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S V, T J, E AP, A MHA. Antibiotic resistance of heterotrophic bacteria from the sediments of adjoining high Arctic fjords, Svalbard. Braz J Microbiol 2024; 55:2371-2383. [PMID: 38767750 PMCID: PMC11405572 DOI: 10.1007/s42770-024-01368-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Accepted: 04/08/2024] [Indexed: 05/22/2024] Open
Abstract
Antibiotic resistance bacteria (ARB) and antibiotic resistance genes (ARGs) are now considered major global threats. The Kongsfjorden and Krossfjorden are the interlinked fjords in the Arctic that are currently experiencing the effects of climate change and receiving input of pollutants from distant and regional sources. The present study focused on understanding the prevalence of antibiotic resistance of retrievable heterotrophic bacteria from the sediments of adjacent Arctic fjords Kongsfjorden and Krossfjorden. A total of 237 bacterial isolates were tested against 16 different antibiotics. The higher resistance observed towards Extended Spectrum β-lactam antibiotic (ESBL) includes ceftazidime (45.56%) followed by trimethoprim (27%) and sulphamethizole (24.05%). The extent of resistance was meagre against tetracycline (2.53%) and gentamycin (2.95%). The 16S rRNA sequencing analysis identified that Proteobacteria (56%) were the dominant antibiotic resistant phyla, followed by Firmicutes (35%), Actinobacteria (8%) and Bacteroidetes. The dominant resistant bacterial isolates are Bacillus cereus (10%), followed by Alcaligenes faecalis (6.47%), Cytobacillus firmus (5.75%) Salinibacterium sp. (5%) and Marinobacter antarcticus (5%). Our study reveals the prevalence of antibiotic resistance showed significant differences in both the inner and outer fjords of Kongsfjorden and Krossfjorden (p < 0.05). This may be the input of antibiotic resistance bacteria released into the fjords from the preserved permafrost due to the melting of glaciers, horizontal gene transfer, and human influence in the Arctic region act as a selection pressure for the development and dissemination of more antibiotic resistant bacteria in Arctic fjords.
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Affiliation(s)
- Vishnupriya S
- Department of Marine Biology, Microbiology, Biochemistry, School of Marine Sciences, Cochin University of Science and Technology (CUSAT), Kochi, India.
| | - Jabir T
- National Centre for Polar and Ocean Research, Ministry of Earth Sciences, Headland Sada, 403 804, Vasco- da-Gama, Goa, India
| | - Akhil Prakash E
- Department of Marine Biology, Microbiology, Biochemistry, School of Marine Sciences, Cochin University of Science and Technology (CUSAT), Kochi, India
| | - Mohamed Hatha A A
- Department of Marine Biology, Microbiology, Biochemistry, School of Marine Sciences, Cochin University of Science and Technology (CUSAT), Kochi, India
- CUSAT NCPOR Centre for Polar Sciences, School of Marine Sciences, Cochin University of Science and Technology (CUSAT), Kochi, India
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2
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Wu H, Wu N, Liu X, Zhang L, Zhao D. Diet Drives Gut Bacterial Diversity of Wild and Semi-Captive Common Cranes ( Grus grus). Animals (Basel) 2024; 14:1566. [PMID: 38891613 PMCID: PMC11171321 DOI: 10.3390/ani14111566] [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: 04/19/2024] [Revised: 05/13/2024] [Accepted: 05/20/2024] [Indexed: 06/21/2024] Open
Abstract
The gut microbiota of wild animals can regulate host physical health to adapt to the environment. High-throughput sequencing from fecal samples was used to analyze the gut microbiota communities in common cranes (Grus grus) without harming them. Herein, we compared the fecal microbiome of fifteen G. grus in Tianjin Tuanbo Bird Natural Reserve (wild group) and six G. grus sampled from Beijing Wildlife Park (semi-captive group) in China, using 16S amplicon sequencing and bioinformatic analysis. The results showed that microbiota diversity and composition varied in different groups, suggesting that the gut microbiota was interactively influenced by diet and the environment. A total of 38 phyla and 776 genera were analyzed in this study. The dominant phyla of the G. grus were Firmicutes and Proteobacteria. Meanwhile, the microbiota richness of the semi-captive group was higher than the wild group. Data on beta diversity highlighted significant differences based on different dietary compositions. Zea mays, Glycine max, and Phragmites australia showed a significant correlation with intestinal bacteria of G. grus. This study provides a comprehensive analysis of diet and microbiomes in semi-captive and wild G. grus living in different environments, thus helping us to evaluate the influence on animal microbiomes and improve conservation efforts for this species.
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Affiliation(s)
- Hong Wu
- Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, College of Life Sciences, Tianjin Normal University, 393 West Binshui Road, Xiqing District, Tianjin 300387, China; (H.W.)
| | - Nan Wu
- Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, College of Life Sciences, Tianjin Normal University, 393 West Binshui Road, Xiqing District, Tianjin 300387, China; (H.W.)
| | - Xinchen Liu
- Beijing Wildlife Park, Daxing District, Beijing 102602, China
| | - Lei Zhang
- Beijing Wildlife Park, Daxing District, Beijing 102602, China
| | - Dapeng Zhao
- Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, College of Life Sciences, Tianjin Normal University, 393 West Binshui Road, Xiqing District, Tianjin 300387, China; (H.W.)
