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Gul N, Qasim M, Khan SN, Rehman KU, Alissa M, Abusalim GS, Alghamdi SA, Alamoudi AJ, Kelabi E, Albaqami FMK. Winged odyssey: Profiling bacterial vistas in migratory avifauna via 16S rRNA sequencing. Microb Pathog 2024; 196:106980. [PMID: 39326805 DOI: 10.1016/j.micpath.2024.106980] [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: 06/28/2024] [Revised: 09/04/2024] [Accepted: 09/23/2024] [Indexed: 09/28/2024]
Abstract
Avian migration is an intrinsic biological phenomenon that involves trans-boundary movements to evade adverse ecological circumstances. During migration, avian gut bacterial taxa may serve as a potential source of bacterial dissemination via fecal contamination at stop-over sites. Therefore, bacterial taxa composition as well as diversities were investigated employing 16S rRNA sequencing in fecal samples collected from flocks of seven migratory avian species visiting southern districts of Khyber Pakhtunkhwa, Pakistan. The analysis revealed that Grus virgo exhibits the highest alpha diversity, followed by Aythya ferina while G. grus reflects lowest diversity among all the migratory avian fecal samples. The findings depicted significant variations in the bacterial beta diversities of migratory avifauna. At phylum level, Firmicutes, Proteobacteria, and Actinobacteriota showed the highest relative abundance in Plegadis falcinellus, Chlamydotis undulata and Aythya ferina respectively. Further exploration within phyla elucidates finer-scale taxonomic differences at the family and genus levels. This study identified potential pathogenic bacteria such as Staphylococcus, Streptococcus, Enterococcus, Proteus, Clostridium sensu stricto 1, Fusobacterium and Escherichia that offers valuable insight into the microbiological hazards associated with migratory birds. Although pathogenicity was not directly assessed, the observed relative abundance of opportunistic bacterial genera suggests continuous surveillance of gut bacterial community during migration to safeguard avian biodiversity and mitigate escalating threats of infection emergence and dissemination.
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Affiliation(s)
- Naila Gul
- Department of Zoology, Kohat University of Science and Technology, Kohat, 26000, Khyber Pakhtunkhwa, Pakistan
| | - Muhammad Qasim
- Department of Microbiology, Kohat University of Science and Technology, Kohat, 26000, Khyber Pakhtunkhwa, Pakistan
| | - Shahid Niaz Khan
- Department of Zoology, Kohat University of Science and Technology, Kohat, 26000, Khyber Pakhtunkhwa, Pakistan.
| | - Khalil Ur Rehman
- Institute of Chemical Sciences, Gomal University, Dera Ismail Khan, KPK, Pakistan.
| | - Mohammed Alissa
- Department of Medical Laboratory, College of Applied Medical Sciences, Prince Sattam bin Abdulaziz University, Al-Kharj, 11942, Saudi Arabia
| | - Ghadah S Abusalim
- Department of Medical Laboratory, College of Applied Medical Sciences, Prince Sattam bin Abdulaziz University, Al-Kharj, 11942, Saudi Arabia
| | - Suad A Alghamdi
- Department of Medical Laboratory, College of Applied Medical Sciences, Prince Sattam bin Abdulaziz University, Al-Kharj, 11942, Saudi Arabia
| | - Abdulmohsin J Alamoudi
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Eman Kelabi
- Departnent of Chemistry, Alwajh College, University of Tabuk, Tabuk, Saudi Arabia
| | - Faisal Miqad K Albaqami
- Department of Biology, Faculty of Science, Islamic University of Madinah, Madinah, 42351, Saudi Arabia
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Vaasjo E, Stothart MR, Black SR, Poissant J, Whiteside DP. The impact of management on the fecal microbiome of endangered greater sage-grouse ( Centrocercus urophasianus) in a zoo-based conservation program. CONSERVATION PHYSIOLOGY 2024; 12:coae052. [PMID: 39113731 PMCID: PMC11304599 DOI: 10.1093/conphys/coae052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 07/09/2024] [Accepted: 07/18/2024] [Indexed: 08/10/2024]
Abstract
Greater sage-grouse (Centrocercus urophasianus) are a critically endangered species in Canada with fewer than 140 individuals remaining on native habitats in southern Alberta and Saskatchewan. In 2014, the Wilder Institute/Calgary Zoo initiated North America's only zoo-based conservation breeding program for this species to bolster declining wild populations through conservation reintroductions. Within the managed population of sage-grouse, morbidity and mortality have primarily been associated with intestinal bacterial infections. As a preliminary study to assess the gastrointestinal health of this species in managed care, the fecal bacterial microbiome of adult and juvenile captive sage-grouse was characterized with 16S rRNA sequencing. The composition of the microbiome at the phylum level in greater sage-grouse is consistent with previous studies of the avian microbiome, with Bacillota as the most abundant phyla, and Actinomycetota, Bacteroidota and Pseudomonadota also being highly abundant. Antibiotic use and sex did not have a significant impact on the diversity or composition of the microbiome, but the management of juvenile sage-grouse did influence the development of the microbiome. Juveniles that were raised outdoors under maternal care developed a microbiome much more similar to adults when compared to chicks that were incubated and hand-raised. The local environment and parental care appear to be important factors influencing the diversity and composition of the gastrointestinal microbiome in this species.
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Affiliation(s)
- Emma Vaasjo
- Faculty of Veterinary Medicine, University of Calgary, 3280 Hospital Dr NW, Calgary, AB T2N 4Z6, Canada
- Animal Health Department, Wilder Institute/Calgary Zoo, 1300 Zoo Rd NE, Calgary, AB T2E 7V6, Canada
| | - Mason R Stothart
- Faculty of Veterinary Medicine, University of Calgary, 3280 Hospital Dr NW, Calgary, AB T2N 4Z6, Canada
| | - Sandra R Black
- Animal Health Department, Wilder Institute/Calgary Zoo, 1300 Zoo Rd NE, Calgary, AB T2E 7V6, Canada
| | - Jocelyn Poissant
- Faculty of Veterinary Medicine, University of Calgary, 3280 Hospital Dr NW, Calgary, AB T2N 4Z6, Canada
| | - Douglas P Whiteside
- Faculty of Veterinary Medicine, University of Calgary, 3280 Hospital Dr NW, Calgary, AB T2N 4Z6, Canada
- Animal Health Department, Wilder Institute/Calgary Zoo, 1300 Zoo Rd NE, Calgary, AB T2E 7V6, Canada
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Sun M, Halimubieke N, Fang B, Valdebenito JO, Xu X, Sheppard SK, Székely T, Zhang T, He S, Lu R, Ward S, Urrutia AO, Liu Y. Gut microbiome in two high-altitude bird populations showed heterogeneity in sex and life stage. FEMS MICROBES 2024; 5:xtae020. [PMID: 39385800 PMCID: PMC11462087 DOI: 10.1093/femsmc/xtae020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 06/21/2024] [Accepted: 07/03/2024] [Indexed: 10/12/2024] Open
Abstract
Gut microbiotas have important impacts on host health, reproductive success, and survival. While extensive research in mammals has identified the exogenous (e.g. environment) and endogenous (e.g. phylogeny, sex, and age) factors that shape the gut microbiota composition and functionality, yet avian systems remain comparatively less understood. Shorebirds, characterized by a well-resolved phylogeny and diverse life-history traits, present an ideal model for dissecting the factors modulating gut microbiota dynamics. Here, we provide an insight into the composition of gut microbiota in two high-altitude (ca. 3200 m above sea level) breeding populations of Kentish plover (Charadrius alexandrinus) and Tibetan sand plover (Charadrius altrifrons) in the Qinghai-Tibetan Plateau, China. By analysing faecal bacterial communities using 16S rRNA sequencing technology, we find a convergence in gut microbial communities between the two species, dominated by Firmicutes, Proteobacteria, and Bacteroidetes. This suggests that the shared breeding environment potentially acts as a significant determinant shaping their gut microbiota. We also show sex- and age-specific patterns of gut microbiota: female adults maintain a higher diversity than males, and juveniles are enriched in Rhizobiaceae and Exiguobacterium due to their vegetative food resource. Our study not only provides a comprehensive descriptive information for future investigations on the diversity, functionality, and determinants of avian microbiomes, but also underscores the importance of microbial communities in broader ecological contexts.
