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Kelly LA, Yost CK, Cooke SJ. Opportunities and challenges with transitioning to non-lethal sampling of wild fish for microbiome research. JOURNAL OF FISH BIOLOGY 2024; 104:912-919. [PMID: 38226503 DOI: 10.1111/jfb.15650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 12/19/2023] [Indexed: 01/17/2024]
Abstract
The microbial communities of fish are considered an integral part of maintaining the overall health and fitness of their host. Research has shown that resident microbes reside on various mucosal surfaces, such as the gills, skin, and gastrointestinal tract, and play a key role in various host functions, including digestion, immunity, and disease resistance. A second, more transient group of microbes reside in the digesta, or feces, and are primarily influenced by environmental factors such as the host diet. The vast majority of fish microbiome research currently uses lethal sampling to analyse any one of these mucosal and/or digesta microbial communities. The present paper discusses the various opportunities that non-lethal microbiome sampling offers, as well as some inherent challenges, with the ultimate goal of creating a sound argument for future researchers to transition to non-lethal sampling of wild fish in microbiome research. Doing so will reduce animal welfare and population impacts on fish while creating novel opportunities to link host microbial communities to an individual's behavior and survival across space and time (e.g., life-stages, seasons). Current lethal sampling efforts constrain our ability to understand the mechanistic ecological consequences of variation in microbiome communities in the wild. Transitioning to non-lethal sampling will open new frontiers in ecological and microbial research.
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Affiliation(s)
- Lisa A Kelly
- Fish Ecology and Conservation Physiology Laboratory, Department of Biology, Institute of Environmental and Interdisciplinary Science, Carleton University, Ottawa, Ontario, Canada
| | - Christopher K Yost
- Department of Biology, University of Regina, Regina, Saskatchewan, Canada
- Institute for Microbial Systems and Society, University of Regina, Regina, Saskatchewan, Canada
| | - Steven J Cooke
- Fish Ecology and Conservation Physiology Laboratory, Department of Biology, Institute of Environmental and Interdisciplinary Science, Carleton University, Ottawa, Ontario, Canada
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2
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Jiang XR, Dai YY, Wang YR, Guo K, Du Y, Gao JF, Lin LH, Li P, Li H, Ji X, Qu YF. Dietary and Sexual Correlates of Gut Microbiota in the Japanese Gecko, Gekko japonicus (Schlegel, 1836). Animals (Basel) 2023; 13:ani13081365. [PMID: 37106928 PMCID: PMC10134999 DOI: 10.3390/ani13081365] [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: 03/01/2023] [Revised: 04/06/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023] Open
Abstract
Numerous studies have demonstrated that multiple intrinsic and extrinsic factors shape the structure and composition of gut microbiota in a host. The disorder of the gut microbiota may trigger various host diseases. Here, we collected fecal samples from wild-caught Japanese geckos (Gekko japonicus) and captive conspecifics fed with mealworms (mealworm-fed geckos) and fruit flies (fly-fed geckos), aiming to examine the dietary and sexual correlates of the gut microbiota. We used 16S rRNA gene sequencing technology to determine the composition of the gut microbiota. The dominant phyla with a mean relative abundance higher than 10% were Verrucomicrobiota, Bacteroidota, and Firmicutes. Gut microbial community richness and diversity were higher in mealworm-fed geckos than in wild geckos. Neither community evenness nor beta diversity of gut microbiota differed among wild, mealworm-fed, and fly-fed geckos. The beta rather than alpha diversity of gut microbiota was sex dependent. Based on the relative abundance of gut bacteria and their gene functions, we concluded that gut microbiota contributed more significantly to the host's metabolic and immune functions. A higher diversity of gut microbiota in mealworm-fed geckos could result from higher chitin content in insects of the order Coleoptera. This study not only provides basic information about the gut microbiota of G. japonicus but also shows that gut microbiota correlates with dietary habits and sex in the species.
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Affiliation(s)
- Xin-Ru Jiang
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Ying-Yu Dai
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Yu-Rong Wang
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Kun Guo
- Zhejiang Provincial Key Laboratory for Water Environment and Marine Biological Resources Protection, College of Life and Environmental Sciences, Wenzhou University, Wenzhou 325035, China
| | - Yu Du
- Hainan Key Laboratory of Herpetological Research, College of Fisheries and Life Science, Hainan Tropical Ocean University, Sanya 572022, China
| | - Jian-Fang Gao
- Herpetological Research Center, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Long-Hui Lin
- Herpetological Research Center, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Peng Li
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Hong Li
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Xiang Ji
- Zhejiang Provincial Key Laboratory for Water Environment and Marine Biological Resources Protection, College of Life and Environmental Sciences, Wenzhou University, Wenzhou 325035, China
| | - Yan-Fu Qu
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
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Kim JE, Tun HM, Bennett DC, Leung FC, Cheng KM. Microbial diversity and metabolic function in duodenum, jejunum and ileum of emu (Dromaius novaehollandiae). Sci Rep 2023; 13:4488. [PMID: 36934111 PMCID: PMC10024708 DOI: 10.1038/s41598-023-31684-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 03/15/2023] [Indexed: 03/20/2023] Open
Abstract
Emus (Dromaius novaehollandiae), a large flightless omnivorous ratite, are farmed for their fat and meat. Emu fat can be rendered into oil for therapeutic and cosmetic use. They are capable of gaining a significant portion of its daily energy requirement from the digestion of plant fibre. Despite of its large body size and low metabolic rate, emus have a relatively simple gastroinstetinal (GI) tract with a short mean digesta retention time. However, little is known about the GI microbial diversity of emus. The objective of this study was to characterize the intraluminal intestinal bacterial community in the different segments of small intestine (duodenum, jejunum, and ileum) using pyrotag sequencing and compare that with the ceca. Gut content samples were collected from each of four adult emus (2 males, 2 females; 5-6 years old) that were free ranged but supplemented with a barley-alfalfa-canola based diet. We amplified the V3-V5 region of 16S rRNA gene to identify the bacterial community using Roche 454 Junior system. After quality trimming, a total of 165,585 sequence reads were obtained from different segments of the small intestine (SI). A total of 701 operational taxonomic units (OTUs) were identified in the different segments of small intestine. Firmicutes (14-99%) and Proteobacteria (0.5-76%) were the most predominant bacterial phyla in the small intestine. Based on species richness estimation (Chao1 index), the average number of estimated OTUs in the small intestinal compartments were 148 in Duodenum, 167 in Jejunum, and 85 in Ileum, respectively. Low number of core OTUs identified in each compartment of small intestine across individual birds (Duodenum: 13 OTUs, Jejunum: 2 OTUs, Ileum: 14 OTUs) indicated unique bacterial community in each bird. Moreover, only 2 OTUs (Escherichia and Sinobacteraceae) were identified as core bacteria along the whole small intestine. PICRUSt analysis has indicated that the detoxification of plant material and environmental chemicals seem to be performed by SI microbiota, especially those in the jejunum. The emu cecal microbiome has more genes than SI segments involving in protective or immune response to enteric pathogens. Microbial digestion and fermentation is mostly in the jejunum and ceca. This is the first study to characterize the microbiota of different compartments of the emu intestines via gut samples and not fecal samples. Results from this study allow us to further investigate the influence of the seasonal and physiological changes of intestinal microbiota on the nutrition of emus and indirectly influence the fatty acid composition of emu fat.
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Affiliation(s)
- Ji Eun Kim
- Avian Research Centre, Faculty of Land and Food Systems, University of British Columbia, 2357 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Hein M Tun
- School of Public Health, Li Ka Shing, Faculty of Medicine, HKU-Pasteur Research Pole, University of Hong Kong, Pok Fu Lam, Hong Kong SAR, China
- JC School of Public Health and Primary Care, Faculty of Medicine, Chinese University of Hong Kong, Sha Tin, Hong Kong SAR, China
| | - Darin C Bennett
- Avian Research Centre, Faculty of Land and Food Systems, University of British Columbia, 2357 Main Mall, Vancouver, BC, V6T 1Z4, Canada
- Animal Science Department, California Polytechnic State University, San Luis Obispo, CA, 93407, USA
| | - Frederick C Leung
- School of Biological Sciences, Faculty of Science, University of Hong Kong, Pok Fu Lam, Hong Kong SAR, China
| | - Kimberly M Cheng
- Avian Research Centre, Faculty of Land and Food Systems, University of British Columbia, 2357 Main Mall, Vancouver, BC, V6T 1Z4, Canada.
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Zhao C, Liu L, Gao L, Bai L. A comprehensive comparison of fecal microbiota in three ecological bird groups of raptors, waders, and waterfowl. Front Microbiol 2022; 13:919111. [PMID: 36003944 PMCID: PMC9393522 DOI: 10.3389/fmicb.2022.919111] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 07/11/2022] [Indexed: 11/13/2022] Open
Abstract
Gut microbiota plays a vital role in maintaining the health and immunity of wild birds. However, less is known about the comparison of fecal microbiota between different ecological groups of wild birds, particularly in the Yellow River National Wetland in Baotou, China, an important transit point for birds migrating all over the East Asia-Australian and Central Asian flyways. In this study, we characterized the fecal microbiota and potential microbial function in nine bird species of raptors, waders, and waterfowl using 16S rRNA gene amplicon sequencing to reveal the microbiota differences and interaction patterns. The results indicated that there was no significant difference in α-diversity, but a significant difference in β-diversity between the three groups of birds. The fecal bacterial microbiota was dominated by Firmicutes, Proteobacteria, Actinobacteria, and Bacteroidetes in all groups of birds. Furthermore, we identified five bacterial genera that were significantly higher in raptors, five genera that were significantly higher in waders, and two genera that were more abundant in waterfowl. The bacterial co-occurrence network results revealed 15 and 26 key genera in raptors and waterfowls, respectively. The microbial network in waterfowl exhibited a stronger correlation pattern than that in raptors. PICRUSt2 predictions indicated that fecal bacterial function was significantly enriched in the antibiotic biosynthesis pathway in all three groups. Metabolic pathways related to cell motility (bacterial chemotaxis and flagellar assembly) were significantly more abundant in raptors than in waders, whereas waders were enriched in lipid metabolism (synthesis and degradation of ketone bodies and fatty acid biosynthesis). The fecal microbiota in waterfowl harbored more abundant vitamin B6 metabolism, RNA polymerase, and tyrosine and tryptophan biosynthesis. This comparative study revealed the microbial community structure, microbial co-occurrence patterns, and potential functions, providing a better understanding of the ecology and conservation of wild birds. Future studies may focus on unraveling metagenomic functions and dynamics along with the migration routine or different seasons by metagenomics or metatranscriptomics.
