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Pisaniello A, Handley KM, White WL, Angert ER, Boey JS, Clements KD. Host individual and gut location are more important in gut microbiota community composition than temporal variation in the marine herbivorous fish Kyphosus sydneyanus. BMC Microbiol 2023; 23:275. [PMID: 37773099 PMCID: PMC10540440 DOI: 10.1186/s12866-023-03025-2] [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: 03/23/2023] [Accepted: 09/19/2023] [Indexed: 09/30/2023] Open
Abstract
BACKGROUND Gut microbiota play a key role in the nutrition of many marine herbivorous fishes through hindgut fermentation of seaweed. Gut microbiota composition in the herbivorous fish Kyphosus sydneyanus (family Kyphosidae) varies between individuals and gut sections, raising two questions: (i) is community composition stable over time, especially given seasonal shifts in storage metabolites of dietary brown algae, and (ii) what processes influence community assembly in the hindgut? RESULTS We examined variation in community composition in gut lumen and mucosa samples from three hindgut sections of K. sydneyanus collected at various time points in 2020 and 2021 from reefs near Great Barrier Island, New Zealand. 16S rRNA gene analysis was used to characterize microbial community composition, diversity and estimated density. Differences in community composition between gut sections remained relatively stable over time, with little evidence of temporal variation. Clostridia dominated the proximal hindgut sections and Bacteroidia the most distal section. Differences were detected in microbial composition between lumen and mucosa, especially at genus level. CONCLUSIONS High variation in community composition and estimated bacterial density among individual fish combined with low variation in community composition temporally suggests that initial community assembly involved environmental selection and random sampling/neutral effects. Community stability following colonisation could also be influenced by historical contingency, where early colonizing members of the community may have a selective advantage. The impact of temporal changes in the algae may be limited by the dynamics of substrate depletion along the gut following feeding, i.e. the depletion of storage metabolites in the proximal hindgut. Estimated bacterial density, showed that Bacteroidota has the highest density (copies/mL) in distal-most lumen section V, where SCFA concentrations are highest. Bacteroidota genera Alistipes and Rikenella may play important roles in the breakdown of seaweed into useful compounds for the fish host.
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Affiliation(s)
- Alessandro Pisaniello
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand.
| | - Kim M Handley
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
| | - W Lindsey White
- School of Science, Auckland University of Technology, Private Bag 92006, Auckland, New Zealand
| | - Esther R Angert
- Department of Microbiology, Cornell University, 123 Wing Drive, Ithaca, NY, 14853, USA
| | - Jian Sheng Boey
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
| | - Kendall D Clements
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand.
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2
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Díaz-Abad L, Bacco-Mannina N, Miguel Madeira F, Serrao EA, Regalla A, Patrício AR, Frade PR. Red, Gold and Green: Microbial Contribution of Rhodophyta and Other Algae to Green Turtle ( Chelonia mydas) Gut Microbiome. Microorganisms 2022; 10:microorganisms10101988. [PMID: 36296266 PMCID: PMC9610419 DOI: 10.3390/microorganisms10101988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 09/28/2022] [Accepted: 09/30/2022] [Indexed: 11/23/2022] Open
Abstract
The fitness of the endangered green sea turtle (Chelonia mydas) may be strongly affected by its gut microbiome, as microbes play important roles in host nutrition and health. This study aimed at establishing environmental microbial baselines that can be used to assess turtle health under altered future conditions. We characterized the microbiome associated with the gastrointestinal tract of green turtles from Guinea Bissau in different life stages and associated with their food items, using 16S rRNA metabarcoding. We found that the most abundant (% relative abundance) bacterial phyla across the gastrointestinal sections were Proteobacteria (68.1 ± 13.9% “amplicon sequence variants”, ASVs), Bacteroidetes (15.1 ± 10.1%) and Firmicutes (14.7 ± 21.7%). Additionally, we found the presence of two red algae bacterial indicator ASVs (the Alphaproteobacteria Brucella pinnipedialis with 75 ± 0% and a Gammaproteobacteria identified as methanotrophic endosymbiont of Bathymodiolus, with <1%) in cloacal compartments, along with six bacterial ASVs shared only between cloacal and local environmental red algae samples. We corroborate previous results demonstrating that green turtles fed on red algae (but, to a lower extent, also seagrass and brown algae), thus, acquiring microbial components that potentially aid them digest these food items. This study is a foundation for better understanding the microbial composition of sea turtle digestive tracts.
