in diet consumed during the breeding season, along with significant differences between nearby breeding colonies. In addition, we found no difference in diet composition between adults and juveniles. Finally, our data revealed a correlation between diet and faecal microbiota composition, even after statistical control for environmental factors affecting both diet and microbiota variation. Our study suggests that variation in diet induce slight but significant microbiota changes in a non-mammalian host relying on a narrow spectrum of items consumed.
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Affiliation(s)
- Lucie Schmiedová
- Department of Zoology, Faculty of Sciences, Charles University, Vinicna 7 CZ-128 44, Prague 2, Czech Republic.
| | - Oldřich Tomášek
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Hana Pinkasová
- Department of Zoology, Faculty of Sciences, Charles University, Vinicna 7 CZ-128 44, Prague 2, Czech Republic
| | - Tomáš Albrecht
- Department of Zoology, Faculty of Sciences, Charles University, Vinicna 7 CZ-128 44, Prague 2, Czech Republic. .,Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic.
| | - Jakub Kreisinger
- Department of Zoology, Faculty of Sciences, Charles University, Vinicna 7 CZ-128 44, Prague 2, Czech Republic
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Bodawatta KH, Klečková I, Klečka J, Pužejová K, Koane B, Poulsen M, Jønsson KA, Sam K. Specific gut bacterial responses to natural diets of tropical birds. Sci Rep 2022; 12:713. [PMID: 35027664 PMCID: PMC8758760 DOI: 10.1038/s41598-022-04808-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 12/28/2021] [Indexed: 12/20/2022] Open
Abstract
The composition of gut bacterial communities is strongly influenced by the host diet in many animal taxa. For birds, the effect of diet on the microbiomes has been documented through diet manipulation studies. However, for wild birds, most studies have drawn on literature-based information to decipher the dietary effects, thereby, overlooking individual variation in dietary intake. Here we examine how naturally consumed diets influence the composition of the crop and cloacal microbiomes of twenty-one tropical bird species, using visual and metabarcoding-based identification of consumed diets and bacterial 16S rRNA microbiome sequencing. We show that diet intakes vary markedly between individuals of the same species and that literature-based dietary guilds grossly underestimate intraspecific diet variability. Furthermore, despite an effect of literature-based dietary guild assignment of host taxa, the composition of natural diets does not align with crop and cloacal microbiome similarity. However, host-taxon specific gut bacterial lineages are positively correlated with specific diet items, indicating that certain microbes associate with different diet components in specific avian hosts. Consequently, microbiome composition is not congruent with the overall consumed diet composition of species, but specific components of a consumed diet lead to host-specific effects on gut bacterial taxa.
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Affiliation(s)
- Kasun H Bodawatta
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
| | - Irena Klečková
- Biology Centre of Czech Academy of Sciences, Institute of Entomology, Branisovska 31, 37005, Ceske Budejovice, Czech Republic
| | - Jan Klečka
- Biology Centre of Czech Academy of Sciences, Institute of Entomology, Branisovska 31, 37005, Ceske Budejovice, Czech Republic
| | - Kateřina Pužejová
- Biology Centre of Czech Academy of Sciences, Institute of Entomology, Branisovska 31, 37005, Ceske Budejovice, Czech Republic.,Faculty of Science, University of South Bohemia, Branisovska 1760, 37005, Ceske Budejovice, Czech Republic
| | - Bonny Koane
- New Guinea Binatang Research Centre, Madang, Papua New Guinea
| | - Michael Poulsen
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Knud A Jønsson
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Katerina Sam
- Biology Centre of Czech Academy of Sciences, Institute of Entomology, Branisovska 31, 37005, Ceske Budejovice, Czech Republic.,Faculty of Science, University of South Bohemia, Branisovska 1760, 37005, Ceske Budejovice, Czech Republic
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11
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Dong S, Xu S, Zhang J, Hussain R, Lu H, Ye Y, Mehmood K, Zhang H, Shang P. First Report of Fecal Microflora of Wild Bar-Headed Goose in Tibet Plateau. Front Vet Sci 2022; 8:791461. [PMID: 35083306 PMCID: PMC8785396 DOI: 10.3389/fvets.2021.791461] [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: 10/08/2021] [Accepted: 11/11/2021] [Indexed: 01/15/2023] Open
Abstract
The bar-headed goose (Anser indicus) has two black spots on its head. It is considered an important bird in China. It breeds in plateau lakes, especially saltwater lakes, and swamp areas. However, the intestinal flora of wild bar-headed geese in the Tibet Autonomous Region is currently not known. In this study, 16S rDNA sequencing was performed on the intestinal microbes of wild bar-headed geese. A total of 513,505 reads of raw data were obtained, and the results analyzed the average number of 128,376 ± 2,392 reads per sample. The microbiota of all samples consists of 10 main bacterial phyla, including Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, Cyanobacteria, Patescibacteria, Deferribacteres, Planctomy-cetes, Fusobacteria, and Tenericutes. The results indicated that Firmicutes (67.34%) was the predominant phylum, followed by Proteobacteria (29.03%) and Cyanobacteria (1.97%). In our research, we identified the intestinal flora of the wild bar-headed goose, which provides valuable information for further research on the gene function of the bar-headed goose and the intestinal flora of wild animals. These findings are also useful and valuable for genetic and high-altitude research in the Tibet Autonomous Region.