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5
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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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Huang Z, Zhu L, Lv J, Pu Z, Zhang L, Chen G, Hu X, Zhang Z, Zhang H. Dietary Effects on Biological Parameters and Gut Microbiota of Harmonia axyridis. Front Microbiol 2022; 12:818787. [PMID: 35154044 PMCID: PMC8828657 DOI: 10.3389/fmicb.2021.818787] [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: 11/22/2021] [Accepted: 12/29/2021] [Indexed: 12/24/2022] Open
Abstract
The multicolored Asian lady beetle (Harmonia axyridis, H. axyridis, Coleoptera, and Coccinellidae) is an effective biocontrol agent against agricultural pests. Previous studies have suggested that amount, type, and the quality of food can directly affect the biological aspects of H. axyridis. In this study, we investigated the influence of the food sources (Acyrthosiphon pisum Harris, Diaphorina citri Kuwayama, and artificial diets) on the gut microbiota diversity and the biology, reproductive variables, and population growth indicators of H. axyridis. Three kinds of diets were considered in this study: (1) HY: the adult of A. pisum Harris (HY group); (2) HM: the adult of D. citri Kuwayama (HM group); (3) HR: artificial diets prepared by blending a portion of fresh homogenized pork liver (15 g), honey (3 g), distilled water (35 ml) (HR group). We found that gut microbiota composition and diversity and the biological parameters differed when H. axyridis was fed with different diets. The abundance of Enterobacteriaceae was the highest in the HM group, followed by HY group, and was the lowest in the HR group. The abundance of Staphylococcaceae was highest in the HR group. Among the gut fungi, Davidiellaceae and Wallemiaceae were the highest and lowest in the HY group; Incertae_sedis were the major gut fungi in the HR group. Meanwhile, the changes of biological parameters may be correlated with the changes of Streptococcaceae abundance, Micrococcaceae abundance, Staphylococcaceae abundance, and Enterobacteriaceae abundance in responds to diet changes. To sum up, these data suggest that different diets can influence the changes in adult H. axyridis gut microbiota, consequently affecting the biological parameters.
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Affiliation(s)
- Zhendong Huang
- The Citrus Research Institute of Zhejiang Province, Taizhou, China
- State Key Laboratory of Agricultural Microbiology, Institute of Urban and Horticultural Entomology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- *Correspondence: Zhendong Huang,
| | - Li Zhu
- The Citrus Research Institute of Zhejiang Province, Taizhou, China
| | - Jia Lv
- The Citrus Research Institute of Zhejiang Province, Taizhou, China
| | - Zhanxu Pu
- The Citrus Research Institute of Zhejiang Province, Taizhou, China
| | - Lipin Zhang
- The Citrus Research Institute of Zhejiang Province, Taizhou, China
| | - Guoqing Chen
- The Citrus Research Institute of Zhejiang Province, Taizhou, China
| | - Xiurong Hu
- The Citrus Research Institute of Zhejiang Province, Taizhou, China
| | - Zhenyu Zhang
- State Key Laboratory of Agricultural Microbiology, Institute of Urban and Horticultural Entomology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Hongyu Zhang
- State Key Laboratory of Agricultural Microbiology, Institute of Urban and Horticultural Entomology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
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7
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Du Y, Chen JQ, Liu Q, Fu JC, Lin CX, Lin LH, Li H, Qu YF, Ji X. Dietary Correlates of Oral and Gut Microbiota in the Water Monitor Lizard, Varanus salvator (Laurenti, 1768). Front Microbiol 2022; 12:771527. [PMID: 35069477 PMCID: PMC8770915 DOI: 10.3389/fmicb.2021.771527] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 11/30/2021] [Indexed: 12/11/2022] Open
Abstract
Numerous studies have demonstrated that food shapes the structure and composition of the host’s oral and gut microbiota. The disorder of oral and gut microbiota may trigger various host diseases. Here, we collected oral and gut samples from wild water monitor lizards (Varanus salvator) and their captive conspecifics fed with bullfrogs, eggs, and depilated chicken, aiming to examine dietary correlates of oral and gut microbiota. We used the 16S rRNA gene sequencing technology to analyze the composition of the microbiota. Proteobacteria and Bacteroidota were the dominant phyla in the oral microbiota, and so were in the gut microbiota. The alpha diversity of microbiota was significantly higher in the gut than in the oral cavity, and the alpha diversity of oral microbiota was higher in captive lizards than in wild conspecifics. Comparing the relative abundance of oral and gut bacteria and their gene functions, differences among different animal groups presumably resulted from human contact in artificial breeding environments and complex food processing. Differences in gene function might be related to the absolute number and/or the taxonomic abundance of oral and gut microorganisms in the wild and the water environment. This study provides not only basic information about the oral and gut microbiota of captive and wild water monitor lizards, but also an inference that feeding on frogs and aquatic products and reducing human exposure help water monitor lizards maintain a microbiota similar to that in the wild environment.
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Affiliation(s)
- Yu Du
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China.,Hainan Key Laboratory of Herpetological Research, College of Fisheries and Life Science, Hainan Tropical Ocean University, Sanya, China.,MOE Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources, Hainan Tropical Ocean University, Sanya, China
| | - Jun-Qiong Chen
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Qian Liu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Jian-Chao Fu
- Hainan Key Laboratory of Herpetological Research, College of Fisheries and Life Science, Hainan Tropical Ocean University, Sanya, China.,MOE Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources, Hainan Tropical Ocean University, Sanya, China
| | - Chi-Xian Lin
- Hainan Key Laboratory of Herpetological Research, College of Fisheries and Life Science, Hainan Tropical Ocean University, Sanya, China.,MOE Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources, Hainan Tropical Ocean University, Sanya, China
| | - Long-Hui Lin
- Hangzhou Key Laboratory for Ecosystem Protection and Restoration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Hong Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Yan-Fu Qu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Xiang Ji
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China.,Hainan Key Laboratory of Herpetological Research, College of Fisheries and Life Science, Hainan Tropical Ocean University, Sanya, China.,Zhejiang Provincial Key Laboratory for Water Environment and Marine Biological Resources Protection, College of Life and Environmental Sciences, Wenzhou University, Wenzhou, China
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8
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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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9
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Wang W, Huang S, Yang L, Zhang G. Comparative Analysis of the Fecal Bacterial Microbiota of Wintering Whooper Swans ( Cygnus Cygnus). Front Vet Sci 2021; 8:670645. [PMID: 34322532 PMCID: PMC8310996 DOI: 10.3389/fvets.2021.670645] [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: 03/18/2021] [Accepted: 06/08/2021] [Indexed: 12/03/2022] Open
Abstract
There are many and diverse intestinal microbiota, and they are closely related to various physiological functions of the body. They directly participate in the host's food digestion, nutrient absorption, energy metabolism, immune response, and many other physiological activities and are also related to the occurrence of many diseases. The intestinal microbiota are extremely important for maintaining normal physical health. In order to explore the composition and differences of the intestinal microbiota of whooper swans in different wintering areas, we collected fecal samples of whooper swans in Sanmenxia, Henan, and Rongcheng, Shandong, and we used the Illumina HiSeq platform to perform high-throughput sequencing of bacterial 16S rRNA genes. Comparison between Sanmenxia and Rongcheng showed no significant differences in ACE, Chao 1, Simpson, and Shannon indices (p > 0.05). Beta diversity results showed significant differences in bacterial communities between two groups [analysis of similarity (ANOSIM): R = 0.80, p = 0.011]. Linear discriminant analysis effect size (LEfSe) analysis showed that at the phylum level, the relative abundance of Actinobacteria was significantly higher in Sanmenxia whooper swans than Rongcheng whooper swans. At the genus level, the amount of Psychrobacter and Carnobacterium in Sanmenxia was significantly higher in Rongcheng, while the relative abundance Catellicoccus and Lactobacillus was significantly higher in Rongcheng than in Sanmenxia. This study analyzed the composition, characteristics, and differences of the intestinal microbiota of the whooper swans in different wintering environments and provided theoretical support for further exploring the relationship between the intestinal microbiota of the whooper swans and the external environment. And it played an important role in the overwintering physiology and ecology, population management, and epidemic prevention and control of whooper swans.
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Affiliation(s)
- Wenxia Wang
- Research Institute of Forestry Policy and Information, Chinese Academy of Forestry, Beijing, China
| | - Songlin Huang
- Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Beijing, China
| | - Liangliang Yang
- Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Beijing, China
| | - Guogang Zhang
- Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Beijing, China
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10
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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: 20] [Impact Index Per Article: 6.7] [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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11
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Jiang D, He X, Valitutto M, Chen L, Xu Q, Yao Y, Hou R, Wang H. Gut microbiota composition and metabolomic profiles of wild and captive Chinese monals (Lophophorus lhuysii). Front Zool 2020; 17:36. [PMID: 33292307 PMCID: PMC7713318 DOI: 10.1186/s12983-020-00381-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 11/16/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The Chinese monal (Lophophorus lhuysii) is an endangered bird species, with a wild population restricted to the mountains in southwest China, and only one known captive population in the world. We investigated the fecal microbiota and metabolome of wild and captive Chinese monals to explore differences and similarities in nutritional status and digestive characteristics. An integrated approach combining 16S ribosomal RNA (16S rRNA) gene sequencing and ultra-high performance liquid chromatography (UHPLC) based metabolomics were used to examine the fecal microbiota composition and the metabolomic profile of Chinese monals. RESULTS The results showed that the alpha diversity of gut microbes in the wild group were significantly higher than that in the captive group and the core bacterial taxa in the two groups showed remarkable differences at phylum, class, order, and family levels. Metabolomic profiling also revealed differences, mainly related to galactose, starch and sucrose metabolism, fatty acid, bile acid biosynthesis and bile secretion. Furthermore, strong correlations between metabolite types and bacterial genus were detected. CONCLUSIONS There were remarkable differences in the gut microbiota composition and metabolomic profile between wild and captive Chinese monals. This study has established a baseline for a normal gut microbiota and metabolomic profile for wild Chinese monals, thus allowing us to evaluate if differences seen in captive organisms have an impact on their overall health and reproduction.