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Affiliation(s)
- Mingwan Sun
- State Key Laboratory of Biocontrol, School of Life Sciences/School of Ecology, Sun Yat-sen University, Guangzhou 510275, China
- Milner Centre for Evolution, Department of Life Science, University of Bath, Bath BA27AY, United Kingdom
| | - Naerhulan Halimubieke
- Milner Centre for Evolution, Department of Life Science, University of Bath, Bath BA27AY, United Kingdom
- Department of Anthropology, University College London, London WC1H 0BW, United Kingdom
| | - Baozhu Fang
- State Key Laboratory of Biocontrol, School of Life Sciences/School of Ecology, Sun Yat-sen University, Guangzhou 510275, China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
| | - José O Valdebenito
- Milner Centre for Evolution, Department of Life Science, University of Bath, Bath BA27AY, United Kingdom
- Bird Ecology Lab, Instituto de Ciencias Marinas y Limnológicas, Universidad Austral de Chile, Independencia 631, Valdivia 5110566, Chile
- Instituto Milenio Biodiversidad de Ecosistemas Antárticos y Subantárticos (BASE), Santiago 8331150, Chile
| | - Xieyang Xu
- State Key Laboratory of Biocontrol, School of Life Sciences/School of Ecology, Sun Yat-sen University, Guangzhou 510275, China
| | - Samuel K Sheppard
- Ineos Oxford Institute, University of Oxford, Oxford OX1 3RE, United Kingdom
| | - Tamás Székely
- Milner Centre for Evolution, Department of Life Science, University of Bath, Bath BA27AY, United Kingdom
- Department of Evolutionary Zoology and Human Biology, University of Debrecen, Debrecen 4032, Hungary
| | - Tongzuo Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining 810008, China
| | - Shunfu He
- Xining National Terrestrial Wildlife Epidemic Monitoring Station, Xining 810008, China
| | - Rong Lu
- Xining National Terrestrial Wildlife Epidemic Monitoring Station, Xining 810008, China
| | - Stephen Ward
- Department of Life Science, University of Bath, Bath BA27AY, United Kingdom
| | - Araxi O Urrutia
- State Key Laboratory of Biocontrol, School of Life Sciences/School of Ecology, Sun Yat-sen University, Guangzhou 510275, China
| | - Yang Liu
- State Key Laboratory of Biocontrol, School of Life Sciences/School of Ecology, Sun Yat-sen University, Guangzhou 510275, China
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Li W, Cheng L, He X, He G, Liu Y, Sang Z, Wang Y, Shao M, Xiong T, Xu H, Zhao J. Gut fungi of black-necked cranes (Grus nigricollis) respond to dietary changes during wintering. BMC Microbiol 2024; 24:232. [PMID: 38951807 PMCID: PMC11218170 DOI: 10.1186/s12866-024-03396-0] [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: 01/03/2024] [Accepted: 06/20/2024] [Indexed: 07/03/2024] Open
Abstract
BACKGROUND Migratory birds exhibit heterogeneity in foraging strategies during wintering to cope with environmental and migratory pressures, and gut bacteria respond to changes in host diet. However, less is known about the dynamics of diet and gut fungi during the wintering period in black-necked cranes (Grus nigricollis). RESULTS In this work, we performed amplicon sequencing of the trnL-P6 loop and ITS1 regions to characterize the dietary composition and gut fungal composition of black-necked cranes during wintering. Results indicated that during the wintering period, the plant-based diet of black-necked cranes mainly consisted of families Poaceae, Solanaceae, and Polygonaceae. Among them, the abundance of Solanaceae, Polygonaceae, Fabaceae, and Caryophyllaceae was significantly higher in the late wintering period, which also led to a more even consumption of various food types by black-necked cranes during this period. The diversity of gut fungal communities and the abundance of core fungi were more conserved during the wintering period, primarily dominated by Ascomycota and Basidiomycota. LEfSe analysis (P < 0.05, LDA > 2) found that Pyxidiophora, Pseudopeziza, Sporormiella, Geotrichum, and Papiliotrema were significantly enriched in early winter, Ramularia and Dendryphion were significantly enriched in mid-winter, Barnettozyma was significantly abundant in late winter, and Pleuroascus was significantly abundant in late winter. Finally, mantel test revealed a significant correlation between winter diet and gut fungal. CONCLUSIONS This study revealed the dynamic changes in the food composition and gut fungal community of black-necked cranes during wintering in Dashanbao. In the late wintering period, their response to environmental and migratory pressures was to broaden their diet, increase the intake of non-preferred foods, and promote a more balanced consumption ratio of various foods. Balanced food composition played an important role in stabilizing the structure of the gut fungal community. While gut fungal effectively enhanced the host's food utilization rate, they may also faced potential risks of introducing pathogenic fungi. Additionally, we recongnized the limitations of fecal testing in studying the composition of animal gut fungal, as it cannot effectively distinguished between fungal taxa from food or soil inadvertently ingested and intestines. Future research on functions such as cultivation and metagenomics may further elucidate the role of fungi in the gut ecosystem.
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Affiliation(s)
- Wenhao Li
- College of Agronomy and Life Sciences, Zhaotong University, Zhaotong, 657000, China
- College of Life Science, Sichuan Agricultural University, No. 46, Xinkang Road, Yucheng District, Ya'an, Sichuan, 625014, China
| | - Lijun Cheng
- College of Agronomy and Life Sciences, Zhaotong University, Zhaotong, 657000, China
- Yunnan Key Laboratory of Gastrodia and Fungi Symbiotic Biology, Zhaotong University, Zhaotong, 657000, China
| | - Xin He
- Sichuan Academy of Grassland Sciences, Chengdu, 610000, China
| | - Guiwen He
- College of Agronomy and Life Sciences, Zhaotong University, Zhaotong, 657000, China
- Yunnan Key Laboratory of Gastrodia and Fungi Symbiotic Biology, Zhaotong University, Zhaotong, 657000, China
| | - Yutong Liu
- Sichuan Academy of Grassland Sciences, Chengdu, 610000, China
| | - Zhenglin Sang
- College of Agronomy and Life Sciences, Zhaotong University, Zhaotong, 657000, China
- Yunnan Key Laboratory of Gastrodia and Fungi Symbiotic Biology, Zhaotong University, Zhaotong, 657000, China
| | - Yuanjian Wang
- Management Bureau of Dashanbao Black-Necked Crane National Nature Reserve, Zhaotong, Yunnan Province, 657000, China
| | - Mingcui Shao
- Management Bureau of Dashanbao Black-Necked Crane National Nature Reserve, Zhaotong, Yunnan Province, 657000, China
| | - Tingsong Xiong
- Management Bureau of Dashanbao Black-Necked Crane National Nature Reserve, Zhaotong, Yunnan Province, 657000, China
| | - Huailiang Xu
- College of Life Science, Sichuan Agricultural University, No. 46, Xinkang Road, Yucheng District, Ya'an, Sichuan, 625014, China.
| | - Junsong Zhao
- College of Agronomy and Life Sciences, Zhaotong University, Zhaotong, 657000, China.
- Yunnan Key Laboratory of Gastrodia and Fungi Symbiotic Biology, Zhaotong University, Zhaotong, 657000, China.
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5
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Grimwood RM, Reyes EMR, Cooper J, Welch J, Taylor G, Makan T, Lim L, Dubrulle J, McInnes K, Holmes EC, Geoghegan JL. From islands to infectomes: host-specific viral diversity among birds across remote islands. BMC Ecol Evol 2024; 24:84. [PMID: 38926829 PMCID: PMC11209962 DOI: 10.1186/s12862-024-02277-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 06/23/2024] [Indexed: 06/28/2024] Open
Abstract
BACKGROUND Accelerating biodiversity loss necessitates monitoring the potential pathogens of vulnerable species. With a third of New Zealand's avifauna considered at risk of extinction, a greater understanding of the factors that influence microbial transmission in this island ecosystem is needed. We used metatranscriptomics to determine the viruses, as well as other microbial organisms (i.e. the infectomes), of seven bird species, including the once critically endangered black robin (Petroica traversi), on two islands in the remote Chatham Islands archipelago, New Zealand. RESULTS We identified 19 likely novel avian viruses across nine viral families. Black robins harboured viruses from the Flaviviridae, Herpesviridae, and Picornaviridae, while introduced starlings (Sturnus vulgaris) and migratory seabirds (Procellariiformes) carried viruses from six additional viral families. Potential cross-species virus transmission of a novel passerivirus (family: Picornaviridae) between native (black robins and grey-backed storm petrels) and introduced (starlings) birds was also observed. Additionally, we identified bacterial genera, apicomplexan parasites, as well as a novel megrivirus linked to disease outbreaks in other native New Zealand birds. Notably, island effects were outweighed by host taxonomy as a significant driver of viral composition, even among sedentary birds. CONCLUSIONS These findings underscore the value of surveillance of avian populations to identify and minimise escalating threats of disease emergence and spread in these island ecosystems. Importantly, they contribute to our understanding of the potential role of introduced and migratory birds in the transmission of microbes and associated diseases, which could impact vulnerable island-endemic species.
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Affiliation(s)
- Rebecca M Grimwood
- Department of Microbiology and Immunology, University of Otago, Dunedin, 9016, New Zealand
| | - Enzo M R Reyes
- Department of Conservation/Te Papa Atawhai, Nelson, New Zealand
| | - Jamie Cooper
- Department of Conservation/Te Papa Atawhai, Nelson, New Zealand
| | - Jemma Welch
- Department of Conservation/Te Papa Atawhai, Nelson, New Zealand
| | - Graeme Taylor
- Department of Conservation/Te Papa Atawhai, Nelson, New Zealand
| | - Troy Makan
- Department of Conservation/Te Papa Atawhai, Nelson, New Zealand
| | - Lauren Lim
- School of Medical Sciences, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Jérémy Dubrulle
- Department of Microbiology and Immunology, University of Otago, Dunedin, 9016, New Zealand
| | - Kate McInnes
- Department of Conservation/Te Papa Atawhai, Nelson, New Zealand
| | - Edward C Holmes
- School of Medical Sciences, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Jemma L Geoghegan
- Department of Microbiology and Immunology, University of Otago, Dunedin, 9016, New Zealand.
- Institute of Environmental Science and Research, Wellington, 5018, New Zealand.
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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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7
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Dunbar A, Drigo B, Djordjevic SP, Donner E, Hoye BJ. Impacts of coprophagic foraging behaviour on the avian gut microbiome. Biol Rev Camb Philos Soc 2024; 99:582-597. [PMID: 38062990 DOI: 10.1111/brv.13036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 11/24/2023] [Accepted: 11/27/2023] [Indexed: 03/06/2024]
Abstract
Avian gut microbial communities are complex and play a fundamental role in regulating biological functions within an individual. Although it is well established that diet can influence the structure and composition of the gut microbiota, foraging behaviour may also play a critical, yet unexplored role in shaping the composition, dynamics, and adaptive potential of avian gut microbiota. In this review, we examine the potential influence of coprophagic foraging behaviour on the establishment and adaptability of wild avian gut microbiomes. Coprophagy involves the ingestion of faeces, sourced from either self (autocoprophagy), conspecific animals (allocoprophagy), or heterospecific animals. Much like faecal transplant therapy, coprophagy may (i) support the establishment of the gut microbiota of young precocial species, (ii) directly and indirectly provide nutritional and energetic requirements, and (iii) represent a mechanism by which birds can rapidly adapt the microbiota to changing environments and diets. However, in certain contexts, coprophagy may also pose risks to wild birds, and their microbiomes, through increased exposure to chemical pollutants, pathogenic microbes, and antibiotic-resistant microbes, with deleterious effects on host health and performance. Given the potentially far-reaching consequences of coprophagy for avian microbiomes, and the dearth of literature directly investigating these links, we have developed a predictive framework for directing future research to understand better when and why wild birds engage in distinct types of coprophagy, and the consequences of this foraging behaviour. There is a need for comprehensive investigation into the influence of coprophagy on avian gut microbiotas and its effects on host health and performance throughout ontogeny and across a range of environmental perturbations. Future behavioural studies combined with metagenomic approaches are needed to provide insights into the function of this poorly understood behaviour.