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Affiliation(s)
- Shixiong Dong
- College of Animal Science, Tibet Agriculture and Animal Husbandry College, Linzhi, China
- The Provincial and Ministerial Co-founded Collaborative Innovation Center for R & D, Tibet Agricultural and Animal Husbandry Resources, Linzhi, China
| | - Shijun Xu
- College of Animal Science, Tibet Agriculture and Animal Husbandry College, Linzhi, China
- The Provincial and Ministerial Co-founded Collaborative Innovation Center for R & D, Tibet Agricultural and Animal Husbandry Resources, Linzhi, China
| | - Jian Zhang
- College of Animal Science, Tibet Agriculture and Animal Husbandry College, Linzhi, China
- The Provincial and Ministerial Co-founded Collaborative Innovation Center for R & D, Tibet Agricultural and Animal Husbandry Resources, Linzhi, China
| | - Riaz Hussain
- Faculty of Veterinary and Animal Sciences, Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Hong Lu
- College of Animal Science, Tibet Agriculture and Animal Husbandry College, Linzhi, China
- The Provincial and Ministerial Co-founded Collaborative Innovation Center for R & D, Tibet Agricultural and Animal Husbandry Resources, Linzhi, China
| | - Yourong Ye
- College of Animal Science, Tibet Agriculture and Animal Husbandry College, Linzhi, China
- The Provincial and Ministerial Co-founded Collaborative Innovation Center for R & D, Tibet Agricultural and Animal Husbandry Resources, Linzhi, China
| | - Khalid Mehmood
- Faculty of Veterinary and Animal Sciences, Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Hui Zhang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Peng Shang
- College of Animal Science, Tibet Agriculture and Animal Husbandry College, Linzhi, China
- The Provincial and Ministerial Co-founded Collaborative Innovation Center for R & D, Tibet Agricultural and Animal Husbandry Resources, Linzhi, China
- *Correspondence: Peng Shang
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12
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Worsley SF, Davies CS, Mannarelli ME, Hutchings MI, Komdeur J, Burke T, Dugdale HL, Richardson DS. Gut microbiome composition, not alpha diversity, is associated with survival in a natural vertebrate population. Anim Microbiome 2021; 3:84. [PMID: 34930493 PMCID: PMC8685825 DOI: 10.1186/s42523-021-00149-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 11/28/2021] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND The vertebrate gut microbiome (GM) can vary substantially across individuals within the same natural population. Although there is evidence linking the GM to health in captive animals, very little is known about the consequences of GM variation for host fitness in the wild. Here, we explore the relationship between faecal microbiome diversity, body condition, and survival using data from the long-term study of a discrete natural population of the Seychelles warbler (Acrocephalus sechellensis) on Cousin Island. To our knowledge, this is the first time that GM differences associated with survival have been fully characterised for a natural vertebrate species, across multiple age groups and breeding seasons. RESULTS We identified substantial variation in GM community structure among sampled individuals, which was partially explained by breeding season (5% of the variance), and host age class (up to 1% of the variance). We also identified significant differences in GM community membership between adult birds that survived, versus those that had died by the following breeding season. Individuals that died carried increased abundances of taxa that are known to be opportunistic pathogens, including several ASVs in the genus Mycobacterium. However, there was no association between GM alpha diversity (the diversity of bacterial taxa within a sample) and survival to the next breeding season, or with individual body condition. Additionally, we found no association between GM community membership and individual body condition. CONCLUSIONS These results demonstrate that components of the vertebrate GM can be associated with host fitness in the wild. However, further research is needed to establish whether changes in bacterial abundance contribute to, or are only correlated with, differential survival; this will add to our understanding of the importance of the GM in the evolution of host species living in natural populations.
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Affiliation(s)
- Sarah F Worsley
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norfolk, NR4 7TJ, UK.
| | - Charli S Davies
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norfolk, NR4 7TJ, UK
| | - Maria-Elena Mannarelli
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norfolk, NR4 7TJ, UK
| | - Matthew I Hutchings
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Jan Komdeur
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, P.O. Box 11103, 9700 CC, Groningen, The Netherlands
| | - Terry Burke
- Department of Animal and Plant Sciences, NERC Biomolecular Analysis Facility, University of Sheffield, Sheffield, S10 2TN, UK
| | - Hannah L Dugdale
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, P.O. Box 11103, 9700 CC, Groningen, The Netherlands
- Faculty of Biological Sciences, School of Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - David S Richardson
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norfolk, NR4 7TJ, UK.
- Nature Seychelles, Roche Caiman, Mahé, Republic of Seychelles.
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13
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Costantini MS, Medeiros MCI, 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] [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 Hawaiʻi, 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 ʻakikiki (Oreomystis bairdi) and the ʻakekeʻe (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 ‘akekeʻe. Additionally, small but stastically significant differences in beta diversity also exist between sampling location and sexes in ʻakikiki. Conclusion ʻAkikiki and ʻakekeʻe 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 Hawai'i at Mānoa, Honolulu, Hawai'i, United States
| | - Matthew C I Medeiros
- School of Life Sciences, University of Hawai'i at Mānoa, Honolulu, Hawai'i, United States.,Pacific Biosciences Research Center, University of Hawai'i at Mānoa, Honolulu, Hawaií, United States
| | - Lisa H Crampton
- Hawai'i Division of Forestry and Wildlife, Hanapepe, Hawai'i, United States.,Pacific Cooperative Studies Unit, University of Hawai'i, Honolulu, Hawai'i, United States
| | - Floyd A Reed
- School of Life Sciences, University of Hawai'i at Mānoa, Honolulu, Hawai'i, United States
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14
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Bodawatta KH, Hird SM, Grond K, Poulsen M, Jønsson KA. Avian gut microbiomes taking flight. Trends Microbiol 2021; 30:268-280. [PMID: 34393028 DOI: 10.1016/j.tim.2021.07.003] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 07/18/2021] [Accepted: 07/20/2021] [Indexed: 02/07/2023]
Abstract
Birds harbor complex gut bacterial communities that may sustain their ecologies and facilitate their biological roles, distribution, and diversity. Research on gut microbiomes in wild birds is surging and it is clear that they are diverse and important - but strongly influenced by a series of environmental factors. To continue expanding our understanding of how the internal ecosystems of birds work in their natural settings, we believe the most pressing needs involve studies on the functional and evolutionary aspects of these symbioses. Here we summarize the state of the field and provide a roadmap for future studies on aspects that are pivotal to understanding the biology of avian gut microbiomes, emphasizing prospects for integrating gut microbiome work in avian conservation and host health monitoring.