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3
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Herder EA, Skeen HR, Lutz HL, Hird SM. Body Size Poorly Predicts Host-Associated Microbial Diversity in Wild Birds. Microbiol Spectr 2023; 11:e0374922. [PMID: 37039681 PMCID: PMC10269867 DOI: 10.1128/spectrum.03749-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 03/12/2023] [Indexed: 04/12/2023] Open
Abstract
The composition and diversity of avian microbiota are shaped by many factors, including host ecologies and environmental variables. In this study, we examine microbial diversity across 214 bird species sampled in Malawi at five major body sites: blood, buccal cavity, gizzard, intestinal tract, and cloaca. Microbial community dissimilarity differed significantly across body sites. Ecological theory predicts that as area increases, so does diversity. We tested the hypothesis that avian microbiota diversity is correlated with body size, used as a proxy for area, using comparative phylogenetic methods. Using Pagel's lambda, we found that few microbial diversity metrics had significant phylogenetic signals. Phylogenetic generalized least squares identified a significant but weak negative correlation between host size and microbial diversity of the blood and a similarly significant but weakly positive correlation between the cloacal microbiota and host size among birds within the order Passeriformes. Phylosymbiosis, or a congruent branching pattern between host phylogeny and their associated microbiota similarity, was tested and found to be weak or not significant in four of the body sites with sufficient sample size (blood, buccal, cloaca, and intestines). Taken together, these results suggest that the avian microbiome is highly variable, with microbiota diversity demonstrating few clear associations with bird size. Finally, the blood microbiota have a unique relationship with host size. IMPORTANCE All animals coexist and interact with microorganisms, including bacteria, archaea, microscopic eukaryotes, and viruses. These microorganisms can have an enormous influence on the biology and health of macro-organisms. However, the general rules that govern these host-associated microbial communities are poorly described, especially in wild animals. In this paper, we investigate the microbial communities of over 200 species of birds from Malawi and characterize five body site bacterial microbiota in depth. Because the evolutionary relationships of the host underlie the relationship between any host-associated microbiota relationships, we use phylogenetic comparative methods to account for this relationship. We find that the size of a host (the bird) and the diversity and composition of the microbiota are largely uncorrelated. We also find that the general pattern of similarity between host phylogeny and microbiota similarity is weak. Together, we see that bird microbiota are not strongly tied to host size or evolutionary history.
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Affiliation(s)
- Elizabeth A. Herder
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Heather R. Skeen
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut, USA
- Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, Illinois, USA
| | - Holly L. Lutz
- Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, Illinois, USA
- Department of Pediatrics, UC San Diego School of Medicine, La Jolla, California, USA
| | - Sarah M. Hird
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
- Institute for Systems Genomics, University of Connecticut, Storrs, Connecticut, USA
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4
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Wang J, Hong M, Long J, Yin Y, Xie J. Differences in intestinal microflora of birds among different ecological types. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.920869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The intestinal microflora of animals plays a key role in metabolism, immunity, and development. Birds distributed across multiple ecological habitats. However, little is known about the differences in the intestinal microflora of birds among different ecological types. In this study, bird feces from different ecological types and orders were collected in Chongqing Zoo, China. In this study, high throughput sequencing of the 16S ribosomal RNA (rRNA) gene (amplicon sequencing) and metagenomics were used to analyze the composition and function differences of gut microbiota communities among different ecological types/orders. Firmicutes and Proteobacteria were the dominant bacteria phyla for all samples but there were significant differences in the α-diversity, community structure and microbial interactions between birds of different ecological types. The function differences involve most aspects of the body functions, especially for environmental information processing, organismal systems, human diseases, genetic information processing, and metabolism. These results suggest that diet and habitat are potential drivers of avian gut microbial aggregation. This preliminary study is of great significance for further research on the intestinal microflora of different ecological types of birds.
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Smith HG, Bean DC, Clarke RH, Loyn R, Larkins JA, Hassell C, Greenhill AR. Presence and antimicrobial resistance profiles of Escherichia coli, Enterococcusspp. and Salmonellasp. in 12 species of Australian shorebirds and terns. Zoonoses Public Health 2022; 69:615-624. [PMID: 35460193 PMCID: PMC9544147 DOI: 10.1111/zph.12950] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 03/13/2022] [Accepted: 04/05/2022] [Indexed: 11/27/2022]
Abstract
Antibiotic resistance is an ongoing threat to both human and animal health. Migratory birds are a potential vector for the spread of novel pathogens and antibiotic resistance genes. To date, there has been no comprehensive study investigating the presence of antibiotic resistance (AMR) in the bacteria of Australian shorebirds or terns. In the current study, 1022 individual birds representing 12 species were sampled across three states of Australia (Victoria, South Australia, and Western Australia) and tested for the presence of phenotypically resistant strains of three bacteria with potential to be zoonotic pathogens; Escherichia coli, Enterococcusspp., and Salmonellasp. In total, 206 E. coli, 266 Enterococcusspp., and 20 Salmonellasp. isolates were recovered, with AMR detected in 42% of E. coli, 85% of Enterococcusspp., and 10% of Salmonellasp. Phenotypic resistance was commonly detected to erythromycin (79% of Enterococcusspp.), ciprofloxacin (31% of Enterococcusspp.) and streptomycin (21% of E. coli). Resident birds were more likely to carry AMR bacteria than migratory birds (p ≤ .001). Bacteria isolated from shorebirds and terns are commonly resistant to at least one antibiotic, suggesting that wild bird populations serve as a potential reservoir and vector for AMR bacteria. However, globally emerging phenotypes of multidrug‐resistant bacteria were not detected in Australian shorebirds. This study provides baseline data of the carriage of AMR bacteria in Australian shorebirds and terns.