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Affiliation(s)
- Dandan Jiang
- Chengdu Research Base of Giant Panda Breeding, Chengdu, 610081, China
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu, 610081, China
- Sichuan Academy of Giant Panda, Chengdu, 610081, China
| | - Xin He
- Chengdu Research Base of Giant Panda Breeding, Chengdu, 610081, China
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu, 610081, China
- Sichuan Academy of Giant Panda, Chengdu, 610081, China
| | - Marc Valitutto
- Chengdu Research Base of Giant Panda Breeding, Chengdu, 610081, China
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu, 610081, China
- Sichuan Academy of Giant Panda, Chengdu, 610081, China
- EcoHealth Alliance, New York, NY, 10012, USA
| | - Li Chen
- Sichuan Fengtongzhai National Nature reserve administration, Yaan, 625700, China
| | - Qin Xu
- Chengdu Research Base of Giant Panda Breeding, Chengdu, 610081, China
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu, 610081, China
- Sichuan Academy of Giant Panda, Chengdu, 610081, China
| | - Ying Yao
- Chengdu Research Base of Giant Panda Breeding, Chengdu, 610081, China
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu, 610081, China
- Sichuan Academy of Giant Panda, Chengdu, 610081, China
| | - Rong Hou
- Chengdu Research Base of Giant Panda Breeding, Chengdu, 610081, China
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu, 610081, China
- Sichuan Academy of Giant Panda, Chengdu, 610081, China
| | - Hairui Wang
- Chengdu Research Base of Giant Panda Breeding, Chengdu, 610081, China.
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu, 610081, China.
- Sichuan Academy of Giant Panda, Chengdu, 610081, China.
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12
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Zhou J, Zhao YT, Dai YY, Jiang YJ, Lin LH, Li H, Li P, Qu YF, Ji X. Captivity affects diversity, abundance, and functional pathways of gut microbiota in the northern grass lizard Takydromus septentrionalis. Microbiologyopen 2020; 9:e1095. [PMID: 32666685 PMCID: PMC7520994 DOI: 10.1002/mbo3.1095] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 05/15/2020] [Accepted: 05/30/2020] [Indexed: 12/14/2022] Open
Abstract
Animals in captivity undergo a range of environmental changes from wild animals. An increasing number of studies show that captivity significantly affects the abundance and community structure of gut microbiota. The northern grass lizard (Takydromus septentrionalis) is an extensively studied lacertid lizard and has a distributional range covering the central and southeastern parts of China. Nonetheless, little is known about the gut microbiota of this species, which may play a certain role in nutrient and energy metabolism as well as immune homeostasis. Here, we examined the differences in the gut microbiota between two groups (wild and captive) of lizards through 16S rRNA sequencing using the Illumina HiSeq platform. The results demonstrated that the dominant microbial components in both groups consisted of Proteobacteria, Firmicutes, and Tenericutes. The two groups did not differ in the abundance of these three phyla. Citrobacter was the most dominant genus in wild lizards, while Morganella was the most dominant genus in captive lizards. Moreover, gene function predictions showed that genes at the KEGG pathway levels2 were more abundant in wild lizards than in captive lizards but, at the KEGG pathway levels1, the differences in gene abundances between wild and captive lizards were not significant. In summary, captivity exerted a significant impact on the gut microbial community structure and diversity in T. septentrionalis, and future work could usefully investigate the causes of these changes using a comparative approach.
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Affiliation(s)
- Jin Zhou
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Yu-Tian Zhao
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Ying-Yu Dai
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Yi-Jin Jiang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Long-Hui Lin
- Hangzhou Key Laboratory for Ecosystem Protection and Restoration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Hong Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Peng Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Yan-Fu Qu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Xiang Ji
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
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13
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Levy H, Fiddaman SR, Vianna JA, Noll D, Clucas GV, Sidhu JKH, Polito MJ, Bost CA, Phillips RA, Crofts S, Miller GD, Pistorius P, Bonnadonna F, Le Bohec C, Barbosa A, Trathan P, Raya Rey A, Frantz LAF, Hart T, Smith AL. Evidence of Pathogen-Induced Immunogenetic Selection across the Large Geographic Range of a Wild Seabird. Mol Biol Evol 2020; 37:1708-1726. [PMID: 32096861 PMCID: PMC7253215 DOI: 10.1093/molbev/msaa040] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Over evolutionary time, pathogen challenge shapes the immune phenotype of the host to better respond to an incipient threat. The extent and direction of this selection pressure depend on the local pathogen composition, which is in turn determined by biotic and abiotic features of the environment. However, little is known about adaptation to local pathogen threats in wild animals. The Gentoo penguin (Pygoscelis papua) is a species complex that lends itself to the study of immune adaptation because of its circumpolar distribution over a large latitudinal range, with little or no admixture between different clades. In this study, we examine the diversity in a key family of innate immune genes-the Toll-like receptors (TLRs)-across the range of the Gentoo penguin. The three TLRs that we investigated present varying levels of diversity, with TLR4 and TLR5 greatly exceeding the diversity of TLR7. We present evidence of positive selection in TLR4 and TLR5, which points to pathogen-driven adaptation to the local pathogen milieu. Finally, we demonstrate that two positively selected cosegregating sites in TLR5 are sufficient to alter the responsiveness of the receptor to its bacterial ligand, flagellin. Taken together, these results suggest that Gentoo penguins have experienced distinct pathogen-driven selection pressures in different environments, which may be important given the role of the Gentoo penguin as a sentinel species in some of the world's most rapidly changing environments.
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Affiliation(s)
- Hila Levy
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | | | - Juliana A Vianna
- Departamento de Ecosistemas y Medio Ambiente, Pontificia Universidad Católica de Chile, Macul, Santiago, Chile
| | - Daly Noll
- Departamento de Ecosistemas y Medio Ambiente, Pontificia Universidad Católica de Chile, Macul, Santiago, Chile
- Departamento de Ciencias Ecológicas, Instituto de Ecología y Biodiversidad, Universidad de Chile, Santiago, Chile
| | - Gemma V Clucas
- Cornell Atkinson Center for a Sustainable Future, Cornell University, Ithaca, NY
- Cornell Lab of Ornithology, Cornell University, Ithaca, NY
| | | | - Michael J Polito
- Department of Oceanography and Coastal Sciences, Louisiana State University, Baton Rouge, LA
| | - Charles A Bost
- Centre d’Etudes Biologiques de Chizé (CEBC), UMR 7372 du CNRS‐Université de La Rochelle, Villiers‐en‐Bois, France
| | | | - Sarah Crofts
- Falklands Conservation, Stanley, Falkland Islands, United Kingdom
| | - Gary D Miller
- Microbiology and Immunology, PALM, University of Western Australia, Crawley, Western Australia, Australia
| | - Pierre Pistorius
- DST/NRF Centre of Excellence at the Percy FitzPatrick Institute for African Ornithology, Department of Zoology, Nelson Mandela University, Port Elizabeth, South Africa
| | - Francesco Bonnadonna
- CEFE UMR 5175, CNRS, Université de Montpellier, Université Paul-Valéry Montpellier, EPHE, Montpellier, France
| | - Céline Le Bohec
- Université de Strasbourg, CNRS, IPHC UMR 7178, Strasbourg, France
- Département de Biologie Polaire, Centre Scientifique de Monaco, Monaco, Principality of Monaco
| | - Andrés Barbosa
- Museo Nacional de Ciencias Naturales, Departamento de Ecología Evolutiva, CSIC, Madrid, Spain
| | - Phil Trathan
- British Antarctic Survey, Cambridge, United Kingdom
| | - Andrea Raya Rey
- Centro Austral de Investigaciones Científicas – Consejo Nacional de Investigaciones Científicas y Técnicas (CADIC-CONICET), Ushuaia, Tierra del Fuego, Argentina
- Instituto de Ciencias Polares, Ambiente y Recursos Naturales, Universidad Nacional de Tierra del Fuego, Ushuaia, Tierra del Fuego, Argentina
- Wildlife Conservation Society, Buenos Aires, Argentina
| | - Laurent A F Frantz
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Tom Hart
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Adrian L Smith
- Department of Zoology, University of Oxford, Oxford, United Kingdom
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14
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Zhang F, Xiang X, Dong Y, Yan S, Song Y, Zhou L. Significant Differences in the Gut Bacterial Communities of Hooded Crane ( Grus monacha) in Different Seasons at a Stopover Site on the Flyway. Animals (Basel) 2020; 10:E701. [PMID: 32316467 PMCID: PMC7222709 DOI: 10.3390/ani10040701] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 04/10/2020] [Accepted: 04/15/2020] [Indexed: 02/08/2023] Open
Abstract
Intestinal bacterial communities form an integral component of the organism. Many factors influence gut bacterial community composition and diversity, including diet, environment and seasonality. During seasonal migration, birds use many habitats and food resources, which may influence their intestinal bacterial community structure. Hooded crane (Grus monacha) is a migrant waterbird that traverses long distances and occupies varied habitats. In this study, we investigated the diversity and differences in intestinal bacterial communities of hooded cranes over the migratory seasons. Fecal samples from hooded cranes were collected at a stopover site in two seasons (spring and fall) in Lindian, China, and at a wintering ground in Shengjin Lake, China. We analyzed bacterial communities from the fecal samples using high throughput sequencing (Illumina Mi-seq). Firmicutes, Proteobacteria, Tenericutes, Cyanobacteria, and Actinobacteria were the dominant phyla across all samples. The intestinal bacterial alpha-diversity of hooded cranes in winter was significantly higher than in fall and spring. The bacterial community composition significantly differed across the three seasons (ANOSIM, P = 0.001), suggesting that seasonal fluctuations may regulate the gut bacterial community composition of migratory birds. This study provides baseline information on the seasonal dynamics of intestinal bacterial community structure in migratory hooded cranes.