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Affiliation(s)
- Kasun H Bodawatta
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
| | - 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
| | - Kirsten Grond
- Department of Biological Sciences, University of Alaska, Anchorage, AK, USA
| | - Michael Poulsen
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Knud A Jønsson
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
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15
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Pekarsky S, Corl A, Turjeman S, Kamath PL, Getz WM, Bowie RCK, Markin Y, Nathan R. Drivers of change and stability in the gut microbiota of an omnivorous avian migrant exposed to artificial food supplementation. Mol Ecol 2021; 30:4723-4739. [PMID: 34260783 DOI: 10.1111/mec.16079] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 06/14/2021] [Accepted: 07/01/2021] [Indexed: 12/21/2022]
Abstract
Human activities shape resources available to wild animals, impacting diet and probably altering their microbiota and overall health. We examined drivers shaping microbiota profiles of common cranes (Grus grus) in agricultural habitats by comparing gut microbiota and crane movement patterns (GPS-tracking) over three periods of their migratory cycle, and by analysing the effect of artificially supplemented food provided as part of a crane-agriculture management programme. We sampled faecal droppings in Russia (nonsupplemented, premigration) and in Israel in late autumn (nonsupplemented, postmigration) and winter (supplemented and nonsupplemented, wintering). As supplemented food is typically homogenous, we predicted lower microbiota diversity and different composition in birds relying on supplementary feeding. We did not observe changes in microbial diversity with food supplementation, as diversity differed only in samples from nonsupplemented wintering sites. However, both food supplementation and season affected bacterial community composition and led to increased abundance of specific genera (mostly Firmicutes). Cranes from the nonsupplemented groups spent most of their time in agricultural fields, probably feeding on residual grain when available, while food-supplemented cranes spent most of their time at the feeding station. Thus, nonsupplemented and food-supplemented diets probably diverge only in winter, when crop rotation and depletion of anthropogenic resources may lead to a more variable diet in nonsupplemented sites. Our results support the role of diet in structuring bacterial communities and show that they undergo both seasonal and human-induced shifts. Movement analyses provide important clues regarding host diet and behaviour towards understanding how human-induced changes shape the gut microbiota in wild animals.
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Affiliation(s)
- Sasha Pekarsky
- Movement Ecology Laboratory, Department of Ecology, Evolution & Behavior, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ammon Corl
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, California, USA
| | - Sondra Turjeman
- Movement Ecology Laboratory, Department of Ecology, Evolution & Behavior, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Pauline L Kamath
- School of Food and Agriculture, University of Maine, Orono, Maine, USA
| | - Wayne M Getz
- Department of Environmental Science, Policy & Management, University of California, Berkeley, California, USA.,School Mathematical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Rauri C K Bowie
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, California, USA.,Department of Integrative Biology, University of California, Berkeley, California, USA
| | - Yuri Markin
- Oksky State Reserve, pos. Brykin Bor, Spassky raion, Ryazanskaya oblast, Russia
| | - Ran Nathan
- Movement Ecology Laboratory, Department of Ecology, Evolution & Behavior, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
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16
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Bodawatta KH, Koane B, Maiah G, Sam K, Poulsen M, Jønsson KA. Species-specific but not phylosymbiotic gut microbiomes of New Guinean passerine birds are shaped by diet and flight-associated gut modifications. Proc Biol Sci 2021; 288:20210446. [PMID: 33878920 DOI: 10.1098/rspb.2021.0446] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Animal hosts have evolved intricate associations with microbial symbionts, where both depend on each other for particular functions. In many cases, these associations lead to phylosymbiosis, where phylogenetically related species harbour compositionally more similar microbiomes than distantly related species. However, evidence for phylosymbiosis is either weak or lacking in gut microbiomes of flying vertebrates, particularly in birds. To shed more light on this phenomenon, we compared cloacal microbiomes of 37 tropical passerine bird species from New Guinea using 16S rRNA bacterial gene sequencing. We show a lack of phylosymbiosis and document highly variable microbiomes. Furthermore, we find that gut bacterial community compositions are species-specific and tend to be shaped by host diet but not sampling locality, potentially driven by the similarities in habitats used by individual species. We further show that flight-associated gut modifications, coupled with individual dietary differences, shape gut microbiome structure and variation, contributing to the lack of phylosymbiosis. These patterns indicate that the stability of symbiosis may depend on microbial functional diversity rather than taxonomic composition. Furthermore, the more variable and fluid host-microbe associations suggest probable disparities in the potential for coevolution between bird host species and microbial symbionts.