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Affiliation(s)
- Hannah G Smith
- Institute of Innovation, Science and Sustainability, Federation University, Churchill, Australia
| | - David C Bean
- Institute of Innovation, Science and Sustainability, Federation University, Churchill, Australia
| | - Rohan H Clarke
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Richard Loyn
- School of Life Sciences, Centre for Freshwater Ecosystems, La Trobe University, Wodonga, Victoria, Australia.,Institute for Land, Water and Society, Charles Sturt University, Albury, New South Wales, Australia
| | - Jo-Ann Larkins
- Institute of Innovation, Science and Sustainability, Federation University, Churchill, Australia.,School of Science, Engineering and Information Technology, Federation University, Ballarat, Victoria, Australia
| | - Chris Hassell
- Global Flyway Network, Broome, Western Australia, Australia.,Australasian Wader Studies Group, Broome, Western Australia, Australia
| | - Andrew R Greenhill
- Institute of Innovation, Science and Sustainability, Federation University, Churchill, Australia
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6
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Akhil Prakash E, Hromádková T, Jabir T, Vipindas PV, Krishnan KP, Mohamed Hatha AA, Briedis M. Dissemination of multidrug resistant bacteria to the polar environment - Role of the longest migratory bird Arctic tern (Sterna paradisaea). THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 815:152727. [PMID: 34974001 DOI: 10.1016/j.scitotenv.2021.152727] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 12/20/2021] [Accepted: 12/23/2021] [Indexed: 06/14/2023]
Abstract
The ever-increasing prevalence of antibiotic-resistant bacteria(ARB), primarily due to the frequent use and misuse of antibiotics, is an issue of serious global concern. Migratory birds have a significant role in dissemination of ARB, as they acquire resistant bacteria from reservoirs and transport them to other environments which are relatively less influenced by anthropogenically. We have investigated the prevalence of ARB in a long-distance migratory bird, the Arctic tern (Sterna paradisaea) captured from the Svalbard Archipelago. The birds were tagged with geolocators to track their extraordinary long migration, and the cloacal samples were collected before the migration and after the migration by recapturing the same birds. The tracking of 12 birds revealed that during the annual cycle they underwent a total of 166 stopovers (11-18, mean = 3.8) and recovery points along the Atlantic Ocean. Twelve major bacterial genera were identified from Arctic tern cloacal samples, which are dominated by Staphylococcus spp. and Aerococcus spp. The bacterial isolates showed resistance against 16 antibiotics (before migration) and 17 antibiotics (after migration) out of 17 antibiotics tested. Resistance to β-lactam and quinolone class of antibiotics were frequent among the bacteria. The study highlights the potential role of Arctic tern in the dissemination of multidrug resistant bacteria across far and wide destinations, especially to the polar environments.
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Affiliation(s)
- E Akhil Prakash
- Department of Marine Biology, Microbiology, and Biochemistry, School of Marine Sciences, Cochin University of Science and Technology (CUSAT), Kochi 682 016, India.
| | - Tereza Hromádková
- Department of Zoology, Faculty of Science, University of South Bohemia, 370 05 České Budějovice, Czech Republic; Centre for Polar Ecology, Faculty of Science, University of South Bohemia, 370 05 České Budějovice, Czech Republic
| | - T Jabir
- National Centre for Polar and Ocean Research, Ministry of Earth Sciences (Government of India), Headland Sada, Vasco-da-Gama, Goa 403 804, India.
| | - P V Vipindas
- National Centre for Polar and Ocean Research, Ministry of Earth Sciences (Government of India), Headland Sada, Vasco-da-Gama, Goa 403 804, India
| | - K P Krishnan
- National Centre for Polar and Ocean Research, Ministry of Earth Sciences (Government of India), Headland Sada, Vasco-da-Gama, Goa 403 804, India; CUSAT-NCPOR Centre for Polar Sciences, Cochin University of Science and Technology (CUSAT), Kochi 682 016, India
| | - A A Mohamed Hatha
- Department of Marine Biology, Microbiology, and Biochemistry, School of Marine Sciences, Cochin University of Science and Technology (CUSAT), Kochi 682 016, India; CUSAT-NCPOR Centre for Polar Sciences, Cochin University of Science and Technology (CUSAT), Kochi 682 016, India.
| | - Martins Briedis
- Department of Bird Migration, Swiss Ornithological Institute, 6204 Sempach, Switzerland; Lab of Ornithology, Institute of Biology, University of Latvia, 1004 Riga, Latvia
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7
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Zhang Z, Yang Z, Zhu L. Gut microbiome of migratory shorebirds: Current status and future perspectives. Ecol Evol 2021; 11:3737-3745. [PMID: 33976772 PMCID: PMC8093701 DOI: 10.1002/ece3.7390] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 02/04/2021] [Accepted: 02/24/2021] [Indexed: 01/26/2023] Open
Abstract
Migratory shorebirds have many unique life history characteristics, such as long-distance travel between breeding sites, stopover sites, and wintering sites. The physiological challenges for migrant energy requirement and immunity may affect their gut microbiome community. Here, we reviewed the specific features (e.g., relatively high proportion of Corynebacterium and Fusobacterium) in the gut microbiome of 18 migratory shorebirds, and the factors (e.g., diet, migration, environment, and phylogeny) affecting the gut microbiome. We discussed possible future studies of the gut microbiome in migratory shorebirds, including the composition and function of the spatial-temporal gut microbiome, and the potential contributions made by the gut microbiome to energy requirement during migration.