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Affiliation(s)
- Lucía Díaz-Abad
- CCMAR—Centre of Marine Sciences, CIMAR, University of Algarve, 8005-139 Faro, Portugal
- IMBRSea, International Master of Science in Marine Biological Resources, IMBRSea Universities Consortium, 9000 Ghent, Belgium
| | | | - Fernando Miguel Madeira
- cE3c—Centre for Ecology, Evolution and Environmental Changes, CHANGE—Global Change and Sustainability Institute, Faculdade de Ciências da Universidade de Lisboa, 1749-016 Lisbon, Portugal
| | - Ester A. Serrao
- CCMAR—Centre of Marine Sciences, CIMAR, University of Algarve, 8005-139 Faro, Portugal
- CIBIO/InBIO—Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, 4485-661 Vairão, Portugal
| | - Aissa Regalla
- IBAP—Instituto da Biodiversidade e das Áreas Protegidas Dr. Alfredo Simão da Silva, Bissau 1220, Guinea-Bissau
| | - Ana R. Patrício
- MARE—Marine and Environmental Sciences Centre, Ispa—Instituto Universitário, 1149-041 Lisbon, Portugal
- Centre for Ecology & Conservation, College of Life and Environmental Sciences, University of Exeter, Penryn TR10 9FE, Cornwall, UK
| | - Pedro R. Frade
- CCMAR—Centre of Marine Sciences, CIMAR, University of Algarve, 8005-139 Faro, Portugal
- Natural History Museum Vienna, 1010 Vienna, Austria
- Correspondence:
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3
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Beale DJ, Bissett A, Nilsson S, Bose U, Nelis JLD, Nahar A, Smith M, Gonzalez-Astudillo V, Braun C, Baddiley B, Vardy S. Perturbation of the gut microbiome in wild-caught freshwater turtles (Emydura macquarii macquarii) exposed to elevated PFAS levels. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 838:156324. [PMID: 35654195 DOI: 10.1016/j.scitotenv.2022.156324] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 05/23/2022] [Accepted: 05/25/2022] [Indexed: 06/15/2023]
Abstract
Per- and polyfluoroalkyl substances (PFAS) are environmentally persistent and pervasive. Understanding the toxicity of PFAS to wildlife is difficult, both due to the complexity of biotic and abiotic perturbations in the taxa under study and the practical and ethical problems associated with studying the impacts of environmental pollutants on free living wildlife. One avenue of inquiry into the effects of environmental pollutants, such as PFAS, is assessing the impact on the host gut microbiome. Here we show the microbial composition and biochemical functional outputs from the gut microbiome of sampled faeces from euthanised and necropsied wild-caught freshwater turtles (Emydura macquarii macquarii) exposed to elevated PFAS levels. The microbial community composition was profiled by 16S rRNA gene sequencing using a Nanopore MinION and the biochemical functional outputs of the gut microbiome were profiled using a combination of targeted central carbon metabolism metabolomics using liquid chromatography coupled to a triple quadrupole mass spectrometer (LC-QqQ-MS) and untargeted metabolomics using liquid chromatography coupled to a quadrupole time of flight mass spectrometer (LC-QToF-MS). Total PFAS was measured in the turtle serum using standard methods. These preliminary data demonstrated a 60-fold PFAS increase in impacted turtles compared to the sampled aquatic environment. The microbiome community was also impacted in the PFAS exposed turtles, with the ratio of Firmicutes-to-Bacteroidetes rising from 1.4 at the reference site to 5.5 at the PFAS impacted site. This ratio increase is indicative of host stress and dysfunction of the gut microbiome that was correlated with the biochemical metabolic function data, metabolites observed that are indications of stress and inflammation in the gut microbiome. Utilising the gut microbiome of sampled faeces collected from freshwater turtles provides a non-destructive avenue for investigating the impacts of PFAS in native wildlife, and provides an avenue to explore other contaminants in higher-order taxa within the environment.
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Affiliation(s)
- David J Beale
- Land and Water, Commonwealth Scientific and Industrial Research Organisation, Ecosciences Precinct, Dutton Park, QLD 4102, Australia.