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Affiliation(s)
- Kasun H Bodawatta
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Bonny Koane
- New Guinea Binatang Research Centre, Madang, Papua New Guinea
| | - Gibson Maiah
- New Guinea Binatang Research Centre, Madang, Papua New Guinea
| | - Katerina Sam
- Biology Centre of Czech Academy of Sciences, Institute of Entomology, Ceske Budejovice, Branisovska 31, 37005, Czech Republic.,Faculty of Science, University of South Bohemia, Ceske Budejovice, Branisovska 1760, 37005, Czech Republic
| | - Michael Poulsen
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Knud A Jønsson
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
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17
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Gunasekaran M, Trabelcy B, Izhaki I, Halpern M. Direct Evidence That Sunbirds' Gut Microbiota Degrades Floral Nectar's Toxic Alkaloids. Front Microbiol 2021; 12:639808. [PMID: 33815326 PMCID: PMC8018289 DOI: 10.3389/fmicb.2021.639808] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 02/08/2021] [Indexed: 12/01/2022] Open
Abstract
Orange-tufted sunbirds (Cinnyris osea) feed on the nectar of the tobacco tree (Nicotiana glauca) which contains toxic pyridine alkaloids characterized by high concentrations of anabasine and much lower concentrations of nicotine. We aimed at determining whether the gut microbiota of sunbirds harbors bacterial species that enable the birds to cope with these toxic alkaloids. An in vivo experiment that included 12 birds showed that inducing dysbiosis in sunbirds’ guts by the addition of sulfamethoxazole and trimethoprim, significantly reduced the birds’ ability to degrade anabasine (n = 3) compared to control birds (n = 3) with undisturbed microbiota. Sunbirds whose gut bacterial communities were altered by the antibacterial agents and who were fed with added nicotine, also showed a lower percentage of nicotine degradation (n = 3) in their excreta compared to the sunbirds with undisturbed microbiota (n = 3), though this difference was not significant. In an in vitro experiment, we studied the ability of Lactococcus lactis, Enterobacter hormaechei, Chryseobacterium gleum, Kocuria palustris, and Methylorubrum populi that were isolated from sunbirds’ excreta, to degrade anabasine and nicotine. By using gas chromatography-mass spectrometry (GC-MS) analysis, we successfully demonstrated, for the first time, the ability of these species to degrade the focal secondary metabolites. Our findings demonstrate the role of gut bacteria in detoxifying toxic secondary metabolites found in the N. glauca nectar. The degradation products may supply the birds with nitrogen which is scarce in nectar-rich diets. These findings support another role of bacteria in mediating the interactions between plants and their pollinators.
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Affiliation(s)
- Mohanraj Gunasekaran
- Department of Evolutionary and Environmental Biology, Faculty of Natural Sciences, University of Haifa, Haifa, Israel
| | - Beny Trabelcy
- Department of Evolutionary and Environmental Biology, Faculty of Natural Sciences, University of Haifa, Haifa, Israel
| | - Ido Izhaki
- Department of Evolutionary and Environmental Biology, Faculty of Natural Sciences, University of Haifa, Haifa, Israel
| | - Malka Halpern
- Department of Evolutionary and Environmental Biology, Faculty of Natural Sciences, University of Haifa, Haifa, Israel.,Department of Biology and Environment, Faculty of Natural Sciences, University of Haifa, Tivon, Israel
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18
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Localization of bacterial communities within gut compartments across Cephalotes turtle ants. Appl Environ Microbiol 2021; 87:AEM.02803-20. [PMID: 33579688 PMCID: PMC8091110 DOI: 10.1128/aem.02803-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Microbial communities within the animal digestive tract often provide important functions for their hosts. The composition of eukaryotes' gut bacteria can be shaped by host diet, vertical bacterial transmission, and physiological variation within the digestive tract. In several ant taxa, recent findings have demonstrated that nitrogen provisioning by symbiotic bacteria makes up for deficiencies in herbivorous diets. Using 16S rRNA amplicon sequencing and qPCR, this study examined bacterial communities at a fine scale across one such animal group, the turtle ant genus Cephalotes We analyzed the composition and colonization density across four portions of the digestive tract to understand how bacterial diversity is structured across gut compartments, potentially allowing for specific metabolic functions of benefit to the host. In addition, we aimed to understand if caste differentiation or host relatedness influences the gut bacterial communities of Cephalotes ants. Microbial communities were found to vary strongly across Cephalotes gut compartments in ways that transcend both caste and host phylogeny. Despite this, caste and host phylogeny still have detectable effects. We demonstrated microbial community divergence across gut compartments, possibly due to the varying function of each gut compartment for digestion.IMPORTANCE Gut compartments play an important role in structuring the microbial community within individual ants. The gut chambers of the turtle ant digestive tract differ remarkably in symbiont abundance and diversity. Furthermore, caste type explains some variation in the microbiome composition. Finally, the evolutionary history of the Cephalotes species structures the microbiome in our study, which elucidates a trend in which related ants maintain related microbiomes, conceivably owing to co-speciation. Amazingly, gut compartment-specific signatures of microbial diversity, relative abundance, composition, and abundance have been conserved over Cephalotes evolutionary history, signifying that this symbiosis has been largely stable for over 50 million years.
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19
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Sottas C, Schmiedová L, Kreisinger J, Albrecht T, Reif J, Osiejuk TS, Reifová R. Gut microbiota in two recently diverged passerine species: evaluating the effects of species identity, habitat use and geographic distance. BMC Ecol Evol 2021; 21:41. [PMID: 33691625 PMCID: PMC7948333 DOI: 10.1186/s12862-021-01773-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 03/01/2021] [Indexed: 01/01/2023] Open
Abstract
Background It has been proposed that divergence in the gut microbiota composition between incipient species could contribute to their reproductive isolation. Nevertheless, empirical evidence for the role of gut microbiota in speciation is scarce. Moreover, it is still largely unknown to what extent closely related species in the early stages of speciation differ in their gut microbiota composition, especially in non-mammalian taxa, and which factors drive the divergence. Here we analysed the gut microbiota in two closely related passerine species, the common nightingale (Luscinia megarhynchos) and the thrush nightingale (Luscinia luscinia). The ranges of these two species overlap in a secondary contact zone, where both species occasionally hybridize and where interspecific competition has resulted in habitat use differentiation. Results We analysed the gut microbiota from the proximal, middle and distal part of the small intestine in both sympatric and allopatric populations of the two nightingale species using sequencing of bacterial 16S rRNA. We found small but significant differences in the microbiota composition among the three gut sections. However, the gut microbiota composition in the two nightingale species did not differ significantly between either sympatric or allopatric populations. Most of the observed variation in the gut microbiota composition was explained by inter-individual differences. Conclusions To our knowledge, this is the first attempt to assess the potential role of the gut microbiota in bird speciation. Our results suggest that neither habitat use, nor geographical distance, nor species identity have strong influence on the nightingale gut microbiota composition. This suggests that changes in the gut microbiota composition are unlikely to contribute to reproductive isolation in these passerine birds. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-021-01773-1.