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Affiliation(s)
- Fengling Zhang
- School of Resources and Environmental Engineering, Anhui University, Hefei 230601, China
- Anhui Province Key Laboratory of Wetland Ecosystem Protection and Restoration (Anhui University), Hefei 230601, China
| | - Xingjia Xiang
- School of Resources and Environmental Engineering, Anhui University, Hefei 230601, China
- Anhui Province Key Laboratory of Wetland Ecosystem Protection and Restoration (Anhui University), Hefei 230601, China
| | - Yuanqiu Dong
- School of Resources and Environmental Engineering, Anhui University, Hefei 230601, China
- Anhui Province Key Laboratory of Wetland Ecosystem Protection and Restoration (Anhui University), Hefei 230601, China
| | - Shaofei Yan
- School of Resources and Environmental Engineering, Anhui University, Hefei 230601, China
- Anhui Province Key Laboratory of Wetland Ecosystem Protection and Restoration (Anhui University), Hefei 230601, China
| | - Yunwei Song
- Shengjin Lake National Nature Reserve of Anhui Province, Dongzhi 247200, China
| | - Lizhi Zhou
- School of Resources and Environmental Engineering, Anhui University, Hefei 230601, China
- Anhui Province Key Laboratory of Wetland Ecosystem Protection and Restoration (Anhui University), Hefei 230601, China
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15
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Bodawatta KH, Puzejova K, Sam K, Poulsen M, Jønsson KA. Cloacal swabs and alcohol bird specimens are good proxies for compositional analyses of gut microbial communities of Great tits (Parus major). Anim Microbiome 2020; 2:9. [PMID: 33499943 PMCID: PMC7807456 DOI: 10.1186/s42523-020-00026-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 02/25/2020] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Comprehensive studies of wild bird microbiomes are often limited by difficulties of sample acquisition. However, widely used non-invasive cloacal swab methods and under-explored museum specimens preserved in alcohol provide promising avenues to increase our understanding of wild bird microbiomes, provided that they accurately portray natural microbial community compositions. To investigate this assertion, we used 16S rRNA amplicon sequencing of Great tit (Parus major) gut microbiomes to compare 1) microbial communities obtained from dissected digestive tract regions and cloacal swabs, and 2) microbial communities obtained from freshly dissected gut regions and from samples preserved in alcohol for 2 weeks or 2 months, respectively. RESULTS We found no significant differences in alpha diversities in communities of different gut regions and cloacal swabs (except in OTU richness between the dissected cloacal region and the cloacal swabs), or between fresh and alcohol preserved samples. However, we did find significant differences in beta diversity and community composition of cloacal swab samples compared to different gut regions. Despite these community-level differences, swab samples qualitatively captured the majority of the bacterial diversity throughout the gut better than any single compartment. Bacterial community compositions of alcohol-preserved specimens did not differ significantly from freshly dissected samples, although some low-abundant taxa were lost in the alcohol preserved specimens. CONCLUSIONS Our findings suggest that cloacal swabs, similar to non-invasive fecal sampling, qualitatively depict the gut microbiota composition without having to collect birds to extract the full digestive tract. The satisfactory depiction of gut microbial communities in alcohol preserved samples opens up for the possibility of using an enormous resource readily available through museum collections to characterize bird gut microbiomes. The use of extensive museum specimen collections of birds for microbial gut analyses would allow for investigations of temporal patterns of wild bird gut microbiomes, including the potential effects of climate change and anthropogenic impacts. Overall, the utilization of cloacal swabs and museum alcohol specimens can positively impact bird gut microbiome research to help increase our understanding of the role and evolution of wild bird hosts and gut microbial communities.
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Affiliation(s)
- Kasun H. Bodawatta
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Katerina Puzejova
- Biology Centre of Czech Academy of Sciences, Institute of Entomology, Branisovska 31, Ceske Budejovice, Czech Republic
- Faculty of Science, University of South Bohemia, Branisovska 1760, Ceske Budejovice, Czech Republic
| | - Katerina Sam
- Biology Centre of Czech Academy of Sciences, Institute of Entomology, Branisovska 31, Ceske Budejovice, Czech Republic
- Faculty of Science, University of South Bohemia, Branisovska 1760, Ceske Budejovice, Czech Republic
| | - Michael Poulsen
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Knud A. Jønsson
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
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16
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Grond K, Santo Domingo JW, Lanctot RB, Jumpponen A, Bentzen RL, Boldenow ML, Brown SC, Casler B, Cunningham JA, Doll AC, Freeman S, Hill BL, Kendall SJ, Kwon E, Liebezeit JR, Pirie-Dominix L, Rausch J, Sandercock BK. Composition and Drivers of Gut Microbial Communities in Arctic-Breeding Shorebirds. Front Microbiol 2019; 10:2258. [PMID: 31649627 PMCID: PMC6795060 DOI: 10.3389/fmicb.2019.02258] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 09/17/2019] [Indexed: 01/02/2023] Open
Abstract
Gut microbiota can have important effects on host health, but explanatory factors and pathways that determine gut microbial composition can differ among host lineages. In mammals, host phylogeny is one of the main drivers of gut microbiota, a result of vertical transfer of microbiota during birth. In birds, it is less clear what the drivers might be, but both phylogeny and environmental factors may play a role. We investigated host and environmental factors that underlie variation in gut microbiota composition in eight species of migratory shorebirds. We characterized bacterial communities from 375 fecal samples collected from adults of eight shorebird species captured at a network of nine breeding sites in the Arctic and sub-Arctic ecoregions of North America, by sequencing the V4 region of the bacterial 16S ribosomal RNA gene. Firmicutes (55.4%), Proteobacteria (13.8%), Fusobacteria (10.2%), and Bacteroidetes (8.1%) dominated the gut microbiota of adult shorebirds. Breeding location was the main driver of variation in gut microbiota of breeding shorebirds (R2 = 11.6%), followed by shorebird host species (R2 = 1.8%), and sampling year (R2 = 0.9%), but most variation remained unexplained. Site variation resulted from differences in the core bacterial taxa, whereas rare, low-abundance bacteria drove host species variation. Our study is the first to highlight a greater importance of local environment than phylogeny as a driver of gut microbiota composition in wild, migratory birds under natural conditions.
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Affiliation(s)
- Kirsten Grond
- Division of Biology, Kansas State University, Manhattan, KS, United States
| | | | - Richard B Lanctot
- Migratory Bird Management, U.S. Fish & Wildlife Service, Anchorage, AK, United States
| | - Ari Jumpponen
- Division of Biology, Kansas State University, Manhattan, KS, United States
| | | | - Megan L Boldenow
- Department of Biology and Wildlife, University of Alaska Fairbanks, Fairbanks, AK, United States
| | | | - Bruce Casler
- Independent Researcher, Nehalem, OR, United States
| | - Jenny A Cunningham
- Department of Fisheries and Wildlife Sciences, University of Missouri, Columbia, MO, United States
| | - Andrew C Doll
- Denver Museum of Nature & Science, Denver, CO, United States
| | - Scott Freeman
- Arctic National Wildlife Refuge, U.S. Fish & Wildlife Service, Fairbanks, AK, United States
| | - Brooke L Hill
- Department of Biology and Wildlife, University of Alaska Fairbanks, Fairbanks, AK, United States
| | - Steven J Kendall
- Arctic National Wildlife Refuge, U.S. Fish & Wildlife Service, Fairbanks, AK, United States
| | - Eunbi Kwon
- Department of Fish and Wildlife Conservation, Virginia Tech, Blacksburg, VA, United States
| | | | | | - Jennie Rausch
- Environment and Climate Change Canada, Yellowknife, NT, Canada
| | - Brett K Sandercock
- Department of Terrestrial Ecology, Norwegian Institute for Nature Research, Trondheim, Norway
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17
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Cockerham S, Lee B, Orben RA, Suryan RM, Torres LG, Warzybok P, Bradley R, Jahncke J, Young HS, Ouverney C, Shaffer SA. Microbial Ecology of the Western Gull (Larus occidentalis). MICROBIAL ECOLOGY 2019; 78:665-676. [PMID: 30891612 DOI: 10.1007/s00248-019-01352-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 02/17/2019] [Indexed: 06/09/2023]
Abstract
Avian species host diverse communities of microorganisms which have important roles in the life of birds, including increased metabolism, protection from disease, and immune system development. Along with high human populations and a diversity of human uses of coastal zones, anthropogenic food sources are becoming increasingly available to some species, including gulls. Anthropogenic associations increase the likelihood of encountering foreign or pathogenic bacteria. Diseases in birds caused by bacteria are a substantial source of avian mortality; therefore, it is essential to characterize the microbiome of seabirds. Here, we determined both core and environmentally derived microbial communities of breeding western gulls (Larus occidentalis) from six colonies in California and Oregon. Using DNA extracted from bacterial swabs of the bill, cloaca, and feet of gulls, 16S rRNA gene sequencing was performed targeting the V4 region. We identified a total of 8542 operational taxonomic units (OTUs) from 75 gulls. Sixty-eight OTUs were identified in gulls from all six colonies with the greatest representation from phyla's of Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria. Overall, microbial richness based on Chao's Abundance-based Coverage Estimator (ACE) index was similar for all colonies (mean = 2347 OTUs) with the smallest coastal colonies having the highest richness (mean = 2626 OTUs) and the largest colonies, located farther off-shore, having the lowest (mean = 2068 OTUs). This survey represents the most in-depth assessment to date of microbes associated with western gulls, and the first study to identify both species-specific and environmentally derived bacteria across multiple populations.