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Affiliation(s)
- Alice Dunbar
- Future Industries Institute (FII), University of South Australia, Mawson Lakes Campus, GPO Box 2471 5095, Adelaide, South Australia, Australia
| | - Barbara Drigo
- Future Industries Institute (FII), University of South Australia, Mawson Lakes Campus, GPO Box 2471 5095, Adelaide, South Australia, Australia
- UniSA STEM, University of South Australia, GPO Box 2471, Adelaide, South Australia, 5001, Australia
| | - Steven P Djordjevic
- Australian Institute for Microbiology and Infection, University of Technology Sydney, PO Box 123, Ultimo, New South Wales, 2007, Australia
- Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, PO Box 123, Ultimo, New South Wales, 2007, Australia
| | - Erica Donner
- Future Industries Institute (FII), University of South Australia, Mawson Lakes Campus, GPO Box 2471 5095, Adelaide, South Australia, Australia
- Cooperative Research Centre for Solving Antimicrobial Resistance in Agribusiness, Food, and Environments (CRC SAAFE), University of South Australia, GPO Box 2471 5095, Adelaide, South Australia, Australia
| | - Bethany J Hoye
- School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, New South Wales, 2522, Australia
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Jiang J, Hu D, Pei E. Integrated omics analysis reveals a correlation between gut microbiota and egg production in captive African penguins (Spheniscus demersus). Anim Reprod Sci 2024; 263:107448. [PMID: 38428346 DOI: 10.1016/j.anireprosci.2024.107448] [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: 11/02/2023] [Revised: 01/24/2024] [Accepted: 02/21/2024] [Indexed: 03/03/2024]
Abstract
The egg production of captive African penguins differs considerably between individuals. An understanding of the physiological differences in African penguins with relatively greater and lesser egg production is meaningful for the captive breeding program of this endangered species. The objective of this study was to investigate differential microbial composition and metabolites in captive African penguins with different egg production. Fecal samples were collected from captive female African penguins during the breeding season. The results of 16 S rRNA gene sequencing showed that African penguins with different egg production had similar microbial diversities, whereas a significant difference was observed between their microbial community structure. African penguins with relatively greater egg production exhibited a higher relative abundance of Alphaproteobacteria, Rhizobiales, Bradyrhizobiaceae, Bradyrhizobium and Bosea. Meanwhile, penguins with relatively lesser egg production had an increased proportion of Klebsiella and Plesiomonas. We further identified a total of 1858 metabolites in female African penguins by liquid chromatography-mass spectrometry analysis. Among these metabolites, 13 kinds of metabolites were found to be significantly differential between African penguins with different egg production. In addition, the correlation analysis revealed that the egg production had significant correlations with most of the differential microbial bacteria and metabolites. Our findings might aid in understanding the potential mechanism underlying the phenomenon of abnormal egg production in captive African penguins, and provide novel insights into the relationship between gut microbiota and reproduction in penguins.
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Affiliation(s)
- Jingle Jiang
- Shanghai Endangered Species Conservation and Research Centre, Shanghai Zoo, Shanghai 200335, China
| | - Di Hu
- Shanghai Endangered Species Conservation and Research Centre, Shanghai Zoo, Shanghai 200335, China
| | - Enle Pei
- Shanghai Endangered Species Conservation and Research Centre, Shanghai Zoo, Shanghai 200335, China.
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9
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Li Z, Duan T, Wang L, Wu J, Meng Y, Bao D, Gao L, Liu L. Comparative analysis of the gut bacteria and fungi in migratory demoiselle cranes ( Grus virgo) and common cranes ( Grus grus) in the Yellow River Wetland, China. Front Microbiol 2024; 15:1341512. [PMID: 38572234 PMCID: PMC10987826 DOI: 10.3389/fmicb.2024.1341512] [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: 11/21/2023] [Accepted: 03/04/2024] [Indexed: 04/05/2024] Open
Abstract
Introduction Gut microbiota are closely related to the nutrition, immunity, and metabolism of the host and play important roles in maintaining the normal physiological activities of animals. Cranes are important protected avian species in China, and they are sensitive to changes in the ecological environment and are thus good environmental indicators. There have been no reports examining gut fungi or the correlation between bacteria and fungi in wild Demoiselle cranes (Grus virgo) and Common cranes (Grus grus). Related research can provide a foundation for the protection of rare wild animals. Methods 16S rRNA and ITS high-throughput sequencing techniques were used to analyze the gut bacterial and fungal diversity of Common and Demoiselle cranes migrating to the Yellow River wetland in Inner Mongolia. Results The results revealed that for gut bacteria α diversity, Chao1 index in Demoiselle cranes was remarkably higher than that in Common cranes (411.07 ± 79.54 vs. 294.92 ± 22.38), while other index had no remarkably differences. There was no remarkable difference in fungal diversity. There were marked differences in the gut microbial composition between the two crane species. At the phylum level, the highest abundance of bacteria in the Common crane and Demoiselle crane samples was Firmicutes, accounting for 87.84% and 74.29%, respectively. The highest abundance of fungi in the guts of the Common and Demoiselle cranes was Ascomycota, accounting for 69.42% and 57.63%, respectively. At the genus level, the most abundant bacterial genus in the Common crane sample was Turicibacter (38.60%), and the most abundant bacterial genus in the Demoiselle crane sample was Catelicoccus (39.18%). The most abundant fungi in the Common crane sample was Penicillium (6.97%), and the most abundant fungi in the Demoiselle crane sample was Saccharomyces (8.59%). Correlation analysis indicated that there was a significant correlation between gut bacteria and fungi. Discussion This study provided a research basis for the protection of cranes. Indeed, a better understanding of the gut microbiota is very important for the conservation and management of wild birds, as it not only helps us to understand their life history and related mechanisms, but also can hinder the spread of pathogenic microorganisms.
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Affiliation(s)
| | | | | | | | | | | | - Li Gao
- Faculty of Biological Science and Technology, Baotou Teacher's College, Baotou, China
| | - Li Liu
- Faculty of Biological Science and Technology, Baotou Teacher's College, Baotou, China
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10
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Hattab J, Marruchella G, Sibra A, Tiscar PG, Todisco G. Canaries' Microbiota: The Gut Bacterial Communities along One Female Reproductive Cycle. Microorganisms 2023; 11:2289. [PMID: 37764133 PMCID: PMC10537324 DOI: 10.3390/microorganisms11092289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 08/31/2023] [Accepted: 09/09/2023] [Indexed: 09/29/2023] Open
Abstract
Investigations of bacterial communities are on the rise both in human and veterinary medicine. Their role in health maintenance and pathogenic mechanisms is in the limelight of infectious, metabolic, and cancer research. Among the most considered, gut bacterial communities take the cake. Their part in animals was assessed mainly to improve animal production, public health, and pet management. In this regard, canaries deserve attention, being a popular pet and source of economic income for bird-keepers, for whom breeding represents a pivotal point. Thus, the present work aimed to follow gut bacterial communities' evolution along on whole reproductive cycle of 12 healthy female canaries. Feces were collected during parental care, molting, and resting phase, and submitted for 16S rRNA sequencing. Data were analyzed and a substantial presence of Lactobacillus aviarius along all the phases, and a relevant shift of microbiota during molting and rest due to an abrupt decrease of the Vermiphilaceae family were detected. Although the meaning of such change is not clear, future research may highlight unforeseen scenarios. Moreover, Lactobacillus aviarius may be deemed for normal bacteria flora restoration in debilitated birds, perhaps improving their health and productivity.
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Affiliation(s)
- Jasmine Hattab
- Department of Veterinary Medicine, University of Teramo, SP18 Piano d’Accio, 64100 Teramo, Italy; (J.H.); (G.M.)
| | - Giuseppe Marruchella
- Department of Veterinary Medicine, University of Teramo, SP18 Piano d’Accio, 64100 Teramo, Italy; (J.H.); (G.M.)
| | - Alessandra Sibra
- APHA—Animal & Plant Health Agency, Building 1, Sevington Inland Border Facility, Ashford TN25 6GE, UK;
| | - Pietro Giorgio Tiscar
- Department of Veterinary Medicine, University of Teramo, SP18 Piano d’Accio, 64100 Teramo, Italy; (J.H.); (G.M.)
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Lu W, Yu H, Liang Y, Zhai S. Effects of White Fish Meal Replaced by Low-Quality Brown Fish Meal with Compound Additives on Growth Performance and Intestinal Health of Juvenile American Eel ( Anguilla rostrata). Animals (Basel) 2023; 13:2873. [PMID: 37760273 PMCID: PMC10526026 DOI: 10.3390/ani13182873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 09/04/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023] Open
Abstract
With a reduced supply and increased price of white fish meal (WFM), the exploration of a practical strategy to replace WFM is urgent for sustainable eel culture. A 70-day feeding trial was conducted to evaluate the effects of replacing WFM with low-quality brown fish meal (LQBFM) with compound additives (CAs) on the growth performance and intestinal health of juvenile American eels (Anguilla rostrata). The 300 fish (11.02 ± 0.02 g/fish) were randomly distributed in triplicate to four groups (control group, LQBFM20+CAs group, LQBFM30+CAs group and LQBFM40+CAs group). They were fed the diets with LQBFM replacing WFM at 0, 20%, 30% and 40%, respectively. The CAs were a mixture of Macleaya cordata extract, grape seed proanthocyanidins and compound acidifiers; its level in the diets of the trial groups was 0.50%. No significant differences were found in the growth performance between the control and LQBFM20+CAs groups (p > 0.05), whereas those values were significantly decreased in LQBFM30+CAs and LQBFM40+CAs groups (p < 0.05). Compared to the control group, the activity of glutamic-pyruvic transaminase was significantly increased in LQBFM30+CAs and LQBFM40+CAs groups, while lysozyme activity and complement 3 level were significantly decreased in those two groups (p < 0.05). There were decreased antioxidant potential and intestinal morphological indexes in the LQBFM30+CAs and LQBFM40+CAs groups, and no significant differences in those parameters were observed between the control group and LQBFM20+CAs group (p > 0.05). The intestinal microbiota at the phylum level or genus level was beneficially regulated in the LQBFM20+CAs group; similar results were not shown in the LQBFM40+CAs group. In conclusion, with 0.50% CA supplementation in the diet, LQBFM could replace 20% of WFM without detrimental effects on the growth and intestinal health of juvenile American eels and replacing 30% and 40%WFM with LQBFM might exert negative effects on this fish species.