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Affiliation(s)
- Zheng Zhang
- Colleges of Life SciencesNanjing Normal UniversityNanjingChina
| | | | - Lifeng Zhu
- Colleges of Life SciencesNanjing Normal UniversityNanjingChina
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8
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Zhang N, Zhou L, Yang Z, Gu J. Effects of Food Changes on Intestinal Bacterial Diversity of Wintering Hooded Cranes ( Grus monacha). Animals (Basel) 2021; 11:ani11020433. [PMID: 33562375 PMCID: PMC7915383 DOI: 10.3390/ani11020433] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 02/01/2021] [Accepted: 02/02/2021] [Indexed: 12/19/2022] Open
Abstract
Simple Summary The intestinal microbiota plays a vital role in the health of animals, and food is an important factor that influences the intestinal microbial community. During the winter months, waterbirds require certain foods to supply them with energy through the cold winter. Due to changes in the plant resources available to waterbirds, their intestinal bacteria will vary accordingly. In this study, we analysed the relationship between food composition and intestinal bacteria in hooded cranes (Grus monacha). We found that food resources from similar habitats were more similar, and the corresponding hooded crane intestinal bacteria were also more similar. The results show that the intestinal bacteria of hooded cranes had a certain adaptability to the type of food being consumed. This study contributes novel insights into the diet of hooded cranes in the winter months, allowing for improved protection and management strategies. Abstract As food is recognised as an important factor affecting the intestinal microbiota, seasonal changes in diet can influence the community composition. The hooded crane (Grus monacha) is an endangered migratory waterbird species, with some of the population wintering in the sallow lakes in the middle and lower Yangtze River floodplain. Their food resources have changed seasonally, with a reduction resulting from wetland degradation. To cope with seasonal changes in food availability, hooded cranes must constantly adjust their foraging strategies to survive. We studied the effect of changes in diet on the intestinal bacterial diversity of hooded cranes at Shengjin Lake, using faecal microanalysis and high-throughput sequencing. The results show that the main foods of hooded cranes were Polygonum criopolitanum, Oryza sativa, and Carex spp., which were significantly related to the composition of the intestinal bacterial community. In addition, foods available from the similar habitats were more similar, and the corresponding hooded crane intestinal bacteria were also more similar. The relative abundance of Lactobacillus acidipiscis in January and March was significantly higher than in November. Our research shows that the intestinal bacteria of hooded cranes actively adapt to diet changes to overcome the negative impact of the reduction in food resources, which is vital to the survival of hooded cranes.
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Affiliation(s)
- Nazhong 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
| | - 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
| | - Zhuqing Yang
- 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
| | - Jingjing Gu
- 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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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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10
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Cruz-López M, Fernández G, Hipperson H, Palacios E, Cavitt J, Galindo-Espinosa D, Gómez Del Angel S, Pruner R, Gonzalez O, Burke T, Küpper C. Allelic diversity and patterns of selection at the major histocompatibility complex class I and II loci in a threatened shorebird, the Snowy Plover (Charadrius nivosus). BMC Evol Biol 2020; 20:114. [PMID: 32912143 PMCID: PMC7488298 DOI: 10.1186/s12862-020-01676-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Accepted: 08/20/2020] [Indexed: 12/02/2022] Open
Abstract
Background Understanding the structure and variability of adaptive loci such as the major histocompatibility complex (MHC) genes is a primary research goal for evolutionary and conservation genetics. Typically, classical MHC genes show high polymorphism and are under strong balancing selection, as their products trigger the adaptive immune response in vertebrates. Here, we assess the allelic diversity and patterns of selection for MHC class I and class II loci in a threatened shorebird with highly flexible mating and parental care behaviour, the Snowy Plover (Charadrius nivosus) across its broad geographic range. Results We determined the allelic and nucleotide diversity for MHC class I and class II genes using samples of 250 individuals from eight breeding population of Snowy Plovers. We found 40 alleles at MHC class I and six alleles at MHC class II, with individuals carrying two to seven different alleles (mean 3.70) at MHC class I and up to two alleles (mean 1.45) at MHC class II. Diversity was higher in the peptide-binding region, which suggests balancing selection. The MHC class I locus showed stronger signatures of both positive and negative selection than the MHC class II locus. Most alleles were present in more than one population. If present, private alleles generally occurred at very low frequencies in each population, except for the private alleles of MHC class I in one island population (Puerto Rico, lineage tenuirostris). Conclusion Snowy Plovers exhibited an intermediate level of diversity at the MHC, similar to that reported in other Charadriiformes. The differences found in the patterns of selection between the class I and II loci are consistent with the hypothesis that different mechanisms shape the sequence evolution of MHC class I and class II genes. The rarity of private alleles across populations is consistent with high natal and breeding dispersal and the low genetic structure previously observed at neutral genetic markers in this species.