| | - Andrew Bissett
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation, Battery Point, TAS 7004, Australia
| | - Sandra Nilsson
- Queensland Alliance for Environmental Health Sciences (QAEHS), The University of Queensland, Woolloongabba, QLD 4102, Australia
| | - Utpal Bose
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Queensland Bioscience Precinct, St Lucia, QLD 4067, Australia
| | - Joost Laurus Dinant Nelis
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Queensland Bioscience Precinct, St Lucia, QLD 4067, Australia
| | - Akhikun Nahar
- Land and Water, Commonwealth Scientific and Industrial Research Organisation, Research and Innovation Park, Acton, ACT 2601, Australia
| | - Matthew Smith
- National Collections and Marine Infrastructure (NCMI), Commonwealth Scientific and Industrial Research Organisation, Battery Point, TAS 7004, Australia
| | | | - Christoph Braun
- Water Quality and Investigation, Science and Technology Division, Department of Environment and Science, Queensland Government, Dutton Park, QLD 4102, Australia
| | - Brenda Baddiley
- Water Quality and Investigation, Science and Technology Division, Department of Environment and Science, Queensland Government, Dutton Park, QLD 4102, Australia
| | - Suzanne Vardy
- Water Quality and Investigation, Science and Technology Division, Department of Environment and Science, Queensland Government, Dutton Park, QLD 4102, Australia
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Kuschke SG. What lives on and in the sea turtle? A literature review of sea turtle bacterial microbiota. Anim Microbiome 2022; 4:52. [PMID: 36076281 PMCID: PMC9461204 DOI: 10.1186/s42523-022-00202-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 08/25/2022] [Indexed: 11/10/2022] Open
Abstract
Within the United States, all populations of sea turtles are listed as threatened or endangered under the Endangered Species Act. Identifying methods of supporting health, preventing disease, and treating disease is essential for conservation and management strategies for all species. Over the last few decades, advances in technology and high throughput sequencing have allowed a proliferation of research into core microbiota and microbiomes in humans and animals. Such investigations have proven that microbiota on and within a host can influence physiology, immunity, and development. Accordingly, a comprehensive understanding of microbiota is essential for unearthing the complex relationships within a microbiome and how those interactions and relationships can be used to promote health and prevent or treat disease. The goal of this review is to summarize the current microbiota research available across all species of sea turtles and identify any emerging trends. Methodological differences made it challenging to draw conclusions across studies, but it is apparent that each anatomical location investigated has a unique core microbiota with some potential overlap. In the future, unifying methodology across microbiota studies will allow broader conclusions to be drawn across all anatomic locations and species of sea turtles. These conclusions will then allow clinicians and conservationists to apply the research results in the field. Additionally, future efforts should include a wider range of organisms including fungi, viruses, parasites, epibiota, and archaea to unveil essential relationships among and between the organisms and host for maintenance of a healthy microbiome.
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5
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Spatial Variation of False Map Turtle (Graptemys pseudogeographica) Bacterial Microbiota in the Lower Missouri River, United States. J HERPETOL 2022. [DOI: 10.1670/20-100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Chen Y, Xia Z, Li H. Comparative analysis of the fecal bacterial communities of hawksbill sea turtles (Eretmochelys imbricata) and green sea turtles (Chelonia mydas). FEMS Microbiol Lett 2022; 369:6659191. [PMID: 35945331 DOI: 10.1093/femsle/fnac073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 05/24/2022] [Accepted: 08/06/2022] [Indexed: 11/13/2022] Open
Abstract
Hawksbill sea turtles (Eretmochelys imbricata) are important for maintaining healthy coral reef ecosystems currently qualify as 'critically endangered' by the IUCN. Their gut microbiota is closely linked to host nutrition and health, however, the gut microbiota of hawksbill sea turtles from a natural reserve remains unclear. Therefore, exploring their microbial community structure in a natural reserve may provide valuable information on strategies for protecting this species. In this study, we investigated hawksbill sea turtle fecal microbial communities from a natural reserve using 16S metagenomics and compared the gut microbiota from fecal samples of hawksbill and green sea turtles (Chelonia mydas). The results indicated that the structure of fecal microbial communities was significantly different between hawksbill and green sea turtles. In hawksbill sea turtles, the three dominant phyla were Bacteroidetes, Firmicutes, and Fusobacteria, whereas the fecal microbial communities of green sea turtles were mainly composed of Firmicutes, Bacteroidetes, and Proteobacteria. Among the hawksbill sea turtle fecal microbes, the predominant genera were Cetobacterium and Rikenell, whereas in green sea turtles, the predominant genera were Bacteroides and Paludibacter. In addition, predictive metagenomic analysis indicated that sugar catabolism was enriched in green sea turtle fecal microbiota, whereas pathways related to secondary metabolite production were enriched in hawksbill sea turtle fecal microbiota. Our study provides preliminary data on the fecal microbiota features of sea turtles from the natural reserve which may contribute to the management of the food requirements and long-term conservation of hawksbill sea turtles.