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Affiliation(s)
- Susan Cockerham
- Department of Biological Sciences, San José State University, One Washington Square, San Jose, CA, 95192-0100, USA.
| | - Becky Lee
- Department of Biological Sciences, San José State University, One Washington Square, San Jose, CA, 95192-0100, USA
| | - Rachael A Orben
- Department of Fisheries and Wildlife, Hatfield Marine Science Center, Oregon State University, Newport, OR, 97365, USA
| | - Robert M Suryan
- Department of Fisheries and Wildlife, Hatfield Marine Science Center, Oregon State University, Newport, OR, 97365, USA
- Alaska Fisheries Science Center, Auke Bay Laboratories, NOAA Fisheries, 17109 Pt. Lena Loop Rd, Juneau, AK, 99801, USA
| | - Leigh G Torres
- Department of Fisheries and Wildlife, Marine Mammal Institute, Oregon State University, Hatfield Marine Science Center, Newport, OR, 97365, USA
| | - Pete Warzybok
- Point Blue Conservation Science, 2030 SE Marine Science Dr., Petaluma, CA, USA
| | - Russell Bradley
- Point Blue Conservation Science, 2030 SE Marine Science Dr., Petaluma, CA, USA
| | - Jaime Jahncke
- Point Blue Conservation Science, 2030 SE Marine Science Dr., Petaluma, CA, USA
| | - Hillary S Young
- Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, CA, USA
| | - Cleber Ouverney
- Department of Biological Sciences, San José State University, One Washington Square, San Jose, CA, 95192-0100, USA
| | - Scott A Shaffer
- Department of Biological Sciences, San José State University, One Washington Square, San Jose, CA, 95192-0100, USA
- Institute of Marine Sciences, University of California, Santa Cruz, CA, USA
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18
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Dong Y, Xiang X, Zhao G, Song Y, Zhou L. Variations in gut bacterial communities of hooded crane ( Grus monacha) over spatial-temporal scales. PeerJ 2019; 7:e7045. [PMID: 31218123 PMCID: PMC6563796 DOI: 10.7717/peerj.7045] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 04/27/2019] [Indexed: 11/20/2022] Open
Abstract
Background Microbes have been recognized as important symbionts to regulate host life. The animal gut harbors abundance and diverse bacteria. Numerous internal and external factors influence intestinal bacterial communities, including diet, seasonal fluctuations and habitat sites. However, the factors that influence the gut bacterial communities of wild bird is poorly characterized. Methods By high-throughput sequencing and statistical analysis, we investigated the variations in gut bacterial communities of the hooded cranes at three wintering stages in Caizi (CZL) and Shengjin Lake (SJL), which are two shallow lakes in the middle and lower Yangtze River floodplain. Results Our results revealed significant differences in gut bacterial community structure and diversity among different sampling sites and wintering stages. Seasonal changes have a significant impact on the gut microbe composition of hooded cranes in the two lakes. ANOSIM analysis demonstrated that the samples in CZL had greater differences in the gut bacterial composition than that in SJL. Our data showed strong evidence that the host's gut filtering might be an important factor in shaping bacterial community according to mean nearest taxon distance (MNTD). The PICRUSt analysis showed that the predicted metagenomes associated with the gut microbiome were carbohydrate metabolism, amino acid metabolism and energy metabolism over the entire wintering period at the two lakes. Conclusions The results demonstrated that both seasonal changes and habitat sites have significant impact on the gut bacterial communities of hooded cranes. In addition, predictive function of gut microbes in hooded cranes varied over time. These results provide new insights into the gut microbial community of the cranes, which serves as a foundation for future studies.
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Affiliation(s)
- Yuanqiu Dong
- School of Resources and Environmental Engineering, Anhui University, Hefei, China.,Anhui Key Laboratory of Wetland Ecosystem Protection and Restoration, Anhui University, Hefei, China
| | - Xingjia Xiang
- School of Resources and Environmental Engineering, Anhui University, Hefei, China.,Anhui Key Laboratory of Wetland Ecosystem Protection and Restoration, Anhui University, Hefei, China
| | - Guanghong Zhao
- School of Resources and Environmental Engineering, Anhui University, Hefei, China.,Anhui Key Laboratory of Wetland Ecosystem Protection and Restoration, Anhui University, Hefei, China
| | - Yunwei Song
- School of Resources and Environmental Engineering, Anhui University, Hefei, China.,Anhui Key Laboratory of Wetland Ecosystem Protection and Restoration, Anhui University, Hefei, China.,Anhui Shengjin Lake National Nature Reserve, Chizhou, China
| | - Lizhi Zhou
- School of Resources and Environmental Engineering, Anhui University, Hefei, China.,Anhui Key Laboratory of Wetland Ecosystem Protection and Restoration, Anhui University, Hefei, China
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19
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Salgado-Flores A, Tveit AT, Wright AD, Pope PB, Sundset MA. Characterization of the cecum microbiome from wild and captive rock ptarmigans indigenous to Arctic Norway. PLoS One 2019; 14:e0213503. [PMID: 30856229 PMCID: PMC6411164 DOI: 10.1371/journal.pone.0213503] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 02/24/2019] [Indexed: 01/17/2023] Open
Abstract
Rock ptarmigans (Lagopus muta) are gallinaceous birds inhabiting arctic and sub-arctic environments. Their diet varies by season, including plants or plant parts of high nutritional value, but also toxic plant secondary metabolites (PSMs). Little is known about the microbes driving organic matter decomposition in the cecum of ptarmigans, especially the last steps leading to methanogenesis. The cecum microbiome in wild rock ptarmigans from Arctic Norway was characterized to unveil their functional potential for PSM detoxification, methanogenesis and polysaccharides degradation. Cecal samples were collected from wild ptarmigans from Svalbard (L. m. hyperborea) and northern Norway (L. m. muta) during autumn/winter (Sept-Dec). Samples from captive Svalbard ptarmigans fed commercial pelleted feed were included to investigate the effect of diet on microbial composition and function. Abundances of methanogens and bacteria were determined by qRT-PCR, while microbial community composition and functional potential were studied using 16S rRNA gene sequencing and shotgun metagenomics. Abundances of bacteria and methanogenic Archaea were higher in wild ptarmigans compared to captive birds. The ceca of wild ptarmigans housed bacterial groups involved in PSM-degradation, and genes mediating the conversion of phenol compounds to pyruvate. Methanomassiliicoccaceae was the major archaeal family in wild ptarmigans, carrying the genes for methanogenesis from methanol. It might be related to increased methanol production from pectin degradation in wild birds due to a diet consisting of primarily fresh pectin-rich plants. Both wild and captive ptarmigans possessed a broad suite of genes for the depolymerization of hemicellulose and non-cellulosic polysaccharides (e.g. starch). In conclusion, there were no physiological and phenotypical dissimilarities in the microbiota found in the cecum of wild ptarmigans on mainland Norway and Svalbard. While substantial differences in the functional potential for PSM degradation and methanogenesis in wild and captive birds seem to be a direct consequence of their dissimilar diets.
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Affiliation(s)
- Alejandro Salgado-Flores
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Langnes, Tromsø, Norway
- * E-mail: (AS); (MS)
| | - Alexander T. Tveit
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Langnes, Tromsø, Norway
| | - Andre-Denis Wright
- College of Agricultural, Human, and Natural Resource Sciences, Washington State University, Pullman, Washington, United States of America
| | - Phil B. Pope
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Aas, Norway
| | - Monica A. Sundset
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Langnes, Tromsø, Norway
- * E-mail: (AS); (MS)
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Xiang X, Zhang F, Fu R, Yan S, Zhou L. Significant Differences in Bacterial and Potentially Pathogenic Communities Between Sympatric Hooded Crane and Greater White-Fronted Goose. Front Microbiol 2019; 10:163. [PMID: 30804919 PMCID: PMC6370644 DOI: 10.3389/fmicb.2019.00163] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 01/22/2019] [Indexed: 01/15/2023] Open
Abstract
The gut microbiota of vertebrates play a crucial role in shaping the health of their hosts. However, knowledge of the avian intestinal microbiota has arguably lagged behind that of many other vertebrates. Here, we examine the intestinal bacterial communities of the hooded crane and the greater white-fronted goose at the Shengjin Lake of China, using high-throughput sequencing (Illumina Mi-Seq), and infer the potential pathogens associated with each species. Intestinal bacterial alpha-diversity in the greater white-fronted goose was significantly higher than that in hooded crane. The intestinal bacterial community compositions were significantly different between the two hosts, suggesting that host interactions with specific communities might have profound implications. In addition, potential pathogens were detected in both guts of the two hosts, suggesting that these wild birds might be at risk of disease and probably spread infectious disease to other sympatric vertebrates. The gut of hooded crane carried more potential pathogens than that of the greater white-fronted goose. The potentially pathogenic community compositions were also significantly different between the two hosts, suggesting the divergence of potentially pathogenic communities between hooded crane, and greater white-fronted goose. Finally, bacterial and potentially pathogenic structures showed strong evidence of phylogenic clustering in both hosts, further demonstrating that each host was associated with preferential and defined bacterial and potentially pathogenic communities. Our results argue that more attention should be paid to investigate avian intestinal pathogens which might increase disease risks for conspecifics and other mixed species, and even poultry and human beings.