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Affiliation(s)
| | | | | | - Shaowei Zhai
- Engineering Research Center of the Modern Industry Technology for Eel, Ministry of Education, Fisheries College of Jimei University, Xiamen 361021, China; (W.L.); (H.Y.); (Y.L.)
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12
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Li W, Zhao J, Tian H, Shen Y, Wang Y, Shao M, Xiong T, Yao Y, Zhang L, Chen X, Xiao H, Xiong Y, Yang S, Tan C, Xu H. Gut microbiota enhance energy accumulation of black-necked crane to cope with impending migration. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12598-x. [PMID: 37249588 DOI: 10.1007/s00253-023-12598-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 05/12/2023] [Accepted: 05/17/2023] [Indexed: 05/31/2023]
Abstract
Less is known about the role of gut microbiota in overwintering environmental adaptation in migratory birds. Here, we performed metagenomic sequencing on fresh fecal samples (n = 24) collected during 4 periods of overwintering (Dec: early; Jan: middle I; Feb: middle II; Mar: late) to characterize gut microbial taxonomic and functional characteristics of black-necked crane (Grus nigricollis). The results demonstrated no significant change in microbial diversity among overwintering periods. Analysis of compositions of microbiomes with bias correction (ANCOM-BC) determined 15 Proteobacteria species enriched in late overwintering period. Based on previous reports, these species are associated with degradation of chitin, cellulose, and lipids. Meanwhile, fatty acid degradation and betalain biosynthesis pathways are enriched in late overwintering period. Furthermore, metagenomic binning obtained 91 high-quality bins (completeness >70% and contamination <10%), 5 of which enriched in late overwintering period. Carnobacterium maltaromaticum, unknown Enterobacteriaceae, and Yersinia frederiksenii have genes for chitin and cellulose degradation, acetate, and glutamate production. Unknown Enterobacteriaceae and Y. frederiksenii hold genes for synthesis of 10 essential amino acids required by birds, and the latter has genes for γ-aminobutyrate production. C. maltaromaticum has genes for pyridoxal synthesis. These results implied the gut microbiota is adapted to the host diet and may help black-necked cranes in pre-migratory energy accumulation by degrading the complex polysaccharide in their diet, supplying essential amino acids and vitamin pyridoxal, and producing acetate, glutamate, and γ-aminobutyrate that could stimulate host feeding. Additionally, enriched Proteobacteria also encoded more carbohydrate-active enzymes (CAZymes) and antibiotic resistance genes (ARGs) in late overwintering period. KEY POINTS: • Differences in gut microbiota function during overwintering period of black-necked cranes depend mainly on changes in core microbiota abundance • Gut microbiota of black-necked crane adapted to the diet during overwintering period • Gut microbiota could help black-necked cranes to accumulate more energy in the late overwintering period.
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Affiliation(s)
- Wenhao Li
- College of Life Science, Sichuan Agricultural University, Ya'an, 625014, China
- College of Agronomy and Life Sciences, Zhaotong University, Zhaotong, 657000, China
| | - Junsong Zhao
- College of Life Science, Sichuan Agricultural University, Ya'an, 625014, China
- College of Agronomy and Life Sciences, Zhaotong University, Zhaotong, 657000, China
| | - Hong Tian
- College of Agronomy and Life Sciences, Zhaotong University, Zhaotong, 657000, China
| | - Yanqiong Shen
- College of Agronomy and Life Sciences, Zhaotong University, Zhaotong, 657000, China
| | - Yuanjian Wang
- Management Bureau of Dashanbao Black-Necked Crane National Nature Reserve, Yunnan Province, Zhaotong, 657000, Yunnan, China
| | - Mingcui Shao
- Management Bureau of Dashanbao Black-Necked Crane National Nature Reserve, Yunnan Province, Zhaotong, 657000, Yunnan, China
| | - Tingsong Xiong
- Management Bureau of Dashanbao Black-Necked Crane National Nature Reserve, Yunnan Province, Zhaotong, 657000, Yunnan, China
| | - Yongfang Yao
- College of Life Science, Sichuan Agricultural University, Ya'an, 625014, China
| | - Lin Zhang
- College of Life Science, Sichuan Agricultural University, Ya'an, 625014, China
| | - Xinyu Chen
- College of Life Science, Sichuan Agricultural University, Ya'an, 625014, China
| | - Hongtao Xiao
- College of Life Science, Sichuan Agricultural University, Ya'an, 625014, China
| | - Ying Xiong
- College of Life Science, Sichuan Agricultural University, Ya'an, 625014, China
| | - Shengzhi Yang
- College of Life Science, Sichuan Agricultural University, Ya'an, 625014, China
| | - Cui Tan
- Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Huailiang Xu
- College of Life Science, Sichuan Agricultural University, Ya'an, 625014, China.
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Kouete MT, Bletz MC, LaBumbard BC, Woodhams DC, Blackburn DC. Parental care contributes to vertical transmission of microbes in a skin-feeding and direct-developing caecilian. Anim Microbiome 2023; 5:28. [PMID: 37189209 PMCID: PMC10184399 DOI: 10.1186/s42523-023-00243-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 03/20/2023] [Indexed: 05/17/2023] Open
Abstract
BACKGROUND Our current understanding of vertebrate skin and gut microbiomes, and their vertical transmission, remains incomplete as major lineages and varied forms of parental care remain unexplored. The diverse and elaborate forms of parental care exhibited by amphibians constitute an ideal system to study microbe transmission, yet investigations of vertical transmission among frogs and salamanders have been inconclusive. In this study, we assess bacteria transmission in Herpele squalostoma, an oviparous direct-developing caecilian in which females obligately attend juveniles that feed on their mother's skin (dermatophagy). RESULTS We used 16S rRNA amplicon-sequencing of the skin and gut of wild caught H. squalostoma individuals (males, females, including those attending juveniles) as well as environmental samples. Sourcetracker analyses revealed that juveniles obtain an important portion of their skin and gut bacteria communities from their mother. The contribution of a mother's skin to the skin and gut of her respective juveniles was much larger than that of any other bacteria source. In contrast to males and females not attending juveniles, only the skins of juveniles and their mothers were colonized by bacteria taxa Verrucomicrobiaceae, Nocardioidaceae, and Erysipelotrichaceae. In addition to providing indirect evidence for microbiome transmission linked to parental care among amphibians, our study also points to noticeable differences between the skin and gut communities of H. squalostoma and that of many frogs and salamanders, which warrants further investigation. CONCLUSION Our study is the first to find strong support for vertical bacteria transmission attributed to parental care in a direct-developing amphibian species. This suggests that obligate parental care may promote microbiome transmission in caecilians.
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Affiliation(s)
- Marcel T Kouete
- School of Natural Resources and Environment, University of Florida, Gainesville, FL, 32611, USA.
- Department of Natural History, Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA.
| | - Molly C Bletz
- Department of Biology, University of Massachusetts, Boston, MA, 02125, USA
| | | | - Douglas C Woodhams
- Department of Biology, University of Massachusetts, Boston, MA, 02125, USA
| | - David C Blackburn
- Department of Natural History, Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
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Lafuente E, Carles L, Walser J, Giulio M, Wullschleger S, Stamm C, Räsänen K. Effects of anthropogenic stress on hosts and their microbiomes: Treated wastewater alters performance and gut microbiome of a key detritivore ( Asellus aquaticus). Evol Appl 2023; 16:824-848. [PMID: 37124094 PMCID: PMC10130563 DOI: 10.1111/eva.13540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 01/24/2023] [Accepted: 02/17/2023] [Indexed: 04/03/2023] Open
Abstract
Human activity is a major driver of ecological and evolutionary change in wild populations and can have diverse effects on eukaryotic organisms as well as on environmental and host-associated microbial communities. Although host-microbiome interactions can be a major determinant of host fitness, few studies consider the joint responses of hosts and their microbiomes to anthropogenic changes. In freshwater ecosystems, wastewater is a widespread anthropogenic stressor that represents a multifarious environmental perturbation. Here, we experimentally tested the impact of treated wastewater on a keystone host (the freshwater isopod Asellus aquaticus) and its gut microbiome. We used a semi-natural flume experiment, in combination with 16S rRNA amplicon sequencing, to assess how different concentrations (0%, 30%, and 80%) of nonfiltered wastewater (i.e. with chemical toxicants, nutrients, organic particles, and microbes) versus ultrafiltered wastewater (i.e. only dissolved pollutants and nutrients) affected host survival, growth, and food consumption as well as mid- and hindgut bacterial community composition and diversity. Our results show that while host survival was not affected by the treatments, host growth increased and host feeding rate decreased with nonfiltered wastewater - potentially indicating that A. aquaticus fed on organic matter and microbes available in nonfiltered wastewater. Furthermore, even though the midgut microbiome (diversity and composition) was not affected by any of our treatments, nonfiltered wastewater influenced bacterial composition (but not diversity) in the hindgut. Ultrafiltered wastewater, on the other hand, affected both community composition and bacterial diversity in the hindgut, an effect that in our system differed between sexes. While the functional consequences of microbiome changes and their sex specificity are yet to be tested, our results indicate that different components of multifactorial stressors (i.e. different constituents of wastewater) can affect hosts and their microbiome in distinct (even opposing) manners and have a substantial impact on eco-evolutionary responses to anthropogenic stressors.