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Affiliation(s)
- Yuan Chen
- School of Life Science, Huizhou University, Huizhou 516007, China
| | - Zhongrong Xia
- Guangdong Huidong Sea Turtle National Nature Reserve Administration, Huidong 516359, Guangdong Province, China
| | - Hongwei Li
- School of Life Science, Huizhou University, Huizhou 516007, China
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7
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Chen Y, Xia Z, Li H. Metagenomic comparison of gut communities between hawksbills (Eretmochelys imbricata) and green sea turtles (Chelonia mydas). Arch Microbiol 2022; 204:450. [PMID: 35780445 DOI: 10.1007/s00203-022-03073-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 06/07/2022] [Accepted: 06/13/2022] [Indexed: 11/29/2022]
Abstract
The gut microbiota is closely linked to host nutrition, immunity, and health. Here, metagenomic analysis was conducted to elucidate the taxonomic and functional diversity of gut communities from hawksbills and green sea turtles. In terms of diversity and abundance, the gut microbiota of herbivorous green sea turtles showed a higher bacterial diversity and richness than that of hawksbills. Firmicutes dominated in all groups; however, the phylum Proteobacteria showed a higher relative abundance in hawksbills. Several metabolic pathways displayed broad prevalence and high relative abundances in the two sea turtle populations. Antibiotic resistance genes (ARGs) responsible for resistance to glycopeptide and tetracycline were the most abundant in all samples. In ARGs, the subtype macB was the most abundant in the two different sea turtle populations; however, evgS, bcrA, and efrA were more abundant in the green sea turtles, while in the hawksbills, tetT and tetB(P) were more abundant. Among mobile genetic elements (MGEs), the abundance of 16 MGE types showed a significant difference between the two sea turtle populations. MGE type transposase and plasmid were the most abundant in the two sea turtle populations. Additionally, gene functions were enriched in carbohydrate esterases, glycoside hydrolases, and polysaccharide lyases in the green sea turtles, whereas genes related to glycosyltransferases and auxiliary activities were highly abundant in hawksbills. These metagenomic profiles provide further insights into the microbial diversities of the two types of sea turtles and provide valuable information for future conservation efforts.
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Affiliation(s)
- Yuan Chen
- School of Life Science, Huizhou University, No. 46 Yanda Road, Huizhou, 516007, China
| | - Zhongrong Xia
- Guangdong Huidong Sea Turtle National Nature Reserve Administration, Huidong, 516359, Guangdong, China
| | - Hongwei Li
- School of Life Science, Huizhou University, No. 46 Yanda Road, Huizhou, 516007, China.
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8
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Hernández M, Ancona S, Díaz De La Vega-Pérez AH, Muñoz-Arenas LC, Hereira-Pacheco SE, Navarro-Noya YE. Is Habitat More Important than Phylogenetic Relatedness for Elucidating the Gut Bacterial Composition in Sister Lizard Species? Microbes Environ 2022; 37. [PMID: 35768277 PMCID: PMC9530725 DOI: 10.1264/jsme2.me21087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The gut microbiota influences the phenotype and fitness of a host; however, limited information is currently available on the diversity and functions of the gut microbiota in wild animals. Therefore, we herein examined the diversity, composition, and potential functions of the gut microbiota in three Sceloporus lizards: Sceloporus aeneus, S. bicanthalis, and S. grammicus, inhabiting different habitats in a mountainous ecosystem. The gut bacterial community of S. bicanthalis from alpine grasslands at 4,150 m a.s.l. exhibited greater taxonomic, phylogenetic, and functional alpha diversities than its sister species S. aeneus from cornfields and human-induced grasslands at 2,600 m a.s.l. Bacteria of the genus Blautia and metabolic functions related to the degradation of aromatic compounds were more abundant in S. bicanthalis than in S. aeneus, whereas Oscillibacter and predicted functions related to amino acid metabolism and fermentation were more abundant in S. aeneus. The structure of the dominant and most prevalent bacteria, i.e., the core microbiota, was similar between the sister species from different habitats, but differed between S. grammicus and S. aeneus cohabiting at 2,600 m a.s.l. and between S. grammicus and S. bicanthalis cohabiting at 4,150 m a.s.l. These results suggest that phylogenetic relatedness defines the core microbiota, while the transient, i.e., non-core, microbiota is influenced by environmental differences in the habitats. Our comparisons between phylogenetically close species provide further evidence for the specialized and complex associations between hosts and the gut microbiota as well as insights into the roles of phylogeny and ecological factors as drivers of the gut microbiota in wild vertebrates.