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Affiliation(s)
- Camille Sottas
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 44, Prague, Czech Republic.
| | - Lucie Schmiedová
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 44, Prague, Czech Republic
| | - Jakub Kreisinger
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 44, Prague, Czech Republic
| | - Tomáš Albrecht
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 44, Prague, Czech Republic.,Institute of Vertebrate Biology, Czech Academy of Sciences, Květná 8, Brno, 603 65, Czech Republic
| | - Jiří Reif
- Faculty of Science, Institute for Environmental Studies, Charles University, Prague, Czech Republic.,Department of Zoology and Laboratory of Ornithology, Faculty of Science, Palacky University, Olomouc, Czech Republic
| | - Tomasz S Osiejuk
- Department of Behavioural Ecology, Institute of Environmental Biology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - Radka Reifová
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 44, Prague, Czech Republic
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20
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Maraci Ö, Antonatou-Papaioannou A, Jünemann S, Castillo-Gutiérrez O, Busche T, Kalinowski J, Caspers BA. The Gut Microbial Composition Is Species-Specific and Individual-Specific in Two Species of Estrildid Finches, the Bengalese Finch and the Zebra Finch. Front Microbiol 2021; 12:619141. [PMID: 33679641 PMCID: PMC7933042 DOI: 10.3389/fmicb.2021.619141] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 01/25/2021] [Indexed: 12/29/2022] Open
Abstract
Microbial communities residing in the gastrointestinal tracts of animals have profound impacts on the physiological processes of their hosts. In humans, host-specific and environmental factors likely interact together to shape gut microbial communities, resulting in remarkable inter-individual differences. However, we still lack a full understanding of to what extent microbes are individual-specific and controlled by host-specific factors across different animal taxa. Here, we document the gut microbial characteristics in two estrildid finch species, the Bengalese finch (Lonchura striata domestica) and the zebra finch (Taeniopygia guttata) to investigate between-species and within-species differences. We collected fecal samples from breeding pairs that were housed under strictly controlled environmental and dietary conditions. All individuals were sampled at five different time points over a range of 120 days covering different stages of the reproductive cycle. We found significant species-specific differences in gut microbial assemblages. Over a period of 3 months, individuals exhibited unique, individual-specific microbial profiles. Although we found a strong individual signature in both sexes, within-individual variation in microbial communities was larger in males of both species. Furthermore, breeding pairs had more similar microbial profiles, compared to randomly chosen males and females. Our study conclusively shows that host-specific factors contribute structuring of gut microbiota.
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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
- Faculty of Technology, Bielefeld University, Bielefeld, Germany
- Center for Biotechnology (CeBiTec), 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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21
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Bodawatta KH, Freiberga I, Puzejova K, Sam K, Poulsen M, Jønsson KA. Flexibility and resilience of great tit (Parus major) gut microbiomes to changing diets. Anim Microbiome 2021; 3:20. [PMID: 33602335 PMCID: PMC7893775 DOI: 10.1186/s42523-021-00076-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 01/12/2021] [Indexed: 12/13/2022] Open
Abstract
Background Gut microbial communities play important roles in nutrient management and can change in response to host diets. The extent of this flexibility and the concomitant resilience is largely unknown in wild animals. To untangle the dynamics of avian-gut microbiome symbiosis associated with diet changes, we exposed Parus major (Great tits) fed with a standard diet (seeds and mealworms) to either a mixed (seeds, mealworms and fruits), a seed, or a mealworm diet for 4 weeks, and examined the flexibility of gut microbiomes to these compositionally different diets. To assess microbiome resilience (recovery potential), all individuals were subsequently reversed to a standard diet for another 4 weeks. Cloacal microbiomes were collected weekly and characterised through sequencing the v4 region of the 16S rRNA gene using Illumina MiSeq. Results Initial microbiomes changed significantly with the diet manipulation, but the communities did not differ significantly between the three diet groups (mixed, seed and mealworm), despite multiple diet-specific changes in certain bacterial genera. Reverting birds to the standard diet led only to a partial recovery in gut community compositions. The majority of the bacterial taxa that increased significantly during diet manipulation decreased in relative abundance after reversion to the standard diet; however, bacterial taxa that decreased during the manipulation rarely increased after diet reversal Conclusions The gut microbial response and partial resilience to dietary changes support that gut bacterial communities of P. major play a role in accommodating dietary changes experienced by wild avian hosts. This may be a contributing factor to the relaxed association between microbiome composition and the bird phylogeny. Our findings further imply that interpretations of wild bird gut microbiome analyses from single-time point sampling, especially for omnivorous species or species with seasonally changing diets, should be done with caution. The partial community recovery implies that ecologically relevant diet changes (e.g., seasonality and migration) open up gut niches that may be filled by previously abundant microbes or replaced by different symbiont lineages, which has important implications for the integrity and specificity of long-term avian-symbiont associations. Supplementary Information The online version contains supplementary material available at 10.1186/s42523-021-00076-6.