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Affiliation(s)
- Medardo Cruz-López
- Posgrado en Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Cd. México, Mexico.
| | - Guillermo Fernández
- Unidad Académica Mazatlán, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Apartado Postal 811, 82040, Mazatlán, Sinaloa, Mexico
| | - Helen Hipperson
- NERC Biomolecular Analysis Facility, Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Eduardo Palacios
- Centro de Investigación Científica y de Educación Superior de Ensenada, Unidad La Paz, Miraflores 334, Col. Bellavista, 23050, La Paz, Baja California Sur, Mexico
| | - John Cavitt
- Avian Ecology Laboratory Department of Zoology, Weber State University, Ogden, UT, 84408, USA
| | - Daniel Galindo-Espinosa
- Departamento Académico de Ciencias Marinas y Costeras, Universidad Autónoma de Baja California Sur, Carretera al Sur km 5.5, A.P. 19-B, 23080, La Paz, B.C.S., Mexico
| | - Salvador Gómez Del Angel
- Posgrado en Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Cd. México, Mexico
| | - Raya Pruner
- Florida Fish and Wildlife Conservation Commission, Fish and Wildlife Research Institute, Panama City, FL, USA
| | - Oscar Gonzalez
- Grupo Aves del Perú, Gómez del Carpio 135, Barrio Medico, 34, Lima, Peru.,Department of Natural Sciences, Emmanuel College, Franklin Springs, GA, 30369, USA
| | - Terry Burke
- NERC Biomolecular Analysis Facility, Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Clemens Küpper
- Max Planck Institute for Ornithology, Eberhard-Gwinner-Strasse, 82319, Seewiesen, Germany.
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11
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Jiang SC, Han M, Chandrasekaran S, Fang Y, Kellogg CA. Assessing the water quality impacts of two Category-5 hurricanes on St. Thomas, Virgin Islands. WATER RESEARCH 2020; 171:115440. [PMID: 31955059 PMCID: PMC7001102 DOI: 10.1016/j.watres.2019.115440] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 12/17/2019] [Accepted: 12/22/2019] [Indexed: 05/12/2023]
Abstract
Managing waterborne and water-related diseases is one of the most critical factors in the aftermath of hurricane-induced natural disasters. The goal of the study was to identify water-quality impairments in order to set the priorities for post-hurricane relief and to guide future decisions on disaster preparation and relief administration. Field investigations were carried out on St. Thomas, U.S. Virgin Islands as soon as the disaster area became accessible after the back-to-back hurricane strikes by Irma and Maria in 2017. Water samples were collected from individual household rain cisterns, the coastal ocean, and street-surface runoffs for microbial concentration. The microbial community structure and the occurrence of potential human pathogens were investigated in samples using next generation sequencing. Loop mediated isothermal amplification was employed to detect fecal indicator bacteria, Enterococcus faecalis. The results showed both fecal indicator bacteria and Legionella genetic markers were prevalent but were low in concentration in the water samples. Among the 22 cistern samples, 86% were positive for Legionella and 82% for Escherichia-Shigella. Enterococcus faecalis was detected in over 68% of the rain cisterns and in 60% of the coastal waters (n = 20). Microbial community composition in coastal water samples was significantly different from cistern water and runoff water. Although identification at bacterial genus level is not direct evidence of human pathogens, our results suggest cistern water quality needs more organized attention for protection of human health, and that preparation and prevention measures should be taken before natural disasters strike.
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Affiliation(s)
- Sunny C Jiang
- Department of Civil and Environmental Engineering, University of California, Irvine, CA, USA.
| | - Muyue Han
- Department of Civil and Environmental Engineering, University of California, Irvine, CA, USA
| | - Srikiran Chandrasekaran
- Department of Civil and Environmental Engineering, University of California, Irvine, CA, USA
| | - Yingcong Fang
- Department of Civil and Environmental Engineering, University of California, Irvine, CA, USA
| | - Christina A Kellogg
- St. Petersburg Coastal and Marine Science Center, U.S. Geological Survey, St. Petersburg, FL, USA
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12
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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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13
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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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14
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Genotypic differences between strains of the opportunistic pathogen Corynebacterium bovis isolated from humans, cows, and rodents. PLoS One 2018; 13:e0209231. [PMID: 30586440 PMCID: PMC6306256 DOI: 10.1371/journal.pone.0209231] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 11/30/2018] [Indexed: 01/21/2023] Open
Abstract
Corynebacterium bovis is an opportunistic bacterial pathogen shown to cause eye and prosthetic joint infections as well as abscesses in humans, mastitis in dairy cattle, and skin disease in laboratory mice and rats. Little is known about the genetic characteristics and genomic diversity of C. bovis because only a single draft genome is available for the species. The overall aim of this study was to sequence and compare the genome of C. bovis isolates obtained from different species, locations, and time points. Whole-genome sequencing was conducted on 20 C. bovis isolates (six human, four bovine, nine mouse and one rat) using the Illumina MiSeq platform and submitted to various comparative analysis tools. Sequencing generated high-quality contigs (over 2.53 Mbp) that were comparable to the only reported assembly using C. bovis DSM 20582T (97.8 ± 0.36% completeness). The number of protein-coding DNA sequences (2,174 ± 12.4) was similar among all isolates. A Corynebacterium genus neighbor-joining tree was created, which revealed Corynebacterium falsenii as the nearest neighbor to C. bovis (95.87% similarity), although the reciprocal comparison shows Corynebacterium jeikeium as closest neighbor to C. falsenii. Interestingly, the average nucleotide identity demonstrated that the C. bovis isolates clustered by host, with human and bovine isolates clustering together, and the mouse and rat isolates forming a separate group. The average number of genomic islands and putative virulence factors were significantly higher (p<0.001) in the mouse and rat isolates as compared to human/bovine isolates. Corynebacterium bovis’ pan-genome contained a total of 3,067 genes of which 1,354 represented core genes. The known core genes of all isolates were primarily related to ‘‘metabolism” and ‘‘information storage/processing.” However, most genes were classified as ‘‘function unknown” or “unclassified”. Surprisingly, no intact prophages were found in any isolate; however, almost all isolates had at least one complete CRISPR-Cas system.