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Affiliation(s)
- Mauricio Hernández
- Doctorado en Ciencias Biológicas, Centro Tlaxcala de Biología de la Conducta, Universidad Autónoma de Tlaxcala
| | - Sergio Ancona
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México
| | | | | | - Stephanie E Hereira-Pacheco
- Estación Científica La Malinche, Centro Tlaxcala de Biología de la Conducta, Universidad Autónoma de Tlaxcala
| | - Yendi E Navarro-Noya
- Laboratorio de Interacciones Bióticas, Centro de Investigación en Ciencias Biológicas, Universidad Autónoma de Tlaxcala
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Ding X, Jin F, Xu J, Zhang S, Chen D, Hu B, Hong Y. The impact of aquaculture system on the microbiome and gut metabolome of juvenile Chinese softshell turtle ( Pelodiscus sinensis). IMETA 2022; 1:e17. [PMID: 38868566 PMCID: PMC10989827 DOI: 10.1002/imt2.17] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 03/03/2022] [Accepted: 03/13/2022] [Indexed: 06/14/2024]
Abstract
The commercial aquatic animal microbiome may markedly affect the successful host's farming in various aquaculture systems. However, very little was known about it. Here, two different aquaculture systems, the rice-fish culture (RFC) and intensive pond culture (IPC) systems, were compared to deconstruct the skin, oral, and gut microbiome, as well as the gut metabolome of juvenile Chinese softshell turtle (Pelodiscus sinensis). Higher alpha-diversity and functional redundancy of P. sinensis microbial community were found in the RFC than those of the IPC. The aquaculture systems have the strongest influence on the gut microbiome, followed by the skin microbiome, and finally the oral microbiome. Source-tracking analysis showed that the RFC's microbial community originated from more unknown sources than that of the IPC across all body regions. Strikingly, the RFC's oral and skin microbiome exhibited a significantly higher proportion of generalists and broader habitat niche breadth than those of the IPC, but not the gut. Null model analysis revealed that the RFC's oral and skin microbial community assembly was governed by a significantly greater proportion of deterministic processes than that of the IPC, but not the gut. We further identified the key gene and microbial contribution to five significantly changed gut metabolites, 2-oxoglutarate, N-acetyl-d-mannosamine, cis-4-hydroxy-d-proline, nicotinamide, and l-alanine, which were significantly correlated with important categories of microbe-mediated processes, including the amino acid metabolism, GABAergic synapse, ABC transporters, biosynthesis of unsaturated fatty acids, as well as citrate cycle. Moreover, different aquaculture systems have a significant impact on the hepatic lipid metabolism and body shape of P. sinensis. Our results provide new insight into the influence of aquaculture systems on the microbial community structure feature and assembly mechanism in an aquatic animal, also highlighting the key microbiome and gene contributions to the metabolite variation in the gut microbiome-metabolome association.
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Affiliation(s)
- Xia Ding
- School of Life SciencesNanchang UniversityNanchangJiangxiChina
| | - Feng Jin
- School of Life SciencesNanchang UniversityNanchangJiangxiChina
| | - Jiawang Xu
- School of Life SciencesNanchang UniversityNanchangJiangxiChina
| | - Shulei Zhang
- School of Life SciencesNanchang UniversityNanchangJiangxiChina
| | - Dongxu Chen
- School of Life SciencesNanchang UniversityNanchangJiangxiChina
| | - Beijuan Hu
- School of Life SciencesNanchang UniversityNanchangJiangxiChina
| | - Yijiang Hong
- School of Life SciencesNanchang UniversityNanchangJiangxiChina
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Filek K, Trotta A, Gračan R, Di Bello A, Corrente M, Bosak S. Characterization of oral and cloacal microbial communities of wild and rehabilitated loggerhead sea turtles (Caretta caretta). Anim Microbiome 2021; 3:59. [PMID: 34479653 PMCID: PMC8417999 DOI: 10.1186/s42523-021-00120-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 08/24/2021] [Indexed: 02/07/2023] Open
Abstract
Background Microbial communities of wild animals are being increasingly investigated to provide information about the hosts’ biology and promote conservation. Loggerhead sea turtles (Caretta caretta) are a keystone species in marine ecosystems and are considered vulnerable in the IUCN Red List, which led to growing efforts in sea turtle conservation by rescue centers around the world. Understanding the microbial communities of sea turtles in the wild and how affected they are by captivity, is one of the stepping stones in improving the conservation efforts. Describing oral and cloacal microbiota of wild animals could shed light on the previously unknown aspects of sea turtle holobiont biology, ecology, and contribute to best practices for husbandry conditions. Results We describe the oral and cloacal microbiota of Mediterranean loggerhead sea turtles by 16S rRNA gene sequencing to compare the microbial communities of wild versus turtles in, or after, rehabilitation at the Adriatic Sea rescue centers and clinics. Our results show that the oral microbiota is more sensitive to environmental shifts than the cloacal microbiota, and that it does retain a portion of microbial taxa regardless of the shift from the wild and into rehabilitation. Additionally, Proteobacteria and Bacteroidetes dominated oral and cloacal microbiota, while Kiritimatiellaeota were abundant in cloacal samples. Unclassified reads were abundant in the aforementioned groups, which indicates high incidence of yet undiscovered bacteria of the marine reptile microbial communities. Conclusions We provide the first insights into the oral microbial communities of wild and rehabilitated loggerhead sea turtles, and establish a framework for quick and non-invasive sampling of oral and cloacal microbial communities, useful for the expansion of the sample collection in wild loggerhead sea turtles. Finally, our investigation of effects of captivity on the gut-associated microbial community provides a baseline for studying the impact of husbandry conditions on turtles’ health and survival upon their return to the wild. Supplementary Information The online version contains supplementary material available at 10.1186/s42523-021-00120-5.