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Affiliation(s)
- Xingjia Xiang
- Anhui Province Key Laboratory of Wetland Ecological Protection and Restoration, School of Resources and Environmental Engineering, Anhui University, Hefei, China
- Anhui Biodiversity Information Center, Hefei, China
| | - Fengling Zhang
- Anhui Province Key Laboratory of Wetland Ecological Protection and Restoration, School of Resources and Environmental Engineering, Anhui University, Hefei, China
- Anhui Biodiversity Information Center, Hefei, China
| | - Rong Fu
- Anhui Province Key Laboratory of Wetland Ecological Protection and Restoration, School of Resources and Environmental Engineering, Anhui University, Hefei, China
- Anhui Biodiversity Information Center, Hefei, China
| | - Shaofei Yan
- Anhui Province Key Laboratory of Wetland Ecological Protection and Restoration, School of Resources and Environmental Engineering, Anhui University, Hefei, China
| | - Lizhi Zhou
- Anhui Province Key Laboratory of Wetland Ecological Protection and Restoration, School of Resources and Environmental Engineering, Anhui University, Hefei, China
- Anhui Biodiversity Information Center, Hefei, China
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21
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Fuirst M, Veit RR, Hahn M, Dheilly N, Thorne LH. Effects of urbanization on the foraging ecology and microbiota of the generalist seabird Larus argentatus. PLoS One 2018; 13:e0209200. [PMID: 30562368 PMCID: PMC6298667 DOI: 10.1371/journal.pone.0209200] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 12/01/2018] [Indexed: 01/22/2023] Open
Abstract
Larus gull species have proven adaptable to urbanization and due to their generalist feeding behaviors, they provide useful opportunities to study how urban environments impact foraging behavior and host-associated microbiota. We evaluated how urbanization influenced the foraging behavior and microbiome characteristics of breeding herring gulls (Larus argentatus) at three different colonies on the east coast of the United States. Study colonies represented high, medium and low degrees of urbanization, respectively. At all colonies, gulls frequently foraged at landfills and in other urban environments, but both the use of urban environments and gull foraging metrics differed with the degree of urbanization. Gulls at the more urban colonies used urban environments more frequently, showed higher rates of site fidelity and took shorter trips. Gulls at less urban colonies used a greater diversity of habitat types and foraged offshore. We observed high microbial diversity at all colonies, though microbial diversity was highest at the least urban colony where gulls used a wider variety of foraging habitats. This suggests that gulls may acquire a wider range of bacteria when visiting a higher variety of foraging sites. Our findings highlight the influence of urban habitats on gull movements and microbiome composition and diversity during the breeding season and represent the first application of amplicon sequence variants, an objective and repeatable method of bacterial classification, to study the microbiota of a seabird species.
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Affiliation(s)
- Matthew Fuirst
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, United States of America
| | - Richard R. Veit
- Department of Biology, College of Staten Island (CSI) CUNY, Staten Island, NY, United States of America
| | - Megan Hahn
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, United States of America
| | - Nolwenn Dheilly
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, United States of America
| | - Lesley H. Thorne
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, United States of America
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22
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Zhu L, Liao R, Wu N, Zhu G, Yang C. Heat stress mediates changes in fecal microbiome and functional pathways of laying hens. Appl Microbiol Biotechnol 2018; 103:461-472. [DOI: 10.1007/s00253-018-9465-8] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Revised: 09/25/2018] [Accepted: 10/08/2018] [Indexed: 12/12/2022]
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Wu Y, Yang Y, Cao L, Yin H, Xu M, Wang Z, Liu Y, Wang X, Deng Y. Habitat environments impacted the gut microbiome of long-distance migratory swan geese but central species conserved. Sci Rep 2018; 8:13314. [PMID: 30190564 PMCID: PMC6127342 DOI: 10.1038/s41598-018-31731-9] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 05/21/2018] [Indexed: 02/07/2023] Open
Abstract
The gut microbime plays an important role in the health of wild animals. This microbial community could be altered by habitat pollution and other human activities that threaten the host organisms. Here, we satellite-tracked a flock of swan geese (Anser cygnoides) migrating from their breeding area (Khukh Lake, Mongolia), with low levels of human activity, to their wintering area (Poyang Lake, China) which has been heavily impacted by human activities. Twenty fecal samples were collected from each site. High-throughput sequencing of 16S and ITS was employed to explore bacterial and fungal composition and diversity of their gut microbiome. Although general composition, alpha-diversity, functional prediction, and the central taxa in the phylogenetic networks showed some similarities between the two habitats, significant divergences were detected in terms of beta-diversity, species abundances, and interaction network topologies. In addition, disease-related and xenobiotic biodegradation pathways, and pathogenic bacteria were significantly increased in bacterial communities from samples at Poyang Lake. Our results reveal that the gut microbiome of swan geese, while somewhat altered after long-distance migration, still maintained a core group of species. We also show that habitat environmental stress could impact these gut microbial communities, suggesting that habitat pollution could indirectly threaten wild animals by altering their gut microbiome.
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Affiliation(s)
- Yueni Wu
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Yuzhan Yang
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Lei Cao
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Meiying Xu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangzhou, China
| | - Zhujun Wang
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Yangying Liu
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Xin Wang
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Ye Deng
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China.
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24
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Liao F, Gu W, Li D, Liang J, Fu X, Xu W, Duan R, Wang X, Jing H, Dai J. Characteristics of microbial communities and intestinal pathogenic bacteria for migrated Larus ridibundus in southwest China. Microbiologyopen 2018; 8:e00693. [PMID: 29978594 PMCID: PMC6460275 DOI: 10.1002/mbo3.693] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 06/18/2018] [Accepted: 06/19/2018] [Indexed: 01/27/2023] Open
Abstract
Larus ridibundus, a migratory wild bird, has become one of the most popular gull species in southwest China in recent years. There has been no information on the gut microbiota and intestinal pathogenic bacteria configuration in wild L. ridibundus, even though the public are in close contact with this bird. In this study, 16S rRNA amplicon‐sequencing methods were used to describe the microbial community structure and intestinal pathogenic bacteria were isolated to identify their characteristics. The taxonomic results revealed that Firmicutes (86%), Proteobacteria (10%), and Tenericutes (3%) were the three most abundant phyla in the gut of L. ridibundus. Enterococcaceae, Enterobacteriaceae, and Mycoplasmataceae were the most predominant families, respectively. The number of operational taxonomic units (OTUs), the richness estimates and diversity indices of microbiota, was statistically different (p < 0.05). However, beta diversity showed that no statistical significance (p > 0.05) between all the fecal samples. The most frequently isolated intestinal pathogenic bacteria from L. ridibundus were enteropathogenic Escherichia coli (32%) and Salmonella (21%). Pulsed‐field gel electrophoresis (PFGE) results of Salmonella species revealed a high degree of similarity between isolates, which was not observed for other species. None of the potentially pathogenic isolates were identical to human‐isolated counterparts suggesting that there was little cross‐infection between humans and gulls, despite close proximity. In brief, this study provided a baseline for future L. ridibundus microbiology analysis, and made an understanding of the intestinal bacterial community structure and diversity.
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Affiliation(s)
- Feng Liao
- Department of Respiratory Medicine, The First People's Hospital of Yunnan Province, Kunming, Yunnan, China.,The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Wenpeng Gu
- Center of Tree Shrew Germplasm Resources, Institute of Medical Biology, The Chinese Academy of Medical Science and Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Yunnan Innovation Team of Standardization and Application Research in Tree Shrew, Kunming, China.,Department of Acute Infectious Diseases Control and Prevention, Yunnan Provincial Centre for Disease Control and Prevention, Kunming, China
| | - Duo Li
- Department of Acute Infectious Diseases Control and Prevention, Yunnan Provincial Centre for Disease Control and Prevention, Kunming, China
| | - Junrong Liang
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, State Key Laboratory for Infectious Disease Prevention and Control, Beijing, China
| | - Xiaoqing Fu
- Department of Acute Infectious Diseases Control and Prevention, Yunnan Provincial Centre for Disease Control and Prevention, Kunming, China
| | - Wen Xu
- Department of Acute Infectious Diseases Control and Prevention, Yunnan Provincial Centre for Disease Control and Prevention, Kunming, China
| | - Ran Duan
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, State Key Laboratory for Infectious Disease Prevention and Control, Beijing, China
| | - Xin Wang
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, State Key Laboratory for Infectious Disease Prevention and Control, Beijing, China
| | - Huaiqi Jing
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, State Key Laboratory for Infectious Disease Prevention and Control, Beijing, China
| | - Jiejie Dai
- Center of Tree Shrew Germplasm Resources, Institute of Medical Biology, The Chinese Academy of Medical Science and Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Yunnan Innovation Team of Standardization and Application Research in Tree Shrew, Kunming, China
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25
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Spergser J, Loncaric I, Tichy A, Fritz J, Scope A. The cultivable autochthonous microbiota of the critically endangered Northern bald ibis (Geronticus eremita). PLoS One 2018; 13:e0195255. [PMID: 29617453 PMCID: PMC5884550 DOI: 10.1371/journal.pone.0195255] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 03/19/2018] [Indexed: 12/31/2022] Open
Abstract
The critically endangered Northern bald ibis (Geronticus eremita) is a migratory bird that became extinct in Europe centuries ago. Since 2014, the Northern bald ibis is subject to an intensive rehabilitation and conservation regime aiming to reintroduce the bird in its original distribution range in Central Europe and concurrently to maintain bird health and increase population size. Hitherto, virtually nothing is known about the microbial communities associated with the ibis species; an information pivotal for the veterinary management of these birds. Hence, the present study was conducted to provide a baseline description of the cultivable microbiota residing in the Northern bald ibis. Samples derived from the choana, trachea, crop and cloaca were examined employing a culturomic approach in order to identify microbes at each sampling site and to compare their frequency among age classes, seasonal appearances and rearing types. In total, 94 microbial species including 14 potentially new bacterial taxa were cultivated from the Northern bald ibis with 36, 58 and 59 bacterial species isolated from the choana, crop and cloaca, respectively. The microbiota of the Northern bald ibis was dominated by members of the phylum Firmicutes, followed by Proteobacteria, Actinobacteria, Bacteroidetes and Fusobacteria, altogether phylotypes commonly observed within avian gut environments. Differences in relative abundances of various microbial taxa were evident among sample types indicating mucosa-specific colonisation properties and tissue tropism. Besides, results of the present study indicate that the composition of microbiota was also affected by age, season (environment) and rearing type. While the prevalence of traditional pathogenic microbial species was extremely low, several opportunists including Clostridium perfringens toxotype A were frequently present in samples indicating that the Northern bald ibis may represent an important animal reservoir for these pathogens. In summary, the presented study provides a first inventory of the cultivable microbiota residing in the critically endangered Northern bald ibis and represents a first step in a wider investigation of the ibis microbiome with the ultimate goal to contribute to the management and survival of this critically endangered bird.