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15
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Kohl KD. An Introductory "How-to" Guide for Incorporating Microbiome Research into Integrative and Comparative Biology. Integr Comp Biol 2018; 57:674-681. [PMID: 28985331 DOI: 10.1093/icb/icx013] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Research on host-associated microbial communities has grown rapidly. Despite the great body of work, inclusion of microbiota-related questions into integrative and comparative biology is still lagging behind other disciplines. The purpose of this paper is to offer an introduction into the basic tools and techniques of host-microbe research. Specifically, what considerations should be made before embarking on such projects (types of samples, types of controls)? How is microbiome data analyzed and integrated with data measured from the hosts? How can researchers experimentally manipulate the microbiome? With this information, integrative and comparative biologists should be able to include host-microbe studies into their research and push the boundaries of both fields.
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Affiliation(s)
- Kevin D Kohl
- Department of Biological Sciences, University of Pittsburgh, 4249 Fifth Avenue, Pittsburgh, PA 15260, USA
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16
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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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17
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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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18
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Proença DN, Francisco R, Kublik S, Schöler A, Vestergaard G, Schloter M, Morais PV. The Microbiome of Endophytic, Wood Colonizing Bacteria from Pine Trees as Affected by Pine Wilt Disease. Sci Rep 2017. [PMID: 28646202 PMCID: PMC5482821 DOI: 10.1038/s41598-017-04141-6] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Pine wilt disease (PWD) is a devastating forest disease present worldwide. In this study we analyzed the effects of the invasion of the pinewood nematode Bursaphelenchus xylophilus, the major pathogen causing PWD, on the endophytic microbiome of adult P. pinaster trees. Wood samples from trees with different degrees of PWD disease were collected at two sites (A and M) in Portugal. Endophytic bacteria were characterized based on directly extracted DNA by fingerprinting and barcoding using the 16S rRNA gene as marker. Furthermore, cultivation-based approaches were used to obtain isolates of the major taxa to study their ecophysiology. The endophytic microbiome from P. pinaster trees differed significantly between the two sampling sites. Main bacterial OTUs belonged to the Proteobacteria (39% (site M) - 97% (site A)), and Firmicutes (0.70% (site A) - 44% (site M)). However, consequences of the invasion with the pathogen were comparable. Interestingly diversity of wood endophytic bacteria increased with the severity of the diseases, with highest diversity levels observed in in the most affected trees. Our results suggest that in the first stages of the disease, the defence mechanisms of plants are repressed by the pathogen, resulting in a colonization of the wood interior by soil microorganisms.
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Affiliation(s)
| | | | - Susanne Kublik
- Research Unit Environmental Genomics, Helmholtz Zentrum München, Munich, Germany
| | - Anne Schöler
- Research Unit Environmental Genomics, Helmholtz Zentrum München, Munich, Germany
| | - Gisle Vestergaard
- Research Unit Environmental Genomics, Helmholtz Zentrum München, Munich, Germany
| | - Michael Schloter
- Research Unit Environmental Genomics, Helmholtz Zentrum München, Munich, Germany.
| | - Paula V Morais
- CEMMPRE, University of Coimbra, Coimbra, Portugal.,Department of Life Sciences, University of Coimbra, Coimbra, Portugal
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19
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Rzymski P, Słodkowicz-Kowalska A, Klimaszyk P, Solarczyk P, Poniedziałek B. Screening of protozoan and microsporidian parasites in feces of great cormorant (Phalacrocorax carbo). ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:9813-9819. [PMID: 28255818 PMCID: PMC5388712 DOI: 10.1007/s11356-017-8652-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 02/16/2017] [Indexed: 06/06/2023]
Abstract
The global population of great cormorants (Phalacrocorax carbo L.) is on the rise. These birds, characterized by rapid metabolism, can deposit large quantities of feces, and because they breed on the land but forage on water, both terrestrial and aquatic environments can be simultaneously affected by their activities. The contribution of great cormorants in the dispersal of bacterial and viral pathogens has been immensely studied; whereas, the occurrence of eukaryotic parasites such as protozoans and microsporidians in these birds is little known. The present study investigated the presence of dispersive stages of potentially zoonotic protozoans belonging to the genera Blastocystis, Giardia and Cryptosporidium, and Microsporidia spores in feces collected from birds inhabiting the breeding colony established at one lake island in Poland, Europe. The feces were examined by coprological techniques (staining with iron hematoxylin, Ziehl-Neelsen, and modified Weber's chromotrope 2R-based trichrome), and with immunofluorescence antibody MERIFLUOR Cryptosporidium/Giardia assay. As found, the Cryptosporidium oocysts were identified rarely in 8% of samples (2/25; 3-5 × 103/g) and no cysts of Giardia and Blastocystis were detected. Microsporidian spores were detected in 4% of samples (1/25) but at very high frequency (4.3 × 104/g). No dispersive stages of parasites were identified in water samples collected from the littoral area near the colony. Despite the profuse defecation of cormorants, their role in the dispersion of the investigated parasites may not be as high as hypothesized.