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Affiliation(s)
- Kasun H Bodawatta
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
| | - Inga Freiberga
- Biology Centre of Czech Academy of Sciences, Institute of Entomology, Ceske Budejovice, Czech Republic
| | - Katerina Puzejova
- Biology Centre of Czech Academy of Sciences, Institute of Entomology, Ceske Budejovice, Czech Republic.,Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic
| | - Katerina Sam
- Biology Centre of Czech Academy of Sciences, Institute of Entomology, Ceske Budejovice, Czech Republic.,Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic
| | - Michael Poulsen
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Knud A Jønsson
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
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22
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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: 5] [Impact Index Per Article: 1.3] [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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23
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Bodawatta KH, Schierbech SK, Petersen NR, Sam K, Bos N, Jønsson KA, Poulsen M. Great Tit ( Parus major) Uropygial Gland Microbiomes and Their Potential Defensive Roles. Front Microbiol 2020; 11:1735. [PMID: 32849371 PMCID: PMC7401573 DOI: 10.3389/fmicb.2020.01735] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 07/02/2020] [Indexed: 12/16/2022] Open
Abstract
The uropygial gland (preen gland) of birds plays an important role in maintaining feather integrity and hygiene. Although a few studies have demonstrated potential defensive roles of bacteria residing within these glands, the diversity and functions of the uropygial gland microbiota are largely unknown. Therefore, we investigated the microbiota of great tit (Parus major) uropygial glands through both isolation of bacteria (culture-dependent) and 16S rRNA amplicon sequencing (culture-independent). Co-culture experiments of selected bacterial isolates with four known feather-degrading bacteria (Bacillus licheniformis, Kocuria rhizophila, Pseudomonas monteilii, and Dermacoccus nishinomiyaensis), two non-feather degrading feather bacteria, one common soil bacterial pathogen and two common fungal pathogens enabled us to evaluate the potential antimicrobial properties of these isolates. Our results show major differences between bacterial communities characterized using culture-dependent and -independent approaches. In the former, we were only able to isolate 12 bacterial genera (dominated by members of the Firmicutes and Actinobacteria), while amplicon sequencing identified 110 bacterial genera (dominated by Firmicutes, Bacteroidetes, and Proteobacteria). Uropygial gland bacterial isolates belonging to the genera Bacillus and Kocuria were able to suppress the growth of four of the nine tested antagonists, attesting to potential defensive roles. However, these bacterial genera were infrequent in our MiSeq results suggesting that the isolated bacteria may not be obligate gland symbionts. Furthermore, bacterial functional predictions using 16S rRNA sequences also revealed the ability of uropygial gland bacteria to produce secondary metabolites with antimicrobial properties, such as terpenes. Our findings support that uropygial gland bacteria may play a role in feather health and that bacterial symbionts might act as defensive microbes. Future investigations of these bacterial communities, with targeted approaches (e.g., bacterial isolation and chemical analyses), are thus warranted to improve our understanding of the evolution and function of these host-microbe interactions.
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Affiliation(s)
- Kasun H. Bodawatta
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Signe K. Schierbech
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Nanna R. Petersen
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Katerina Sam
- Biology Centre of Czech Academy of Sciences, Institute of Entomology, České Budějovice, Czechia
- Faculty of Science, University of South Bohemia, České Budějovice, Czechia
| | - Nick Bos
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - 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
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24
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Trevelline BK, Sosa J, Hartup BK, Kohl KD. A bird's-eye view of phylosymbiosis: weak signatures of phylosymbiosis among all 15 species of cranes. Proc Biol Sci 2020; 287:20192988. [PMID: 32183630 DOI: 10.1098/rspb.2019.2988] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
In numerous animal clades, the evolutionary history of host species drives patterns of gut microbial community structure, resulting in more divergent microbiota with increasing phylogenetic distance between hosts. This phenomenon, termed phylosymbiosis, has been observed in diverse evolutionary lineages, but has been difficult to detect in birds. Previous tests of phylosymbiosis among birds have been conducted using wild individuals, and thus interspecific differences in diet and environment may have masked a phylogenetic signal. Therefore, we tested for phylosymbiosis among all 15 species of cranes (family Gruidae) housed in the same captive environment and maintained on identical diets. 16S rRNA sequencing revealed that crane species harbour distinct gut microbiota. Overall, we detected marginally significant patterns of phylosymbiosis, the strength of which was increased when including the estimates of absolute microbial abundance (rather than relative abundance) derived from microbial densities determined by flow cytometry. Using this approach, we detected the statistically significant signatures of phylosymbiosis only after removing male cranes from our analysis, suggesting that using mixed-sex animal cohorts may prevent the detection of phylosymbiosis. Though weak compared with mammals (and especially insects), these results provide evidence of phylosymbiosis in birds. We discuss the potential differences between birds and mammals, such as transmission routes and host filtering, that may underlie the differences in the strength of phylosymbiosis.