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Affiliation(s)
- Klara Filek
- Department of Biology, Faculty of Science, University of Zagreb, Rooseveltov trg 6, 10 000, Zagreb, Croatia
| | - Adriana Trotta
- Department of Veterinary Medicine, University of Bari "Aldo Moro", Str. Prov. Per Casamassima Km 3, 70010, Valenzano, BA, Italy
| | - Romana Gračan
- Department of Biology, Faculty of Science, University of Zagreb, Rooseveltov trg 6, 10 000, Zagreb, Croatia
| | - Antonio Di Bello
- Department of Veterinary Medicine, University of Bari "Aldo Moro", Str. Prov. Per Casamassima Km 3, 70010, Valenzano, BA, Italy
| | - Marialaura Corrente
- Department of Veterinary Medicine, University of Bari "Aldo Moro", Str. Prov. Per Casamassima Km 3, 70010, Valenzano, BA, Italy
| | - Sunčica Bosak
- Department of Biology, Faculty of Science, University of Zagreb, Rooseveltov trg 6, 10 000, Zagreb, Croatia.
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11
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McNally KL, Mott CR, Guertin JR, Bowen JL. Microbial communities of wild-captured Kemp’s ridley (Lepidochelys kempii) and green sea turtles (Chelonia mydas). ENDANGER SPECIES RES 2021. [DOI: 10.3354/esr01116] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Conservation efforts for endangered sea turtle species, such as Kemp’s ridley turtles Lepidochelys kempii and green turtles Chelonia mydas, may benefit from information on the microbial communities that contribute to host health. Previous studies examining host-associated microbiomes of these species have been limited in geographic region, life stage, and/or health. Here, we characterized the microbiome of the oral cavity and cloaca from wild-captured Kemp’s ridley and green turtles off the west coast of Florida, USA, by using Illumina sequencing to analyze the 16S rRNA gene. Microbial communities were distinct between body sites as well as between turtle species, suggesting that the turtle species is more important than the local environment in determining the microbiome of sea turtles. We identified the core microbiome for each species at each body site and determined that there were very few bacteria shared among the oral samples of both species, and no taxa co-occurred in the cloaca samples among both species. The core microbiome of the green turtle cloaca was primarily from the order Clostridiales, which plays an important role in digestion for other herbivorous species. Due to high prevalence of fibropapillomatosis in the green turtles (90%), we also investigated the correlation between the microbiome and the severity of fibropapillomatosis, and we identified changes in beta diversity associated with the total number of tumors. This study provides the first glimpse of the microbiome in 2 sympatric species of sea turtle and sheds an important species-specific light on the microbiome of these endangered species.
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Affiliation(s)
- KL McNally
- Animal Health Department, New England Aquarium, Boston, Massachusetts 02110, USA
- University of Massachusetts, Boston, Massachusetts 20125, USA
| | - CR Mott
- Inwater Research Group, Inc., Jensen Beach, Florida 34957, USA
| | - JR Guertin
- Inwater Research Group, Inc., Jensen Beach, Florida 34957, USA
| | - JL Bowen
- Department of Marine and Environmental Sciences, Marine Science Center, Northeastern University, Nahant, Massachusetts 01908, USA
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12
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Levin D, Raab N, Pinto Y, Rothschild D, Zanir G, Godneva A, Mellul N, Futorian D, Gal D, Leviatan S, Zeevi D, Bachelet I, Segal E. Diversity and functional landscapes in the microbiota of animals in the wild. Science 2021; 372:science.abb5352. [PMID: 33766942 DOI: 10.1126/science.abb5352] [Citation(s) in RCA: 82] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 07/17/2020] [Accepted: 03/09/2021] [Indexed: 12/11/2022]
Abstract
Animals in the wild are able to subsist on pathogen-infected and poisonous food and show immunity to various diseases. These may be due to their microbiota, yet we have a poor understanding of animal microbial diversity and function. We used metagenomics to analyze the gut microbiota of more than 180 species in the wild, covering diverse classes, feeding behaviors, geographies, and traits. Using de novo metagenome assembly, we constructed and functionally annotated a database of more than 5000 genomes, comprising 1209 bacterial species of which 75% are unknown. The microbial composition, diversity, and functional content exhibit associations with animal taxonomy, diet, activity, social structure, and life span. We identify the gut microbiota of wild animals as a largely untapped resource for the discovery of therapeutics and biotechnology applications.