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Affiliation(s)
- Elvira Lafuente
- Eawag: Swiss Federal Institute of Aquatic Science and TechnologyDübendorfSwitzerland
- Instituto Gulbenkian de CiênciaOeirasPortugal
| | - Louis Carles
- Eawag: Swiss Federal Institute of Aquatic Science and TechnologyDübendorfSwitzerland
| | - Jean‐Claude Walser
- Department of Environmental Systems Science D‐USYS, Genetic Diversity CentreSwiss Federal Institute of Technology (ETH), ZürichZürichSwitzerland
| | - Marco Giulio
- Eawag: Swiss Federal Institute of Aquatic Science and TechnologyDübendorfSwitzerland
| | - Simon Wullschleger
- Eawag: Swiss Federal Institute of Aquatic Science and TechnologyDübendorfSwitzerland
| | - Christian Stamm
- Eawag: Swiss Federal Institute of Aquatic Science and TechnologyDübendorfSwitzerland
| | - Katja Räsänen
- Eawag: Swiss Federal Institute of Aquatic Science and TechnologyDübendorfSwitzerland
- Department of Biological and Environmental ScienceUniversity of JyväskyläJyväskyläFinland
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Liukkonen M, Hukkanen M, Cossin-Sevrin N, Stier A, Vesterinen E, Grond K, Ruuskanen S. No evidence for associations between brood size, gut microbiome diversity and survival in great tit (Parus major) nestlings. Anim Microbiome 2023; 5:19. [PMID: 36949549 PMCID: PMC10031902 DOI: 10.1186/s42523-023-00241-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 03/13/2023] [Indexed: 03/24/2023] Open
Abstract
BACKGROUND The gut microbiome forms at an early stage, yet data on the environmental factors influencing the development of wild avian microbiomes is limited. As the gut microbiome is a vital part of organismal health, it is important to understand how it may connect to host performance. The early studies with wild gut microbiome have shown that the rearing environment may be of importance in gut microbiome formation, yet the results vary across taxa, and the effects of specific environmental factors have not been characterized. Here, wild great tit (Parus major) broods were manipulated to either reduce or enlarge the original brood soon after hatching. We investigated if brood size was associated with nestling bacterial gut microbiome, and whether gut microbiome diversity predicted survival. Fecal samples were collected at mid-nestling stage and sequenced with the 16S rRNA gene amplicon sequencing, and nestling growth and survival were measured. RESULTS Gut microbiome diversity showed high variation between individuals, but this variation was not significantly explained by brood size or body mass. Additionally, we did not find a significant effect of brood size on body mass or gut microbiome composition. We also demonstrated that early handling had no impact on nestling performance or gut microbiome. Furthermore, we found no significant association between gut microbiome diversity and short-term (survival to fledging) or mid-term (apparent juvenile) survival. CONCLUSIONS We found no clear association between early-life environment, offspring condition and gut microbiome. This suggests that brood size is not a significantly contributing factor to great tit nestling condition, and that other environmental and genetic factors may be more strongly linked to offspring condition and gut microbiome. Future studies should expand into other early-life environmental factors e.g., diet composition and quality, and parental influences.
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Affiliation(s)
- Martta Liukkonen
- Department of Biological and Environmental Science, University of Jyväskylä, Jyvaskyla, Finland.
| | - Mikaela Hukkanen
- Department of Biology, University of Turku, Turku, Finland
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | | | - Antoine Stier
- Department of Biology, University of Turku, Turku, Finland
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023 LEHNA, 69622, Lyon, France
- Institut Pluridisciplinaire Hubert Curien, UMR7178, Université de Strasbourg, CNRS, Strasbourg, France
| | | | - Kirsten Grond
- Department of Biological Sciences, University of Alaska Anchorage, Anchorage, AK, 99508, USA
| | - Suvi Ruuskanen
- Department of Biological and Environmental Science, University of Jyväskylä, Jyvaskyla, Finland
- Department of Biology, University of Turku, Turku, Finland
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Intestinal Microbiota of Anser fabalis Wintering in Two Lakes in the Middle and Lower Yangtze River Floodplain. Animals (Basel) 2023; 13:ani13040707. [PMID: 36830494 PMCID: PMC9952484 DOI: 10.3390/ani13040707] [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: 01/06/2023] [Revised: 02/12/2023] [Accepted: 02/14/2023] [Indexed: 02/19/2023] Open
Abstract
The intestinal microbiota of migratory birds participate in the life activities of the host and are affected by external environmental factors. The difference in habitat environment provides diversity in external environmental selection pressure for the same overwintering waterfowl, which may be reflected in their intestinal microbiota. Caizi lake and Shengjin Lake in the Middle and Lower Yangtze River Floodplain are the main habitats for migratory waterfowl in winter, especially the Anser fabalis (A. fabalis). It is important to explore the changes in intestinal microbiota composition and function of A. fabalis in the early overwintering period to clarify the effect of habitat size and protection status on intestinal microbiota. In this study, the composition and structural characteristics of the intestinal microbiota of A. fabalis in Shengjin Lake (SL) and Caizi Lake (CL) were preliminarily explored in order to obtain data for the migratory birds. In both SL and CL groups, 16S rRNA amplicon sequencing analysis showed that Firmicutes was the dominant bacterial phylum, but the relative abundance showed significant differences. Lactobacillus was the most abundant genus in both SL and CL groups. At the species level, the abundance of L. aviaries was the highest, with a relative abundance in both SL and CL groups of more than 34%. When comparing the average relative abundance of the 15 most abundant genera, it was found that Subdoligranulum, Exiguobacterium, and Terrisporobacter had higher abundances in the intestinal microbiota of CL A. fabalis, while Streptococcus and Rothia had higher abundances in the intestinal microbiota of SL A. fabalis. There was only a positive correlation between Bacteroidota and Proteobacteria in the intestinal microbiota flora of SL A. fabalis, and the species were closely related. At the same time, there were positive and negative correlations between Firmicutes and Actinomycetes. However, CL is mainly associated with a positive correlation between Firmicutes and Actinomycetes, and there are also a small number of connections between Firmicutes. PICRUSt1 prediction analysis revealed that the Clusters of Orthologous Groups (COG) functions of SL and CL involve energy production and transformation, amino acid transport and metabolism, carbohydrate transport and metabolism, and transcription. Understanding the changes in intestinal microbiota in Aves during the overwintering period is of great importance to explore the adaptation mechanism of migratory Aves to the overwintering environment. This work provides basic data for an A. fabalis intestinal microbiota study.
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Cloacal microbiota are biogeographically structured in larks from desert, tropical and temperate areas. BMC Microbiol 2023; 23:40. [PMID: 36765278 PMCID: PMC9921332 DOI: 10.1186/s12866-023-02768-2] [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: 03/07/2022] [Accepted: 01/11/2023] [Indexed: 02/12/2023] Open
Abstract
BACKGROUND In contrast with macroorganisms, that show well-documented biogeographical patterns in distribution associated with local adaptation of physiology, behavior and life history, strong biogeographical patterns have not been found for microorganisms, raising questions about what determines their biogeography. Thus far, large-scale biogeographical studies have focused on free-living microbes, paying little attention to host-associated microbes, which play essential roles in physiology, behavior and life history of their hosts. Investigating cloacal gut microbiota of closely-related, ecologically similar free-living songbird species (Alaudidae, larks) inhabiting desert, temperate and tropical regions, we explored influences of geographical location and host species on α-diversity, co-occurrence of amplicon sequence variants (ASVs) and genera, differentially abundant and dominant bacterial taxa, and community composition. We also investigated how geographical distance explained differences in gut microbial community composition among larks. RESULTS Geographic location did not explain variation in richness and Shannon diversity of cloacal microbiota in larks. Out of 3798 ASVs and 799 bacterial genera identified, 17 ASVs (< 0.5%) and 43 genera (5%) were shared by larks from all locations. Desert larks held fewer unique ASVs (25%) than temperate zone (31%) and tropical larks (34%). Five out of 33 detected bacterial phyla dominated lark cloacal gut microbiomes. In tropical larks three bacterial classes were overrepresented. Highlighting the distinctiveness of desert lark microbiota, the relative abundances of 52 ASVs differed among locations, which classified within three dominant and 11 low-abundance phyla. Clear and significant phylogenetic clustering in cloacal microbiota community composition (unweighted UniFrac) showed segregation with geography and host species, where microbiota of desert larks were distinct from those of tropical and temperate regions. Geographic distance was nonlinearly associated with pairwise unweighted UniFrac distances. CONCLUSIONS We conclude that host-associated microbiota are geographically structured in a group of widespread but closely-related bird species, following large-scale macro-ecological patterns and contrasting with previous findings for free-living microbes. Future work should further explore if and to what extent geographic variation in host-associated microbiota can be explained as result of co-evolution between gut microbes and host adaptive traits, and if and how acquisition from the environmental pool of bacteria contributes to explaining host-associated communities.