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Affiliation(s)
- Piotr Rzymski
- Department of Environmental Medicine, Faculty of Health Sciences, Poznan University of Medical Sciences, Poznań, Poland.
| | - Anna Słodkowicz-Kowalska
- Department of Biology and Medical Parasitology, Faculty of Medicine I, Poznan University of Medical Sciences, Poznań, Poland
| | - Piotr Klimaszyk
- Department of Water Protection, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - Piotr Solarczyk
- Department of Biology and Medical Parasitology, Faculty of Medicine I, Poznan University of Medical Sciences, Poznań, Poland
| | - Barbara Poniedziałek
- Department of Environmental Medicine, Faculty of Health Sciences, Poznan University of Medical Sciences, Poznań, Poland
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20
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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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21
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Escallón C, Becker MH, Walke JB, Jensen RV, Cormier G, Belden LK, Moore IT. Testosterone levels are positively correlated with cloacal bacterial diversity and the relative abundance of Chlamydiae in breeding male rufous‐collared sparrows. Funct Ecol 2016. [DOI: 10.1111/1365-2435.12696] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Camilo Escallón
- Department of Biological Sciences Virginia Tech 2119 Derring Hall Blacksburg Virginia 24061 USA
| | - Matthew H. Becker
- Department of Biological Sciences Virginia Tech 2119 Derring Hall Blacksburg Virginia 24061 USA
| | - Jenifer B. Walke
- Department of Biological Sciences Virginia Tech 2119 Derring Hall Blacksburg Virginia 24061 USA
| | - Roderick V. Jensen
- Department of Biological Sciences Virginia Tech 2119 Derring Hall Blacksburg Virginia 24061 USA
| | - Guy Cormier
- Georgia Advanced Computing Resource Center The University of Georgia 4098C Stegeman Coliseum Athens Georgia 30602 USA
| | - Lisa K. Belden
- Department of Biological Sciences Virginia Tech 2119 Derring Hall Blacksburg Virginia 24061 USA
| | - Ignacio T. Moore
- Department of Biological Sciences Virginia Tech 2119 Derring Hall Blacksburg Virginia 24061 USA
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22
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Rasch J, Krüger S, Fontvieille D, Ünal CM, Michel R, Labrosse A, Steinert M. Legionella-protozoa-nematode interactions in aquatic biofilms and influence of Mip on Caenorhabditis elegans colonization. Int J Med Microbiol 2016; 306:443-51. [PMID: 27288243 DOI: 10.1016/j.ijmm.2016.05.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Revised: 05/03/2016] [Accepted: 05/24/2016] [Indexed: 02/08/2023] Open
Abstract
Legionella pneumophila, the causative agent of Legionnaireś disease, is naturally found in aquatic habitats. The intracellular life cycle within protozoa pre-adapted the "accidental" human pathogen to also infect human professional phagocytes like alveolar macrophages. Previous studies employing the model organism Caenorhabditis elegans suggest that also nematodes might serve as a natural host for L. pneumophila. Here, we report for the first time from a natural co-habitation of L. pneumophila and environmental nematode species within biofilms of a warm water spring. In addition, we identified the protozoan species Oxytricha bifaria, Stylonychia mytilus, Ciliophrya sp. which have never been described as potential interaction partners of L. pneumophila before. Modeling and dissection of the Legionella-protozoa-nematode interaction revealed that C. elegans ruptures Legionella-infected amoebal cells and by this means incorporate the pathogen. Further infection studies revealed that the macrophage infectivity potentiator (Mip) protein of L. pneumophila, which is known to bind collagen IV during human lung infection, promotes the colonization of the intestinal tract of L4 larvae of C. elegans and negatively influences the life span of the worms. The Mip-negative L. pneumophila mutant exhibited a 32-fold reduced colonization rate of the nematodes after 48h when compared to the wild-type strain. Taken together, these studies suggest that nematodes may serve as natural hosts for L. pneumophila, promote their persistence and dissemination in the environment, and co-evolutionarily pre-adapt the pathogen for interactions with extracellular constituents of human lung tissue.
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Affiliation(s)
- Janine Rasch
- Institut für Mikrobiologie, Technische Universität Braunschweig, Germany
| | - Stefanie Krüger
- Institut für Mikrobiologie, Technische Universität Braunschweig, Germany
| | | | - Can M Ünal
- Institut für Mikrobiologie, Technische Universität Braunschweig, Germany
| | - Rolf Michel
- Central Institute of the Federal Armed Forces Medical Services, Koblenz, Germany
| | | | - Michael Steinert
- Institut für Mikrobiologie, Technische Universität Braunschweig, Germany; Helmholtz Center for Infection Research, Braunschweig, Germany.
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Meissner W, Dynowska M, Góralska K, Rzyska H. Mallards (Anas platyrhynchos) staying in urban environments have higher levels of microfungi biota diversity than do birds from non-urban areas. FUNGAL ECOL 2015. [DOI: 10.1016/j.funeco.2015.07.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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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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Waite DW, Taylor MW. Characterizing the avian gut microbiota: membership, driving influences, and potential function. Front Microbiol 2014; 5:223. [PMID: 24904538 PMCID: PMC4032936 DOI: 10.3389/fmicb.2014.00223] [Citation(s) in RCA: 277] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Accepted: 04/28/2014] [Indexed: 12/18/2022] 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 important roles in providing the host with nutrition and protection from pathogens. Although many studies have investigated the role of particular microbes in the guts of avian species, there has been no attempt to unify the results of previous, sequence-based studies to examine the factors that shape the avian gut microbiota as a whole. In this study, we present the first meta-analysis of the avian gut microbiota, using 16S rRNA gene sequences obtained from a range of publicly available clone-library and amplicon pyrosequencing data. We investigate community membership and structure, as well as probe the roles of some of the key biological factors that influence the gut microbiota of other vertebrates, such as host phylogeny, location within the gut, diet, and association with humans. Our results indicate that, across avian studies, the microbiota demonstrates a similar phylum-level composition to that of mammals. Host bird species is the most important factor in determining community composition, although sampling site, diet, and captivity status also contribute. These analyses provide a first integrated look at the composition of the avian microbiota, and serve as a foundation for future studies in this area.