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Affiliation(s)
- Joachim Spergser
- Institute of Microbiology, Department of Pathobiology, University of Veterinary Medicine, Vienna, Austria
- * E-mail:
| | - Igor Loncaric
- Institute of Microbiology, Department of Pathobiology, University of Veterinary Medicine, Vienna, Austria
| | - Alexander Tichy
- Bioinformatics and Biostatistics Platform, Department of Biomedical Sciences, University of Veterinary Medicine, Vienna, Austria
| | | | - Alexandra Scope
- Clinical Unit of Internal Medicine Small Animals, Department/Clinic for Companion Animals and Horses, University of Veterinary Medicine, Vienna, Austria
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26
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van Veelen HPJ, Salles JF, Tieleman BI. Microbiome assembly of avian eggshells and their potential as transgenerational carriers of maternal microbiota. ISME JOURNAL 2018; 12:1375-1388. [PMID: 29445132 DOI: 10.1038/s41396-018-0067-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 12/01/2017] [Accepted: 12/21/2017] [Indexed: 02/07/2023]
Abstract
The microbiome is essential for development, health and homeostasis throughout an animal's life. Yet, the origins and transmission processes governing animal microbiomes remain elusive for non-human vertebrates, oviparous vertebrates in particular. Eggs may function as transgenerational carriers of the maternal microbiome, warranting characterisation of egg microbiome assembly. Here, we investigated maternal and environmental contributions to avian eggshell microbiota in wild passerine birds: woodlark Lullula arborea and skylark Alauda arvensis. Using 16S rRNA gene sequencing, we demonstrated in both lark species, at the population and within-nest levels, that bacterial communities of freshly laid eggs were distinct from the female cloacal microbiome. Instead, soil-borne bacteria appeared to thrive on freshly laid eggs, and eggshell microbiota composition strongly resembled maternal skin, body feather and nest material communities, sources in direct contact with laid eggs. Finally, phylogenetic structure analysis and microbial source tracking underscored species sorting from directly contacting sources rather than in vivo-transferred symbionts. The female-egg-nest system allowed an integrative assessment of avian egg microbiome assembly, revealing mixed modes of symbiont acquisition not previously documented for vertebrate eggs. Our findings illuminated egg microbiome origins, which suggested a limited potential of eggshells for transgenerational transmission, encouraging further investigation of eggshell microbiome functions in vertebrates.
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Affiliation(s)
- H Pieter J van Veelen
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, P.O. box 11103, 9700 CC, Groningen, The Netherlands.
| | - Joana Falcão Salles
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, P.O. box 11103, 9700 CC, Groningen, The Netherlands
| | - B Irene Tieleman
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, P.O. box 11103, 9700 CC, Groningen, The Netherlands
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27
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Videvall E, Strandh M, Engelbrecht A, Cloete S, Cornwallis CK. Measuring the gut microbiome in birds: Comparison of faecal and cloacal sampling. Mol Ecol Resour 2017; 18:424-434. [PMID: 29205893 DOI: 10.1111/1755-0998.12744] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2017] [Revised: 11/17/2017] [Accepted: 11/20/2017] [Indexed: 12/22/2022]
Abstract
The gut microbiomes of birds and other animals are increasingly being studied in ecological and evolutionary contexts. Numerous studies on birds and reptiles have made inferences about gut microbiota using cloacal sampling; however, it is not known whether the bacterial community of the cloaca provides an accurate representation of the gut microbiome. We examined the accuracy with which cloacal swabs and faecal samples measure the microbiota in three different parts of the gastrointestinal tract (ileum, caecum, and colon) using a case study on juvenile ostriches, Struthio camelus, and high-throughput 16S rRNA sequencing. We found that faeces were significantly better than cloacal swabs in representing the bacterial community of the colon. Cloacal samples had a higher abundance of Gammaproteobacteria and fewer Clostridia relative to the gut and faecal samples. However, both faecal and cloacal samples were poor representatives of the microbial communities in the caecum and ileum. Furthermore, the accuracy of each sampling method in measuring the abundance of different bacterial taxa was highly variable: Bacteroidetes was the most highly correlated phylum between all three gut sections and both methods, whereas Actinobacteria, for example, was only strongly correlated between faecal and colon samples. Based on our results, we recommend sampling faeces, whenever possible, as this sample type provides the most accurate assessment of the colon microbiome. The fact that neither sampling technique accurately portrayed the bacterial community of the ileum nor the caecum illustrates the difficulty in noninvasively monitoring gut bacteria located further up in the gastrointestinal tract. These results have important implications for the interpretation of avian gut microbiome studies.
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Affiliation(s)
- Elin Videvall
- Department of Biology, Lund University, Lund, Sweden
| | - Maria Strandh
- Department of Biology, Lund University, Lund, Sweden
| | - Anel Engelbrecht
- Directorate Animal Sciences, Western Cape Department of Agriculture, Elsenburg, South Africa
| | - Schalk Cloete
- Directorate Animal Sciences, Western Cape Department of Agriculture, Elsenburg, South Africa.,Department of Animal Sciences, Stellenbosch University, Matieland, South Africa
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28
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Zhao G, Zhou L, Dong Y, Cheng Y, Song Y. The gut microbiome of hooded cranes (Grus monacha) wintering at Shengjin Lake, China. Microbiologyopen 2017; 6. [PMID: 28127902 PMCID: PMC5458448 DOI: 10.1002/mbo3.447] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 12/12/2016] [Accepted: 12/20/2016] [Indexed: 12/18/2022] Open
Abstract
Gut microbes of animals play critical roles in processes such as digestion and immunity. Therefore, identifying gut microbes will shed light on understanding the annual life of animal species, particularly those that are threatened or endangered. In the present study, we conducted nucleotide sequence analyses of the 16S rRNA genes of gut microbiome of the hooded cranes (Grus monacha) wintering at Shengjin Lake, China, by Illumina high‐throughput sequencing technology. We acquired 503,398 high‐quality sequences and 785 operational taxonomic units (OTUs) from 15 fecal samples from different cranes, representing 22 phyla that were dominated by Firmicutes, Proteobacteria, and Actinobacteria. A total of 305 genera were identified that were dominated by Clostridium, Lysinibacillus, and Enterobacter. The core gut microbiome comprised 26 genera, including many probiotic species such as Clostridium, Bacillus, Cellulosilyticum, and Cellulomonas that could catabolize cellulose. The findings reported here contribute to our knowledge of the microbiology of hooded cranes and will likely advance efforts to protect waterbirds that inhabit Shengjin Lake Reserve during winter.
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Affiliation(s)
- Guanghong Zhao
- School of Resources and Environmental Engineering, Anhui University, Hefei, China
| | - Lizhi Zhou
- School of Resources and Environmental Engineering, Anhui University, Hefei, China
| | - Yuanqiu Dong
- School of Resources and Environmental Engineering, Anhui University, Hefei, China
| | - Yuanyuan Cheng
- School of Resources and Environmental Engineering, Anhui University, Hefei, China
| | - Yunwei Song
- School of Resources and Environmental Engineering, Anhui University, Hefei, China.,Shengjin Lake National Nature Reserve of Anhui Province, Chizhou, China
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29
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Wang W, Zheng S, Sharshov K, Sun H, Yang F, Wang X, Li L, Xiao Z. Metagenomic profiling of gut microbial communities in both wild and artificially reared Bar-headed goose (Anser indicus). Microbiologyopen 2016; 6. [PMID: 27998035 PMCID: PMC5387313 DOI: 10.1002/mbo3.429] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 10/17/2016] [Accepted: 10/27/2016] [Indexed: 12/28/2022] Open
Abstract
Bar-headed goose (Anser indicus), a species endemic to Asia, has become one of the most popular species in recent years for rare bird breeding industries in several provinces of China. There has been no information on the gut metagenome configuration in both wild and artificially reared Bar-headed geese, even though the importance of gut microbiome in vertebrate nutrient and energy metabolism, immune homeostasis and reproduction is widely acknowledged. In this study, metagenomic methods have been used to describe the microbial community structure and composition of functional genes associated with both wild and artificially reared Bar-headed goose. Taxonomic analyses revealed that Firmicutes, Proteobacteria, Actinobacteria and Bacteroidetes were the four most abundant phyla in the gut of Bar-headed geese. Bacteroidetes were significantly abundant in the artificially reared group compared to wild group. Through functional profiling, we found that artificially reared Bar-headed geese had higher bacterial gene content related to carbohydrate transport and metabolism, energy metabolism and coenzyme transport, and metabolism. A comprehensive gene catalog of Bar-headed geese metagenome was built, and the metabolism of carbohydrate, amino acid, nucleotide, and energy were found to be the four most abundant categories. These results create a baseline for future Bar-headed goose microbiology research, and make an original contribution to the artificial rearing of this bird.
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Affiliation(s)
- Wen Wang
- Center of GrowthMetabolism and AgingKey Laboratory of Bio‐Resource and Eco‐Environment of Ministry of EducationCollege of Life Sciences and State Key Laboratory of BiotherapySichuan UniversityChengduChina
- Key Laboratory of Adaptation and Evolution of Plateau BiotaNorthwest Institute of Plateau BiologyChinese Academy of SciencesXi'ningChina
| | - Sisi Zheng
- Key Laboratory of Adaptation and Evolution of Plateau BiotaNorthwest Institute of Plateau BiologyChinese Academy of SciencesXi'ningChina
- University of Chinese Academy of SciencesBeijingChina
| | - Kirill Sharshov
- Research Institute of Experimental and Clinical MedicineNovosibirskRussia
| | - Hao Sun
- Key Laboratory of Adaptation and Evolution of Plateau BiotaNorthwest Institute of Plateau BiologyChinese Academy of SciencesXi'ningChina
| | - Fang Yang
- Key Laboratory of Adaptation and Evolution of Plateau BiotaNorthwest Institute of Plateau BiologyChinese Academy of SciencesXi'ningChina
| | - Xuelian Wang
- Key Laboratory of Adaptation and Evolution of Plateau BiotaNorthwest Institute of Plateau BiologyChinese Academy of SciencesXi'ningChina
| | - Laixing Li
- Key Laboratory of Adaptation and Evolution of Plateau BiotaNorthwest Institute of Plateau BiologyChinese Academy of SciencesXi'ningChina
| | - Zhixiong Xiao
- Center of GrowthMetabolism and AgingKey Laboratory of Bio‐Resource and Eco‐Environment of Ministry of EducationCollege of Life Sciences and State Key Laboratory of BiotherapySichuan UniversityChengduChina
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Effects of captivity and artificial breeding on microbiota in feces of the red-crowned crane (Grus japonensis). Sci Rep 2016; 6:33350. [PMID: 27628212 PMCID: PMC5024133 DOI: 10.1038/srep33350] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 08/26/2016] [Indexed: 01/25/2023] Open
Abstract
Reintroduction of the threatened red-crowned crane has been unsuccessful. Although gut microbiota correlates with host health, there is little information on gut microbiota of cranes under different conservation strategies. The study examined effects of captivity, artificial breeding and life stage on gut microbiota of red-crown cranes. The gut microbiotas of wild, captive adolescent, captive adult, artificially bred adolescent and artificially bred adult cranes were characterized by next-generation sequencing of 16S rRNA gene amplicons. The gut microbiotas were dominated by three phyla: Firmicutes (62.9%), Proteobacteria (29.9%) and Fusobacteria (9.6%). Bacilli dominated the 'core' community consisting of 198 operational taxonomic units (OTUs). Both captivity and artificial breeding influenced the structures and diversities microbiota of the gut. Especially, wild cranes had distinct compositions of gut microbiota from captive and artificially bred cranes. The greatest alpha diversity was found in captive cranes, while wild cranes had the least. According to the results of ordination analysis, influences of captivity and artificial breeding were greater than that of life stage. Overall, captivity and artificial breeding influenced the gut microbiota, potentially due to changes in diet, vaccination, antibiotics and living conditions. Metagenomics can serve as a supplementary non-invasive screening tool for disease control.