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Gao Z, Song H, Dong H, Ji X, Lei Z, Tian Y, Wu Y, Zou H. Comparative analysis of intestinal flora between rare wild red-crowned crane and white-naped crane. Front Microbiol 2022; 13:1007884. [PMID: 36532425 PMCID: PMC9752901 DOI: 10.3389/fmicb.2022.1007884] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 11/14/2022] [Indexed: 10/17/2024] Open
Abstract
INTRODUCTION Animal intestines are extremely rich in microbial ecosystems. Numerous studies in different fields, such as epidemiology and histology, have revealed that gut microorganisms considerably mediate the survival and reproduction of animals. However, gut microbiology studies of homogeneously distributed wild cranes are still rare. This study aimed to understand the structural composition of the gut microbial community of wild cranes and elucidate the potential roles of the microorganisms. METHODS We used high-throughput sequencing to analyze the gut microbial community structure of wild cranes in the Zhalong Nature Reserve. RESULTS A total of 1,965,683 valid tags and 5248 OTUs were obtained from 32 fecal samples. Twenty-six bacteria phyla and 523 genera were annotated from the intestinal tract of the red-crowned crane. Twenty-five bacteria phyla and 625 genera were annotated from the intestine of the white-naped crane. Firmicutes, Proteobacteria, and Bacteroidetes are the dominant bacterial phyla in the intestinal tract of red-crowned cranes, while Catellicoccus, Lactobacillus, Neisseria, and Streptococcus were the dominant genera. The dominant bacterial phyla in the intestinal tract of white-naped cranes were Firmicutes, Proteobacteria, Bacteroidetes, Epsilonbacteraeota, Actinobacteria, and Fusobacteria. However, the dominant genera were Catellicoccus, Lactobacillus, Neisseria, Campylobacter, Streptococcus, Anaerobiospirillum, Romboutsia, Turicibacter, Haemophilus, and Lautropia. Firmicutes had significantly higher relative abundance in the intestine of the red-crowned than white-naped cranes (P < 0.05). However, the relative abundance of Actinobacteria and Bacteroidetes was significantly higher (P < 0.05) in the intestines of white-naped than red-crowned cranes. The diversity of the intestinal flora between the two crane species was significantly different (P < 0.05). Besides, the alpha diversity of the intestinal flora was higher for white-naped than red-crowned cranes. Eight of the 41 functional pathways differed in the gut of both crane species (P < 0.05). DISCUSSION Both species live in the same area and have similar feeding and behavioral characteristics. Therefore, host differences are possibly the main factors influencing the structural and functional differences in the composition of the gut microbial community. This study provides important reference data for constructing a crane gut microbial assessment system. The findings have implications for studying deeper relationships between crane gut microbes and genetics, nutrition, immunity, and disease.
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Affiliation(s)
- Zhongsi Gao
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
| | - Hongwei Song
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
| | - Haiyan Dong
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
| | - Xiaolong Ji
- Department of Genetics, College of Life Science, Northeast Forestry University, Harbin, China
| | - Zefeng Lei
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
| | - Ye Tian
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
| | - Yining Wu
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
| | - Hongfei Zou
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
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19
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Yan R, Lu M, Zhang L, Yao J, Li S, Jiang Y. Effect of sex on the gut microbiota characteristics of passerine migratory birds. Front Microbiol 2022; 13:917373. [PMID: 36118231 PMCID: PMC9478027 DOI: 10.3389/fmicb.2022.917373] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 08/05/2022] [Indexed: 11/23/2022] Open
Abstract
The gut microbiota, considered the “invisible organ” in the host animal, has been extensively studied recently. However, knowledge about the gut microbiota characteristics of passerine migratory birds during migration is limited. This study investigated the gut microbiota characteristics of three dominant migratory bird species (namely orange-flanked bluetail Tarsiger cyanurus, yellow-throated bunting Emberiza elegans, and black-faced bunting Emberiza spodocephala) in the same niche during spring migration and whether they were bird sex-specific. The compositions of gut microbiota species in these three migratory bird species and their male and female individuals were found to be similar. The main bacterial phyla were Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes, and the main genera were Lactobacillus, Acinetobacter, Rickettsiella, and Mycobacterium; however, their relative abundance was different. Moreover, some potential pathogens and beneficial bacteria were found in all the three bird species. Alpha diversity analysis showed that in T. cyanurus, the richness and diversity of the gut microbiota were higher in male individuals than in female individuals, while the opposite was true for E. elegans and E. spodocephala. The alpha diversity analysis showed significant differences between male and female individuals of E. elegans (p < 0.05). The beta diversity analysis also revealed that the gut microbial community structure differed significantly between the male and female individuals of the three migratory bird species.
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Affiliation(s)
- Rongfei Yan
- College of Animal Science and Technology, College of Veterinary Medicine, Jilin Agricultural University, Changchun, China
| | - Meixia Lu
- School of Life Sciences, Jilin Agricultural University, Changchun, China
| | - Lishi Zhang
- College of Animal Science and Technology, College of Veterinary Medicine, Jilin Agricultural University, Changchun, China
| | - Jiyuan Yao
- College of Animal Science and Technology, College of Veterinary Medicine, Jilin Agricultural University, Changchun, China
| | - Shi Li
- College of Animal Science and Technology, College of Veterinary Medicine, Jilin Agricultural University, Changchun, China
| | - Yunlei Jiang
- College of Animal Science and Technology, College of Veterinary Medicine, Jilin Agricultural University, Changchun, China
- *Correspondence: Yunlei Jiang,
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20
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Sun F, Chen J, Liu K, Tang M, Yang Y. The avian gut microbiota: Diversity, influencing factors, and future directions. Front Microbiol 2022; 13:934272. [PMID: 35992664 PMCID: PMC9389168 DOI: 10.3389/fmicb.2022.934272] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 07/08/2022] [Indexed: 11/13/2022] Open
Abstract
The gut microbiota is viewed as the “second genome” of animals, sharing intricate relationships with their respective hosts. Because the gut microbial community and its diversity are affected by many intrinsic and extrinsic factors, studying intestinal microbes has become an important research topic. However, publications are dominated by studies on domestic or captive birds, while research on the composition and response mechanism of environmental changes in the gut microbiota of wild birds remains scarce. Therefore, it is important to understand the co-evolution of host and intestinal bacteria under natural conditions to elucidate the diversity, maintenance mechanisms, and functions of gut microbes in wild birds. Here, the existing knowledge of gut microbiota in captive and wild birds is summarized, along with previous studies on the composition and function, research methods employed, and factors influencing the avian gut microbial communities. Furthermore, research hotspots and directions were also discussed to identify the dynamics of the avian gut microbiota, aiming to contribute to studies of avian microbiology in the future.
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21
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Zhang K, Wang X, Gong X, Sui J. Gut Microbiome Differences in Rescued Common Kestrels (Falco tinnunculus) Before and After Captivity. Front Microbiol 2022; 13:858592. [PMID: 35794924 PMCID: PMC9251364 DOI: 10.3389/fmicb.2022.858592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 05/19/2022] [Indexed: 11/13/2022] Open
Abstract
Gut microbes significantly impact animal health, yet research on the gut microbiota of most birds, especially raptors, is lacking. This study investigated the effects of dietary and environmental changes on the composition and abundance of gut microbiota in 17 rescued common kestrels (Falco tinnunculus) through 16S rRNA gene high-throughput sequencing of microorganisms in the feces of the birds. Firmicutes (relative abundance, 43.63%), Proteobacteria (37.26%), Actinobacteria (7.31%), and Bacteroidetes (5.48%) were the dominant phyla in the gut microbiota of the common kestrels. A comparison of the gut microbiota before and after captivity revealed that community composition and abundance of the common kestrel gut microbiota differed among different living conditions including diet and environment. At the phylum level, the abundance of Firmicutes was higher (P < 0.05), and that of Proteobacteria was lower (P < 0.05), after captivity (54.62 and 27.16%, respectively) compared with before captivity (33.67 and 46.41%, respectively), but no significant differences were found among other phyla. At the genus level, the abundance of Lactobacillus was higher (P < 0.05) after captivity (15.77%) compared with the abundance before captivity (5.02%). Hierarchical clustering and principal component analyses showed that common kestrels in different living conditions exhibited differences (P < 0.05) in gut microbiota at phylum and genus levels. Functional prediction of gene sequences using PICRUSt2 further revealed that pathways related to glucose metabolism and amino acid metabolism were enhanced (P < 0.05) after captivity. Collectively, the findings from this study demonstrated that the relative abundance of specific microbes in the gut of the rescued common kestrels either increased or decreased, and that dietary and environment changes might be the predominant factors affecting the gut microbiota of these birds during rescue or captivity.
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22
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Houtz JL, Taff CC, Vitousek MN. Gut Microbiome as a Mediator of Stress Resilience: A Reactive Scope Model Framework. Integr Comp Biol 2022; 62:41-57. [PMID: 35544275 DOI: 10.1093/icb/icac030] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Stress resilience is defined as the ability to rebound to a homeostatic state after exposure to a perturbation. Organisms modulate various physiological mediators to respond to unpredictable changes in their environment. The gut microbiome is a key example of a physiological mediator that coordinates a myriad of host functions including counteracting stressors. Here, we highlight the gut microbiome as a mediator of host stress resilience in the framework of the reactive scope model. The reactive scope model integrates physiological mediators with unpredictable environmental changes to predict how animals respond to stressors. We provide examples of how the gut microbiome responds to stressors within the four ranges of the reactive scope model (i.e., predictive homeostasis, reactive homeostasis, homeostatic overload, and homeostatic failure). We identify measurable metrics of the gut microbiome that could be used to infer the degree to which the host is experiencing chronic stress, including microbial diversity, flexibility, and gene richness. The goal of this perspective piece is to highlight the underutilized potential of measuring the gut microbiome as a mediator of stress resilience in wild animal hosts.
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Affiliation(s)
- Jennifer L Houtz
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, USA
| | - Conor C Taff
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, USA
| | - Maren N Vitousek
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, USA
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23
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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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24
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Davies CS, Worsley SF, Maher KH, Komdeur J, Burke T, Dugdale HL, Richardson DS. Immunogenetic variation shapes the gut microbiome in a natural vertebrate population. MICROBIOME 2022; 10:41. [PMID: 35256003 PMCID: PMC8903650 DOI: 10.1186/s40168-022-01233-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 01/20/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND The gut microbiome (GM) can influence many biological processes in the host, impacting its health and survival, but the GM can also be influenced by the host's traits. In vertebrates, Major Histocompatibility Complex (MHC) genes play a pivotal role in combatting pathogens and are thought to shape the host's GM. Despite this-and the documented importance of both GM and MHC variation to individual fitness-few studies have investigated the association between the GM and MHC in the wild. RESULTS We characterised MHC class I (MHC-I), MHC class II (MHC-II) and GM variation in individuals within a natural population of the Seychelles warbler (Acrocephalus sechellensis). We determined how the diversity and composition of the GM varied with MHC characteristics, in addition to environmental factors and other host traits. Our results show that the presence of specific MHC alleles, but not MHC diversity, influences both the diversity and composition of the GM in this population. MHC-I alleles, rather than MHC-II alleles, had the greatest impact on the GM. GM diversity was negatively associated with the presence of three MHC-I alleles (Ase-ua3, Ase-ua4, Ase-ua5), and one MHC-II allele (Ase-dab4), while changes in GM composition were associated with the presence of four different MHC-I alleles (Ase-ua1, Ase-ua7, Ase-ua10, Ase-ua11). There were no associations between GM diversity and TLR3 genotype, but GM diversity was positively correlated with genome-wide heterozygosity and varied with host age and field period. CONCLUSIONS These results suggest that components of the host's immune system play a role in shaping the GM of wild animals. Host genotype-specifically MHC-I and to a lesser degree MHC-II variation-can modulate the GM, although whether this occurs directly, or indirectly through effects on host health, is unclear. Importantly, if immune genes can regulate host health through modulation of the microbiome, then it is plausible that the microbiome could also influence selection on immune genes. As such, host-microbiome coevolution may play a role in maintaining functional immunogenetic variation within natural vertebrate populations. Video abstract.