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Affiliation(s)
- David W Waite
- Centre for Microbial Innovation, School of Biological Sciences, Faculty of Science, The University of Auckland Auckland, New Zealand
| | - Michael W Taylor
- Centre for Microbial Innovation, School of Biological Sciences, Faculty of Science, The University of Auckland Auckland, New Zealand
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de Abreu PM, Farias PG, Paiva GS, Almeida AM, Morais PV. Persistence of microbial communities including Pseudomonas aeruginosa in a hospital environment: a potential health hazard. BMC Microbiol 2014; 14:118. [PMID: 24885173 PMCID: PMC4049484 DOI: 10.1186/1471-2180-14-118] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Accepted: 04/14/2014] [Indexed: 01/26/2023] Open
Abstract
Background The persistence of microbial communities and how they change in indoor environments is of immense interest to public health. Moreover, hospital acquired infections are significant contributors to morbidity and mortality. Evidence suggests that, in hospital environments agent transfer between surfaces causes healthcare associated infections in humans, and that surfaces are an important transmission route and may act as a reservoir for some of the pathogens. This study aimed to evaluate the diversity of microorganisms that persist on noncritical equipment and surfaces in a main hospital in Portugal, and are able to grow in selective media for Pseudomonas, and relate them with the presence of Pseudomonas aeruginosa. Results During 2 years, a total of 290 environmental samples were analyzed, in 3 different wards. The percentage of equipment in each ward that showed low contamination level varied between 22% and 38%, and more than 50% of the equipment sampled was highly contaminated. P. aeruginosa was repeatedly isolated from sinks (10 times), from the taps’ biofilm (16 times), and from the showers and bedside tables (two times). Two ERIC clones were isolated more than once. The contamination level of the different taps analyzed showed correlation with the contamination level of the hand gels support, soaps and sinks. Ten different bacteria genera were frequently isolated in the selective media for Pseudomonas. Organisms usually associated with nosocomial infections as Stenotrophomonas maltophilia, Enterococcus feacalis, Serratia nematodiphila were also repeatedly isolated on the same equipment. Conclusions The environment may act as a reservoir for at least some of the pathogens implicated in nosocomial infections. The bacterial contamination level was related to the presence of humidity on the surfaces, and tap water (biofilm) was a point of dispersion of bacterial species, including potentially pathogenic organisms. The materials of the equipment sampled could not be related to the microbial contamination level. The presence of a disinfectant in the isolation medium suggests that the number of microorganism in the environment could be higher and shows the diversity of disinfectant resistant species. The statistical analysis suggests that the presence of bacteria could increase the risk of transmission by hand manipulation.
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Affiliation(s)
| | | | | | | | - Paula Vasconcelos Morais
- IMAR - Marine and Environmental Research Centre, University of Coimbra, 3004-517 Coimbra, Portugal.
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Complete Genome Sequence of Corynebacterium falsenii DSM 44353 To Study the Evolution of Corynebacterium Cluster 3 Species. GENOME ANNOUNCEMENTS 2014; 2:2/2/e00158-14. [PMID: 24604654 PMCID: PMC3945510 DOI: 10.1128/genomea.00158-14] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Corynebacterium falsenii is a member of the natural microflora of wild and domesticated birds and is rarely detected in human clinical specimens. The chromosomal sequence of the type strain C. falsenii DSM 44353 comprises 2,677,607 bp and provides detailed insights into the evolution of Corynebacterium species assigned to the highly diverse cluster 3.
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Intestinal microbiota and species diversity of Campylobacter and Helicobacter spp. in migrating shorebirds in Delaware Bay. Appl Environ Microbiol 2014; 80:1838-47. [PMID: 24413599 DOI: 10.1128/aem.03793-13] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Using 16S rRNA gene sequencing analysis, we examined the bacterial diversity and the presence of opportunistic bacterial pathogens (i.e., Campylobacter and Helicobacter) in red knot (Calidris canutus; n = 40), ruddy turnstone (Arenaria interpres; n = 35), and semipalmated sandpiper (Calidris pusilla; n = 22) fecal samples collected during a migratory stopover in Delaware Bay. Additionally, we studied the occurrence of Campylobacter spp., enterococci, and waterfowl fecal source markers using quantitative PCR (qPCR) assays. Of 3,889 16S rRNA clone sequences analyzed, the bacterial community was mostly composed of Bacilli (63.5%), Fusobacteria (12.7%), Epsilonproteobacteria (6.5%), and Clostridia (5.8%). When epsilonproteobacterium-specific 23S rRNA gene clone libraries (i.e., 1,414 sequences) were analyzed, the sequences were identified as Campylobacter (82.3%) or Helicobacter (17.7%) spp. Specifically, 38.4%, 10.1%, and 26.0% of clone sequences were identified as C. lari (>99% sequence identity) in ruddy turnstone, red knot, and semipalmated sandpiper clone libraries, respectively. Other pathogenic species of Campylobacter, such as C. jejuni and C. coli, were not detected in excreta of any of the three bird species. Most Helicobacter-like sequences identified were closely related to H. pametensis (>99% sequence identity) and H. anseris (92% sequence identity). qPCR results showed that the occurrence and abundance of Campylobacter spp. was relatively high compared to those of fecal indicator bacteria, such as Enterococcus spp., E. faecalis, and Catellicoccus marimammalium. Overall, the results provide insights into the complexity of the shorebird gut microbial community and suggest that these migratory birds are important reservoirs of pathogenic Campylobacter species.
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