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Affiliation(s)
| | | | | | - Daphna Rothschild
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, 7610001 Israel.,Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 7610001, Israel.,Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA.,Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | | | - Anastasia Godneva
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, 7610001 Israel.,Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | | | | | | | - Sigal Leviatan
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, 7610001 Israel.,Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - David Zeevi
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, 7610001 Israel.,Center for Studies in Physics and Biology, Rockefeller University, New York, NY 10065, USA
| | - Ido Bachelet
- Wild Biotech, Rehovot, Israel.,Augmanity, Rehovot, Israel
| | - Eran Segal
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, 7610001 Israel. .,Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
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13
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Qu YF, Wu YQ, Zhao YT, Lin LH, Du Y, Li P, Li H, Ji X. The invasive red-eared slider turtle is more successful than the native Chinese three-keeled pond turtle: evidence from the gut microbiota. PeerJ 2020; 8:e10271. [PMID: 33194431 PMCID: PMC7603792 DOI: 10.7717/peerj.10271] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 10/08/2020] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND The mutualistic symbiosis between the gut microbial communities (microbiota) and their host animals has attracted much attention. Many factors potentially affect the gut microbiota, which also varies among host animals. The native Chinese three-keeled pond turtle (Chinemys reevesii) and the invasive red-eared slider turtle (Trachemys scripta elegans) are two common farm-raised species in China, with the latter generally considered a more successful species. However, supporting evidence from the gut microbiota has yet to be collected. METHODS We collected feces samples from these two turtle species raised in a farm under identical conditions, and analyzed the composition and relative abundance of the gut microbes using bacterial 16S rRNA sequencing on the Roach/454 platform. RESULTS The gut microbiota was mainly composed of Bacteroidetes and Firmicutes at the phylum level, and Porphyromonadaceae, Bacteroidaceae and Lachnospiraceae at the family level in both species. The relative abundance of the microbes and gene functions in the gut microbiota differed between the two species, whereas alpha or beta diversity did not. Microbes of the families Bacteroidaceae, Clostridiaceae and Lachnospiraceae were comparatively more abundant in C. reevesii, whereas those of the families Porphyromonadaceae and Fusobacteriaceae were comparatively more abundant in T. s. elegans. In both species the gut microbiota had functional roles in enhancing metabolism, genetic information processing and environmental information processing according to the Kyoto Encyclopedia of Genes and Genomes database. The potential to gain mass is greater in T. s. elegans than in C. reevesii, as revealed by the fact that the Firmicutes/Bacteroidetes ratio was lower in the former species. The percentage of human disease-related functional genes was lower in T. s. elegans than in C. reevesii, presumably suggesting an enhanced potential to colonize new habitats in the former species.
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Affiliation(s)
- Yan-Fu Qu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
| | - Yan-Qing Wu
- National Key Laboratory of Environmental Protection and Biosafety, Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing, Jiangsu, China
| | - Yu-Tian Zhao
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
| | - Long-Hui Lin
- Hangzhou Key Laboratory for Ecosystem Protection and Restoration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Yu Du
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
- Hainan Key Laboratory of Herpetological Research, College of Fisheries and Life Science, Hainan Tropical Ocean University, Sanya, Hainan, China
| | - Peng Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
| | - Hong Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
| | - Xiang Ji
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
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14
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Sandri C, Correa F, Spiezio C, Trevisi P, Luise D, Modesto M, Remy S, Muzungaile MM, Checcucci A, Zaborra CA, Mattarelli P. Fecal Microbiota Characterization of Seychelles Giant Tortoises ( Aldabrachelys gigantea) Living in Both Wild and Controlled Environments. Front Microbiol 2020; 11:569249. [PMID: 33193160 PMCID: PMC7641630 DOI: 10.3389/fmicb.2020.569249] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 09/15/2020] [Indexed: 12/15/2022] Open
Abstract
A microbiome is defined as a complex collection of microorganisms and their genetic material. Studies regarding gut microbiomes of different animals have provided ecological and evolutionary information showing a strong link between health and disease. Very few studies have compared the gut microbiota of animals housed under controlled conditions and those in wild habitats. Little research has been performed on the reptile gut microbiota, and what studies do exist are mainly focused on carnivorous reptiles. The aim of this study was first to describe the overall microbiota structure of Aldabra giant tortoises (Aldabrachelys gigantea) and, second, to compare the microbiota of tortoises living under natural conditions and tortoises living in controlled environments, such as zoological and botanical parks, in Italy and in the Seychelles. Seventeen fecal samples were collected from giant tortoises located on Curieuse Island (CI, n = 8), at the Botanical Garden (BG, n = 3) in Mahé (Seychelles Islands) and at Parco Natura Viva-Garda Zoological Park (PNV, n = 6) in Verona (Italy). The V3-V4 region of the 16S rRNA gene was amplified in order to characterize the gut microbiota profile. Overall, the major phyla identified were Bacteroidetes 42%, Firmicutes 32%, and Spirochaetes 9%. A higher microbial diversity (alpha indices) was observed for the BG samples as compared to the PNV samples (Shannon: 5.39 vs. 4.43; InvSimpson: 80.7 vs. 25; Chao1: 584 vs. 377 p < 0.05). The results in the present study showed a significant difference in beta diversity between the samples from CI, BG, and PNV (p = 0.001), suggesting a different bacterial fecal profile of giant tortoises at the different habitats. This study provided novel insights into the effects of different environmental conditions on the gut microbial communities of giant tortoises. In particular, differences were reported regarding the bacterial gut community structure between tortoises in natural and in controlled environments. These results could help to improve the management of giant tortoises under human care, thus enhancing ex-situ conservation efforts far from the species geographic range.