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Affiliation(s)
- Charli S Davies
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norfolk, NR4 7TJ, UK.
- NERC Biomolecular Analysis Facility, Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK.
| | - Sarah F Worsley
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norfolk, NR4 7TJ, UK
| | - Kathryn H Maher
- NERC Biomolecular Analysis Facility, Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Jan Komdeur
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, P.O. Box 11103, 9700 CC, Groningen, The Netherlands
| | - Terry Burke
- NERC Biomolecular Analysis Facility, Department of Animal and Plant Sciences, 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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25
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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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26
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Franz M, Whyte L, Atwood TC, Laidre KL, Roy D, Watson SE, Góngora E, McKinney MA. Distinct gut microbiomes in two polar bear subpopulations inhabiting different sea ice ecoregions. Sci Rep 2022; 12:522. [PMID: 35017585 PMCID: PMC8752607 DOI: 10.1038/s41598-021-04340-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 12/13/2021] [Indexed: 11/09/2022] Open
Abstract
Gut microbiomes were analyzed by 16S rRNA gene metabarcoding for polar bears (Ursus maritimus) from the southern Beaufort Sea (SB), where sea ice loss has led to increased use of land-based food resources by bears, and from East Greenland (EG), where persistent sea ice has allowed hunting of ice-associated prey nearly year-round. SB polar bears showed a higher number of total (940 vs. 742) and unique (387 vs. 189) amplicon sequence variants and higher inter-individual variation compared to EG polar bears. Gut microbiome composition differed significantly between the two subpopulations and among sex/age classes, likely driven by diet variation and ontogenetic shifts in the gut microbiome. Dietary tracer analysis using fatty acid signatures for SB polar bears showed that diet explained more intrapopulation variation in gut microbiome composition and diversity than other tested variables, i.e., sex/age class, body condition, and capture year. Substantial differences in the SB gut microbiome relative to EG polar bears, and associations between SB gut microbiome and diet, suggest that the shifting foraging habits of SB polar bears tied to sea ice loss may be altering their gut microbiome, with potential consequences for nutrition and physiology.
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Affiliation(s)
- Megan Franz
- Department of Natural Resource Sciences, McGill University, Sainte-Anne-de-Bellevue, QC, H9X 3V9, Canada
| | - Lyle Whyte
- Department of Natural Resource Sciences, McGill University, Sainte-Anne-de-Bellevue, QC, H9X 3V9, Canada
| | - Todd C Atwood
- United States Geological Survey (USGS), Alaska Science Center, University Drive, Anchorage, AK, 99508, USA
| | - Kristin L Laidre
- Polar Science Center, Applied Physics Laboratory, University of Washington, Seattle, WA, USA
- Greenland Institute of Natural Resources, P.O. Box 570, Nuuk, Greenland
| | - Denis Roy
- Department of Natural Resource Sciences, McGill University, Sainte-Anne-de-Bellevue, QC, H9X 3V9, Canada
| | - Sophie E Watson
- School of Biosciences, Cardiff University, The Sir Martin Evans Building, Museum Avenue, Cardiff, UK
| | - Esteban Góngora
- Department of Natural Resource Sciences, McGill University, Sainte-Anne-de-Bellevue, QC, H9X 3V9, Canada
| | - Melissa A McKinney
- Department of Natural Resource Sciences, McGill University, Sainte-Anne-de-Bellevue, QC, H9X 3V9, Canada.
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27
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Minich D, Madden C, Navarro MA, Glowacki L, French-Kim K, Chan W, Evans MV, Soares K, Mrofchak R, Madan R, Ballash GA, LaPerle K, Paul S, Vodovotz Y, Uzal FA, Martinez M, Hausmann J, Junge RE, Hale VL. Gut microbiota and age shape susceptibility to clostridial enteritis in lorikeets under human care. Anim Microbiome 2022; 4:7. [PMID: 35000619 PMCID: PMC8744333 DOI: 10.1186/s42523-021-00148-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 12/07/2021] [Indexed: 12/14/2022] Open
Abstract
Background Enteritis is a common cause of morbidity and mortality in lorikeets that can be challenging to diagnose and treat. In this study, we examine gut microbiota in two lorikeet flocks with enteritis (Columbus Zoo and Aquarium—CZA; Denver Zoo—DZ). Since 2012, the CZA flock has experienced repeated outbreaks of enteritis despite extensive diet, husbandry, and clinical modifications. In 2018, both CZA and DZ observed a spike in enteritis. Recent research has revealed that the gut microbiota can influence susceptibility to enteropathogens. We hypothesized that a dysbiosis, or alteration in the gut microbial community, was making some lorikeets more susceptible to enteritis, and our goal was to characterize this dysbiosis and determine the features that predicted susceptibility.
Results We employed 16S rRNA sequencing to characterize the cloacal microbiota in lorikeets (CZA n = 67, DZ n = 24) over time. We compared the microbiota of healthy lorikeets, to lorikeets with enteritis, and lorikeets susceptible to enteritis, with “susceptible” being defined as healthy birds that subsequently developed enteritis. Based on sequencing data, culture, and toxin gene detection in intestinal contents, we identified Clostridium perfringens type A (CZA and DZ) and C. colinum (CZA only) at increased relative abundances in birds with enteritis. Histopathology and immunohistochemistry further identified the presence of gram-positive bacilli and C. perfringens, respectively, in the necrotizing intestinal lesions. Finally, using Random Forests and LASSO models, we identified several features (young age and the presence of Rhodococcus fascians and Pseudomonas umsongensis) associated with susceptibility to clostridial enteritis. Conclusions We identified C. perfringens type A and C. colinum associated with lorikeet necrohemorrhagic enteritis at CZA and DZ. Susceptibility testing of isolates lead to an updated clinical treatment plan which ultimately resolved the outbreaks at both institutions. This work provides a foundation for understanding gut microbiota features that are permissive to clostridial colonization and host factors (e.g. age, prior infection) that shape responses to infection. Supplementary Information The online version contains supplementary material available at 10.1186/s42523-021-00148-7.
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Affiliation(s)
- David Minich
- Department of Veterinary Preventive Medicine, Ohio State University College of Veterinary Medicine, 1902 Coffey Rd., Columbus, OH, 43210, USA
| | - Christopher Madden
- Department of Veterinary Preventive Medicine, Ohio State University College of Veterinary Medicine, 1902 Coffey Rd., Columbus, OH, 43210, USA
| | - Mauricio A Navarro
- California Animal Health & Food Safety Lab, University of California, Davis, San Bernardino, CA, USA.,Instituto de Patología Animal, Facultad de Ciencias Veterinarias, Universidad Austral de Chile, Valdivia, Chile
| | - Leo Glowacki
- Ohio State University College of Arts and Sciences, Columbus, OH, USA
| | - Kristen French-Kim
- Department of Veterinary Preventive Medicine, Ohio State University College of Veterinary Medicine, 1902 Coffey Rd., Columbus, OH, 43210, USA
| | - Willow Chan
- Ohio State University College of Food, Agricultural, and Environmental Sciences, Columbus, OH, USA
| | - Morgan V Evans
- Department of Veterinary Preventive Medicine, Ohio State University College of Veterinary Medicine, 1902 Coffey Rd., Columbus, OH, 43210, USA.,Ohio State University College of Public Health, Columbus, OH, USA
| | - Kilmer Soares
- Department of Veterinary Preventive Medicine, Ohio State University College of Veterinary Medicine, 1902 Coffey Rd., Columbus, OH, 43210, USA.,Department of Animal Science, College of Agricultural Sciences (CCA), Federal University of Paraiba (UFPB), Areia, PB, Brazil
| | - Ryan Mrofchak
- Department of Veterinary Preventive Medicine, Ohio State University College of Veterinary Medicine, 1902 Coffey Rd., Columbus, OH, 43210, USA
| | - Rushil Madan
- Department of Veterinary Preventive Medicine, Ohio State University College of Veterinary Medicine, 1902 Coffey Rd., Columbus, OH, 43210, USA
| | - Gregory A Ballash
- Department of Veterinary Preventive Medicine, Ohio State University College of Veterinary Medicine, 1902 Coffey Rd., Columbus, OH, 43210, USA
| | - Krista LaPerle
- Department of Veterinary Preventive Medicine, Ohio State University College of Veterinary Medicine, 1902 Coffey Rd., Columbus, OH, 43210, USA.,Comparative Pathology & Digital Imaging Shared Resource, Ohio State University, Columbus, OH, USA
| | - Subhadeep Paul
- Ohio State University College of Arts and Sciences, Columbus, OH, USA
| | - Yael Vodovotz
- Ohio State University College of Food, Agricultural, and Environmental Sciences, Columbus, OH, USA
| | - Francisco A Uzal
- California Animal Health & Food Safety Lab, University of California, Davis, San Bernardino, CA, USA
| | - Margaret Martinez
- Department of Veterinary Preventive Medicine, Ohio State University College of Veterinary Medicine, 1902 Coffey Rd., Columbus, OH, 43210, USA.,The Marine Mammal Center, Sausalito, CA, USA
| | | | | | - Vanessa L Hale
- Department of Veterinary Preventive Medicine, Ohio State University College of Veterinary Medicine, 1902 Coffey Rd., Columbus, OH, 43210, USA.