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Affiliation(s)
- Brian K Trevelline
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jahree Sosa
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Barry K Hartup
- Department of Conservation Medicine, International Crane Foundation, Baraboo, WI, USA.,School of Veterinary Medicine, University of Wisconsin, Madison, WI, USA
| | - Kevin D Kohl
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
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25
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Bodawatta KH, Puzejova K, Sam K, Poulsen M, Jønsson KA. Cloacal swabs and alcohol bird specimens are good proxies for compositional analyses of gut microbial communities of Great tits (Parus major). Anim Microbiome 2020; 2:9. [PMID: 33499943 PMCID: PMC7807456 DOI: 10.1186/s42523-020-00026-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 02/25/2020] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Comprehensive studies of wild bird microbiomes are often limited by difficulties of sample acquisition. However, widely used non-invasive cloacal swab methods and under-explored museum specimens preserved in alcohol provide promising avenues to increase our understanding of wild bird microbiomes, provided that they accurately portray natural microbial community compositions. To investigate this assertion, we used 16S rRNA amplicon sequencing of Great tit (Parus major) gut microbiomes to compare 1) microbial communities obtained from dissected digestive tract regions and cloacal swabs, and 2) microbial communities obtained from freshly dissected gut regions and from samples preserved in alcohol for 2 weeks or 2 months, respectively. RESULTS We found no significant differences in alpha diversities in communities of different gut regions and cloacal swabs (except in OTU richness between the dissected cloacal region and the cloacal swabs), or between fresh and alcohol preserved samples. However, we did find significant differences in beta diversity and community composition of cloacal swab samples compared to different gut regions. Despite these community-level differences, swab samples qualitatively captured the majority of the bacterial diversity throughout the gut better than any single compartment. Bacterial community compositions of alcohol-preserved specimens did not differ significantly from freshly dissected samples, although some low-abundant taxa were lost in the alcohol preserved specimens. CONCLUSIONS Our findings suggest that cloacal swabs, similar to non-invasive fecal sampling, qualitatively depict the gut microbiota composition without having to collect birds to extract the full digestive tract. The satisfactory depiction of gut microbial communities in alcohol preserved samples opens up for the possibility of using an enormous resource readily available through museum collections to characterize bird gut microbiomes. The use of extensive museum specimen collections of birds for microbial gut analyses would allow for investigations of temporal patterns of wild bird gut microbiomes, including the potential effects of climate change and anthropogenic impacts. Overall, the utilization of cloacal swabs and museum alcohol specimens can positively impact bird gut microbiome research to help increase our understanding of the role and evolution of wild bird hosts and gut microbial communities.
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Affiliation(s)
- Kasun H. Bodawatta
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Katerina Puzejova
- Biology Centre of Czech Academy of Sciences, Institute of Entomology, Branisovska 31, Ceske Budejovice, Czech Republic
- Faculty of Science, University of South Bohemia, Branisovska 1760, Ceske Budejovice, Czech Republic
| | - Katerina Sam
- Biology Centre of Czech Academy of Sciences, Institute of Entomology, Branisovska 31, Ceske Budejovice, Czech Republic
- Faculty of Science, University of South Bohemia, Branisovska 1760, Ceske Budejovice, Czech Republic
| | - Michael Poulsen
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Knud A. Jønsson
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
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26
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Teyssier A, Matthysen E, Hudin NS, de Neve L, White J, Lens L. Diet contributes to urban-induced alterations in gut microbiota: experimental evidence from a wild passerine. Proc Biol Sci 2020; 287:20192182. [PMID: 32019440 DOI: 10.1098/rspb.2019.2182] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Urban sprawl increasingly affects the ecology of natural populations, including host-microbiota interactions, with observed differences in the gut microbiota between urban and rural hosts. While different mechanisms could explain this pattern, dietary uptake constitutes a likely candidate. To assess the contribution of diet in explaining urban-rural variation in gut microbiota, we performed an aviary experiment in which urban and rural house sparrows were fed with mimics of urban or rural diets. Before the experiment, rural sparrows hosted more diverse gut communities, with a higher relative abundance of Enterococcaceae and Staphylococcaceae and lower abundance of genes involved in xenobiotic degradation and lipid metabolism than their urban counterparts. The experimental diets significantly altered gut microbiota α- and β-diversity and taxonomic composition, with the strongest shifts occurring in individuals exposed to contrasting diets. Overall, diet-induced shifts resembled initial differences between free-ranging urban and rural hosts. Furthermore, rural diet had a positive impact on urban host body mass but only in hosts with the highest initial gut diversity. Overall, our results indicate that diet constitutes an important factor contributing to differences in gut microbiota along the urbanization gradient and provide new insights on possible fitness consequences of a reduced gut diversity in urban settings.
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Affiliation(s)
- Aimeric Teyssier
- Terrestrial Ecology Unit, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium.,Evolutionary Ecology Group, Department of Biology, University of Antwerp, Wilrijk, Belgium.,Evolution and Diversité Biologique, UMR 5174 CNRS-Université Paul Sabatier-IRD, 118 route de Narbonne, 31062 Toulouse, France
| | - Erik Matthysen
- Evolutionary Ecology Group, Department of Biology, University of Antwerp, Wilrijk, Belgium
| | - Noraine Salleh Hudin
- Terrestrial Ecology Unit, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium.,Department of Biological Sciences, Faculty of Science and Mathematics, Universiti Pendidikan Sultan Idris, 35900 Tanjong Malim, Perak, Malaysia
| | - Liesbeth de Neve
- Terrestrial Ecology Unit, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Joël White
- Evolution and Diversité Biologique, UMR 5174 CNRS-Université Paul Sabatier-IRD, 118 route de Narbonne, 31062 Toulouse, France.,ENSFEA, 2 route de Narbonne, 31326 Castanet-Tolosan, France
| | - Luc Lens
- Terrestrial Ecology Unit, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium
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27
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Laviad-Shitrit S, Izhaki I, Lalzar M, Halpern M. Comparative Analysis of Intestine Microbiota of Four Wild Waterbird Species. Front Microbiol 2019; 10:1911. [PMID: 31481943 PMCID: PMC6711360 DOI: 10.3389/fmicb.2019.01911] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 08/05/2019] [Indexed: 01/07/2023] Open
Abstract
Waterbirds are ubiquitous and globally distributed. Yet, studies on wild waterbirds' gut microbiota are still rare. Our aim was to explore and compare the gut microbial community composition of wild waterbird species. Four wild waterbird species that are either wintering or all-year residents in Israel were studied: great cormorants, little egrets, black-crowned night herons and black-headed gulls. For each bird, three intestinal sections were sampled; anterior, middle and posterior. No significant differences were found among the microbiota compositions in the three intestine sections of each individual bird. Each waterbird species had a unique microbial composition. The gut microbiota of the black-headed gulls' fundamentally deviated from that of the other bird species, probably due to a very high abundance (58.8%) of the genus Catellicoccus (Firmicutes). Our results suggest a correlation between the waterbird species' phylogeny and their intestine microbial community hierarchical tree, which evinced phylosymbiosis. This recent coinage stands for eco-evolutionary patterns between the host phylogeny and its microbiota composition. We conclude that eco-evolutionary processes termed phylosymbiosis may occur between wild waterbird species and their gut microbial community composition.