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Yang Y, Deng Y, Cao L. Characterising the interspecific variations and convergence of gut microbiota in Anseriformes herbivores at wintering areas. Sci Rep 2016; 6:32655. [PMID: 27600170 PMCID: PMC5013396 DOI: 10.1038/srep32655] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 08/12/2016] [Indexed: 02/07/2023] Open
Abstract
Microorganisms in vertebrate guts have been recognized as important symbionts influencing host life. However, it remains unclear about the gut microbiota in long-distance migratory Anseriformes herbivores, which could be functionally important for these wetland-dependent animals. We collected faeces of the greater white-fronted goose (GWFG), bean goose (BG) and swan goose (SG) from Shengjin Lake (SJL) and Poyang Lake (PYL) in the Yangtze River Floodplain, China. High-throughput sequencing of 16S rRNA V4 region was employed to depict the composition and structure of geese gut microbiota during wintering period. The dominant bacterial phyla across all samples were Firmicutes, Proteobacteria and Actinobacteria, but significant variations were detected among different goose species and sampling sites, in terms of α diversity, community structures and microbial interactions. We found a significant correlation between diet and the microbial community structure in GWFG-SJL samples. These results demonstrated that host species and diet are potential drivers of goose gut microbiota assemblies. Despite these variations, functions of geese gut microbiota were similar, with great abundances of potential genes involved in nutrient metabolism. This preliminary study would be valuable for future, exhaustive investigations of geese gut microbiota and their interactions with host.
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Affiliation(s)
- Yuzhan Yang
- School of Life Sciences, University of Science and Technology of China, Huangshan Road, Hefei, 230026, China
| | - Ye Deng
- Research Center of Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Lei Cao
- Research Center of Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
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Colston TJ, Jackson CR. Microbiome evolution along divergent branches of the vertebrate tree of life: what is known and unknown. Mol Ecol 2016; 25:3776-800. [DOI: 10.1111/mec.13730] [Citation(s) in RCA: 223] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Revised: 05/25/2016] [Accepted: 05/30/2016] [Indexed: 02/06/2023]
Affiliation(s)
- Timothy J. Colston
- Department of Biology The University of Mississippi University MS 38677 USA
| | - Colin R. Jackson
- Department of Biology The University of Mississippi University MS 38677 USA
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Wang W, Zheng S, Sharshov K, Cao J, Sun H, Yang F, Wang X, Li L. Distinctive gut microbial community structure in both the wild and farmed Swan goose (Anser cygnoides). J Basic Microbiol 2016; 56:1299-1307. [DOI: 10.1002/jobm.201600155] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 05/29/2016] [Indexed: 01/22/2023]
Affiliation(s)
- Wen Wang
- Key Laboratory of Adaptation and Evolution of Plateau Biota; Northwest Institute of Plateau Biology; Chinese Academy of Sciences; Xi'ning Qinghai P.R. China
- Center of Growth, Metabolism and Aging; College of Life Sciences; Sichuan University; Chengdu Sichuan P.R. China
| | - Sisi Zheng
- Key Laboratory of Adaptation and Evolution of Plateau Biota; Northwest Institute of Plateau Biology; Chinese Academy of Sciences; Xi'ning Qinghai P.R. China
- University of Chinese Academy of Sciences; Beijing P.R. China
| | - Kirill Sharshov
- Research Institute of Experimental and Clinical Medicine; Novosibirsk Russia
| | - Jian Cao
- Key Laboratory of Adaptation and Evolution of Plateau Biota; Northwest Institute of Plateau Biology; Chinese Academy of Sciences; Xi'ning Qinghai P.R. China
- University of Chinese Academy of Sciences; Beijing P.R. China
| | - Hao Sun
- Key Laboratory of Adaptation and Evolution of Plateau Biota; Northwest Institute of Plateau Biology; Chinese Academy of Sciences; Xi'ning Qinghai P.R. China
| | - Fang Yang
- Key Laboratory of Adaptation and Evolution of Plateau Biota; Northwest Institute of Plateau Biology; Chinese Academy of Sciences; Xi'ning Qinghai P.R. China
| | - Xuelian Wang
- Key Laboratory of Adaptation and Evolution of Plateau Biota; Northwest Institute of Plateau Biology; Chinese Academy of Sciences; Xi'ning Qinghai P.R. China
| | - Laixing Li
- Key Laboratory of Adaptation and Evolution of Plateau Biota; Northwest Institute of Plateau Biology; Chinese Academy of Sciences; Xi'ning Qinghai P.R. China
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Barbosa A, Balagué V, Valera F, Martínez A, Benzal J, Motas M, Diaz JI, Mira A, Pedrós-Alió C. Age-Related Differences in the Gastrointestinal Microbiota of Chinstrap Penguins (Pygoscelis antarctica). PLoS One 2016; 11:e0153215. [PMID: 27055030 PMCID: PMC4824521 DOI: 10.1371/journal.pone.0153215] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 03/26/2016] [Indexed: 11/30/2022] Open
Abstract
The gastrointestinal tract microbiota is known to play very important roles in the well being of animals. It is a complex community composed by hundreds of microbial species interacting closely among them and with their host, that is, a microbial ecosystem. The development of high throughput sequencing techniques allows studying the diversity of such communities in a realistic way and considerable work has been carried out in mammals and some birds such as chickens. Wild birds have received less attention and in particular, in the case of penguins, only a few individuals of five species have been examined with molecular techniques. We collected cloacal samples from Chinstrap penguins in the Vapour Col rookery in Deception Island, Antarctica, and carried out pyrosequencing of the V1-V3 region of the 16S rDNA in samples from 53 individuals, 27 adults and 26 chicks. This provided the first description of the Chinstrap penguin gastrointestinal tract microbiota and the most extensive in any penguin species. Firmicutes, Bacteoridetes, Proteobacteria, Fusobacteria, Actinobacteria, and Tenericutes were the main components. There were large differences between chicks and adults. The former had more Firmicutes and the latter more Bacteroidetes and Proteobacteria. In addition, adults had richer and more diverse bacterial communities than chicks. These differences were also observed between parents and their offspring. On the other hand, nests explained differences in bacterial communities only among chicks. We suggest that environmental factors have a higher importance than genetic factors in the microbiota composition of chicks. The results also showed surprisingly large differences in community composition with other Antarctic penguins including the congeneric Adélie and Gentoo penguins.
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Affiliation(s)
- Andrés Barbosa
- Departamento de Ecología Evolutiva, Museo Nacional de Ciencias Naturales, CSIC, Madrid, Spain
| | - Vanessa Balagué
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Barcelona, Spain
| | - Francisco Valera
- Departamento de Ecología Funcional y Evolutiva, Estación Experimental de Zonas Áridas, CSIC, Almería, Spain
| | - Ana Martínez
- Instituto de Investigaciones en Materiales, Universidad Nacional Autónoma de México, México DF, México
| | - Jesús Benzal
- Departamento de Ecología Funcional y Evolutiva, Estación Experimental de Zonas Áridas, CSIC, Almería, Spain
| | - Miguel Motas
- Facultad de Veterinaria, Universidad de Murcia, Murcia, Spain
| | - Julia I. Diaz
- Centro de Estudios Parasitológicos y de Vectores, CCT La Plata (CONICET-UNLP), La Plata, Argentina
| | - Alex Mira
- Department of Genomics and Health, FISABIO Foundation, Center for Advanced Research in Public Health, Valencia, Spain
| | - Carlos Pedrós-Alió
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Barcelona, Spain
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Waite DW, Taylor MW. Exploring the avian gut microbiota: current trends and future directions. Front Microbiol 2015; 6:673. [PMID: 26191057 PMCID: PMC4490257 DOI: 10.3389/fmicb.2015.00673] [Citation(s) in RCA: 168] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2015] [Accepted: 06/19/2015] [Indexed: 01/16/2023] Open
Abstract
Birds represent a diverse and evolutionarily successful lineage, occupying a wide range of niches throughout the world. Like all vertebrates, avians harbor diverse communities of microorganisms within their guts, which collectively fulfill crucial roles in providing the host with nutrition and protection from pathogens. Across the field of avian microbiology knowledge is extremely uneven, with several species accounting for an overwhelming majority of all microbiological investigations. These include agriculturally important birds, such as chickens and turkeys, as well as birds of evolutionary or conservation interest. In our previous study we attempted the first meta-analysis of the avian gut microbiota, using 16S rRNA gene sequences obtained from a range of publicly available data sets. We have now extended our analysis to explore the microbiology of several key species in detail, to consider the avian microbiota within the context of what is known about other vertebrates, and to identify key areas of interest in avian microbiology for future study.
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Affiliation(s)
| | - Michael W. Taylor
- Centre for Microbial Innovation, School of Biological Sciences, University of AucklandAuckland, New Zealand
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