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Velando A, Noguera JC, Aira M, Domínguez J. Gut microbiome and telomere length in gull hatchlings. Biol Lett 2021; 17:20210398. [PMID: 34637637 DOI: 10.1098/rsbl.2021.0398] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
In many animals, recent evidence indicates that the gut microbiome may be acquired during early development, with possible consequences on newborns' health. Thus, it has been hypothesized that a healthy microbiome protects telomeres and genomic integrity against cellular stress. However, the link between the early acquired microbiome and telomere dynamics has not hitherto been investigated. In birds, this link may also be potentially modulated by the transfer of maternal glucocorticoids, since these substances dysregulate microbiome composition during postnatal development. Here, we examined the effect of the interplay between the microbiome and stress hormones on the telomere length of yellow-legged gull hatchlings by using a field experiment in which we manipulated the corticosterone content in eggs. We found that the hatchling telomere length was related to microbiome composition, but this relationship was not affected by the corticosterone treatment. Hatchlings with a microbiome dominated by potential commensal bacteria (i.e. Catellicoccus and Cetobacterium) had larger telomeres, suggesting that an early establishment of the species-specific microbiome during development may have important consequences on offspring health and survival.
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Affiliation(s)
- Alberto Velando
- Grupo de Ecoloxía Animal (GEA), Centro de Investigación Mariña, Universidade de Vigo, Vigo, Spain
| | - Jose Carlos Noguera
- Grupo de Ecoloxía Animal (GEA), Centro de Investigación Mariña, Universidade de Vigo, Vigo, Spain
| | - Manuel Aira
- Grupo de Ecoloxía Animal (GEA), Centro de Investigación Mariña, Universidade de Vigo, Vigo, Spain
| | - Jorge Domínguez
- Grupo de Ecoloxía Animal (GEA), Centro de Investigación Mariña, Universidade de Vigo, Vigo, Spain
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29
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Skeen HR, Cooper NW, Hackett SJ, Bates JM, Marra PP. Repeated sampling of individuals reveals impact of tropical and temperate habitats on microbiota of a migratory bird. Mol Ecol 2021; 30:5900-5916. [PMID: 34580952 DOI: 10.1111/mec.16170] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 08/26/2021] [Accepted: 09/02/2021] [Indexed: 01/04/2023]
Abstract
Migratory animals experiencing substantial change in diet and habitat across the annual cycle may have corresponding shifts in host-associated microbial diversity. Using automated telemetry and radio tags to recapture birds, we examined gut microbiota structure in the same population and often same individual of Kirtland's Warblers (Setophaga kirtlandii) initially sampled on their wintering grounds in The Bahamas and subsequently resampled within their breeding territories in Michigan, USA. Initial sampling occurred in March and April and resampling occurred in May, June and early July. The composition of the most abundant phyla and classes of the warblers' microbiota is similar to that of other migratory birds. However, we detected notable variation in abundance and diversity of numerous bacterial taxa, including a decrease in microbial richness and significant differences in microbial communities when comparing the microbiota of birds first captured in The Bahamas to that of birds recaptured in Michigan. This is observed at the individual and population level. Furthermore, we found that 22 bacterial genera exhibit heightened abundance within specific sampling periods and are probably associated with diet and environmental change. Finally, we described a small, species-specific shared microbial profile that spans multiple time periods and environments within the migratory cycle. Our research highlights that the avian gut microbiota is dynamic over time, most significantly impacted by changing environments associated with migration. These results support the need for full annual cycle monitoring of migratory bird microbiota to improve understanding of seasonal host movement ecologies and response to recurrent physiological stressors.
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Affiliation(s)
- Heather R Skeen
- Committee on Evolutionary Biology, University of Chicago, Chicago, Illinois, USA.,Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, Illinois, USA
| | - Nathan W Cooper
- Migratory Bird Center, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, District of Columbia, USA.,Department of Biology and McCourt School of Public Policy, Georgetown University, Washington, District of Columbia, USA
| | - Shannon J Hackett
- Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, Illinois, USA
| | - John M Bates
- Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, Illinois, USA
| | - Peter P Marra
- Department of Biology and McCourt School of Public Policy, Georgetown University, Washington, District of Columbia, USA
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30
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Duda MP, Hargan KE, Michelutti N, Blais JM, Grooms C, Gilchrist HG, Mallory ML, Robertson GJ, Smol JP. Reconstructing Long-Term Changes in Avian Populations Using Lake Sediments: Opening a Window Onto the Past. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.698175] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The lack of long-term monitoring data for many wildlife populations is a limiting factor in establishing meaningful and achievable conservation goals. Even for well-monitored species, time series are often very short relative to the timescales required to understand a population’s baseline conditions before the contemporary period of increased human impacts. To fill in this critical information gap, techniques have been developed to use sedimentary archives to provide insights into long-term population dynamics over timescales of decades to millennia. Lake and pond sediments receiving animal inputs (e.g., feces, feathers) typically preserve a record of ecological and environmental information that reflects past changes in population size and dynamics. With a focus on bird-related studies, we review the development and use of several paleolimnological proxies to reconstruct past colony sizes, including trace metals, isotopes, lipid biomolecules, diatoms, pollen and non-pollen palynomorphs, invertebrate sub-fossils, pigments, and others. We summarize how animal-influenced sediments, cored from around the world, have been successfully used in addressing some of the most challenging questions in conservation biology, namely: How dynamic are populations on long-term timescales? How may populations respond to climate change? How have populations responded to human intrusion? Finally, we conclude with an assessment of the current state of the field, challenges to overcome, and future potential for research.
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31
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Zhu Y, Li Y, Yang H, He K, Tang K. Establishment of Gut Microbiome During Early Life and Its Relationship With Growth in Endangered Crested Ibis ( Nipponia nippon). Front Microbiol 2021; 12:723682. [PMID: 34434183 PMCID: PMC8382091 DOI: 10.3389/fmicb.2021.723682] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 07/20/2021] [Indexed: 12/13/2022] Open
Abstract
Gut microbiota during early life could influence host fitness in vertebrates. Studies on how gut microbiota colonize the gut in birds using frequent sampling during early developmental stages and how shifts in microbiota diversity influence host growth are lacking. Here, we examine the microbiome profiles of 151 fecal samples from 14 young crested ibis (Nipponia nippon), an endangered bird species, collected longitudinally across 13 time points during the early stages of development and investigated their correlation with host growth. Gut diversity showed a non-linear change during development, which involved multiple colonization and extinction events, mainly associated with Proteobacteria and Firmicutes. Gut microbiota in young crested ibis became more similar with increasing age. In addition, gut microbiota exhibited a strong temporal structure and two specific developmental stages; the beginning of the latter stage coincided with the introduction of fresh loach, with a considerable increase in the relative abundance of Fusobacteria and several Firmicutes, which may be involved in lipid metabolism. Crested ibis chick growth rate was negatively correlated with gut microbiota diversity and negatively associated with the abundance of Halomonadaceae, Streptococci, Corynebacteriaceae, and Dietziaceae. Our findings highlight the importance of frequent sampling when studying microbiome development during early stages of development of vertebrates. The role of microbial diversity in host growth during the early stages of development of birds warrants further investigations.
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Affiliation(s)
- Ying Zhu
- Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, China
| | - Yudong Li
- Sichuan Province Laboratory for Natural Resources Protection and Sustainable Utilization, Sichuan Provincial Academy of Natural Resource Sciences, Chengdu, China
| | - Haiqiong Yang
- Emei Breeding Center for Crested Ibis, Emei, Chengdu, China
| | - Ke He
- College of Animal Sciences and Technology, Zhejiang A&F University, Hangzhou, China
| | - Keyi Tang
- College of Life Sciences, Sichuan Normal University, Chengdu, China
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32
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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: 45] [Impact Index Per Article: 15.0] [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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33
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Góngora E, Elliott KH, Whyte L. Gut microbiome is affected by inter-sexual and inter-seasonal variation in diet for thick-billed murres (Uria lomvia). Sci Rep 2021; 11:1200. [PMID: 33441848 PMCID: PMC7806582 DOI: 10.1038/s41598-020-80557-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 12/14/2020] [Indexed: 01/29/2023] Open
Abstract
The role of the gut microbiome is increasingly being recognized by health scientists and veterinarians, yet its role in wild animals remains understudied. Variations in the gut microbiome could be the result of differential diets among individuals, such as variation between sexes, across seasons, or across reproductive stages. We evaluated the hypothesis that diet alters the avian gut microbiome using stable isotope analysis (SIA) and 16S rRNA gene sequencing. We present the first description of the thick-billed murre (Uria lomvia) fecal microbiome. The murre microbiome was dominated by bacteria from the genus Catellicoccus, ubiquitous in the guts of many seabirds. Microbiome variation was explained by murre diet in terms of proportion of littoral carbon, trophic position, and sulfur isotopes, especially for the classes Actinobacteria, Bacilli, Bacteroidia, Clostridia, Alphaproteobacteria, and Gammaproteobacteria. We also observed differences in the abundance of bacterial genera such as Catellicoccus and Cetobacterium between sexes and reproductive stages. These results are in accordance with behavioural observations of changes in diet between sexes and across the reproductive season. We concluded that the observed variation in the gut microbiome may be caused by individual prey specialization and may also be reinforced by sexual and reproductive stage differences in diet.
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Affiliation(s)
- Esteban Góngora
- Department of Natural Resource Sciences, McGill University, 21111 Lakeshore Road, Sainte-Anne-de-Bellevue, H9X 3V9, Canada.
| | - Kyle H Elliott
- Department of Natural Resource Sciences, McGill University, 21111 Lakeshore Road, Sainte-Anne-de-Bellevue, H9X 3V9, Canada
| | - Lyle Whyte
- Department of Natural Resource Sciences, McGill University, 21111 Lakeshore Road, Sainte-Anne-de-Bellevue, H9X 3V9, Canada
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