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Affiliation(s)
- Sivan Laviad-Shitrit
- Department of Evolutionary and Environmental Biology, Faculty of Natural Sciences, University of Haifa, Haifa, Israel
| | - Ido Izhaki
- Department of Evolutionary and Environmental Biology, Faculty of Natural Sciences, University of Haifa, Haifa, Israel
| | - Maya Lalzar
- Bioinformatics Service Unit, University of Haifa, Haifa, Israel
| | - Malka Halpern
- Department of Evolutionary and Environmental Biology, Faculty of Natural Sciences, University of Haifa, Haifa, Israel.,Department of Biology and Environment, Faculty of Natural Sciences, University of Haifa at Oranim, Tivon, Israel
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28
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Shi Z, Rothrock MJ, Ricke SC. Applications of Microbiome Analyses in Alternative Poultry Broiler Production Systems. Front Vet Sci 2019; 6:157. [PMID: 31179291 PMCID: PMC6543280 DOI: 10.3389/fvets.2019.00157] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Accepted: 05/07/2019] [Indexed: 01/01/2023] Open
Abstract
While most of the focus on poultry microbiome research has been directed toward conventional poultry production, there is increasing interest in characterizing microbial populations originating from alternative or non-conventional poultry production. This is in part due to the growing general popularity in locally produced foods and more specifically the attractiveness of free-range or pasture raised poultry. Most of the focus of microbiome characterization in pasture flock birds has been on live bird production, primarily on the gastrointestinal tract. Interest in environmental impacts on production responses and management strategies have been key factors for comparative microbiome studies. This has important ramifications since these birds are not only raised under different conditions, but the grower cycle can be longer and in some cases slower growing breeds used. The impact of different feed additives is also of interest with some microbiome-based studies having examined the effect of feeding these additives to birds grown under pasture flock conditions. In the future, microbiome research approaches offer unique opportunities to develop better live bird management strategies and design optimal feed additive approaches for pasture flock poultry production systems.
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Affiliation(s)
- Zhaohao Shi
- Center for Food Safety, Food Science Department, University of Arkansas, Fayetteville, AR, United States
| | - Michael J Rothrock
- Egg Safety and Quality Research Unit, U.S. National Poultry Research Center, USDA-ARS, Athens, GA, United States
| | - Steven C Ricke
- Center for Food Safety, Food Science Department, University of Arkansas, Fayetteville, AR, United States
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29
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Abstract
Understanding functional capacities of gut microbiomes is important to improve our understanding of symbiotic associations. Here, we use peptide-based functional annotation to show that the gut microbiomes of fungus-farming termites code for a wealth of enzymes that likely target the fungal diet the termites eat. Comparisons to other termites showed that fungus-growing termite guts have relatively more fungal cell wall-degrading enzyme genes, whereas wood-feeding termite gut communities have relatively more plant cell wall-degrading enzyme genes. Across termites with different diets, the dominant biomass-degrading enzymes are predominantly coded for by the most abundant bacterial taxa, suggesting tight links between diet and gut community compositions. Termites forage on a range of substrates, and it has been suggested that diet shapes the composition and function of termite gut bacterial communities. Through comparative analyses of gut metagenomes in nine termite species with distinct diets, we characterize bacterial community compositions and use peptide-based functional annotation method to determine biomass-degrading enzymes and the bacterial taxa that encode them. We find that fungus-growing termite guts have relatively more fungal cell wall-degrading enzyme genes, while wood-feeding termite gut communities have relatively more plant cell wall-degrading enzyme genes. Interestingly, wood-feeding termite gut bacterial genes code for abundant chitinolytic enzymes, suggesting that fungal biomass within the decaying wood likely contributes to gut bacterial or termite host nutrition. Across diets, the dominant biomass-degrading enzymes are predominantly coded for by the most abundant bacterial taxa, suggesting tight links between diet and gut community composition, with the most marked difference being the communities coding for the mycolytic capacity of the fungus-growing termite gut. IMPORTANCE Understanding functional capacities of gut microbiomes is important to improve our understanding of symbiotic associations. Here, we use peptide-based functional annotation to show that the gut microbiomes of fungus-farming termites code for a wealth of enzymes that likely target the fungal diet the termites eat. Comparisons to other termites showed that fungus-growing termite guts have relatively more fungal cell wall-degrading enzyme genes, whereas wood-feeding termite gut communities have relatively more plant cell wall-degrading enzyme genes. Across termites with different diets, the dominant biomass-degrading enzymes are predominantly coded for by the most abundant bacterial taxa, suggesting tight links between diet and gut community compositions.
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