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Affiliation(s)
- Camillo Sandri
- Department of Agricultural and Food Science, University of Bologna, Bologna, Italy
- Department of Animal Health Care and Management, Parco Natura Viva – Garda Zoological Park, Verona, Italy
| | - Federico Correa
- Department of Agricultural and Food Science, University of Bologna, Bologna, Italy
| | - Caterina Spiezio
- Department of Animal Health Care and Management, Parco Natura Viva – Garda Zoological Park, Verona, Italy
| | - Paolo Trevisi
- Department of Agricultural and Food Science, University of Bologna, Bologna, Italy
| | - Diana Luise
- Department of Agricultural and Food Science, University of Bologna, Bologna, Italy
| | - Monica Modesto
- Department of Agricultural and Food Science, University of Bologna, Bologna, Italy
| | - Selby Remy
- Seychelles National Parks Authority, Victoria, Seychelles
| | - Marie-May Muzungaile
- Biodiversity Conservation and Management Division, Ministry of Environment, Energy and Climate Change, Victoria, Seychelles
| | - Alice Checcucci
- Department of Agricultural and Food Science, University of Bologna, Bologna, Italy
| | - Cesare Avesani Zaborra
- Department of Animal Health Care and Management, Parco Natura Viva – Garda Zoological Park, Verona, Italy
| | - Paola Mattarelli
- Department of Agricultural and Food Science, University of Bologna, Bologna, Italy
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15
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Ahasan MS, Waltzek TB, Owens L, Ariel E. Characterisation and comparison of the mucosa-associated bacterial communities across the gastrointestinal tract of stranded green turtles, Chelonia mydas. AIMS Microbiol 2020; 6:361-378. [PMID: 33364533 PMCID: PMC7755585 DOI: 10.3934/microbiol.2020022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Accepted: 10/08/2020] [Indexed: 01/02/2023] Open
Abstract
Chelonia mydas are primarily herbivorous long-distance migratory sea turtles that contribute to marine ecosystems. Extensive research has been conducted to restore the populations of green turtles. Little is known about their gut microbiota which plays a vital role in their health. We investigated the mucosa-associated bacterial communities across the gastrointestinal (GI) tract of a total four (3, juvenile and 1, adult) stranded green turtles. Samples taken from four GI regions including oesophagus, stomach, small intestine and large intestine were analysed by high-throughput sequencing targeting hypervariable V1-V3 regions of the bacterial 16S rRNA gene. Bacterial diversity and richness decreased longitudinally along the GI tract from oesophagus to the small intestine of stranded turtles. The large intestine showed a higher bacterial diversity and richness compared to small intestine. The bacterial community of green turtles' GI tract was largely dominated by Firmicutes, Proteobacteria, Actinobacteria, Bacteroidetes and Fusobacteria. Aerobic and facultative anaerobic bacteria prevailed primarily in the oesophagus while anaerobes (Lachnospiraceae, Peptostreptococcaceae and Ruminococcaceae) constituted the bulk of large intestinal microbiota. Firmicutes dominated the GI tract except within the small intestine where Proteobacteria prevailed. At the OTU level, six percent of the total OTUs (>1% relative abundance) were common in all GI regions. This is a comprehensive characterisation of bacterial microbiota across the GI tract in green turtles which will provide a reference for future studies on turtle gut microbiome and their metabolism to improve their health and nutrition during rehabilitation.
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Affiliation(s)
- Mohammad Shamim Ahasan
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, 4811, Qld, Australia.,Faculty of Veterinary and Animal Sciences, Hajee Mohammad Danesh Science and Technology University, Dinajpur 5200, Rangpur, Bangladesh
| | - Thomas B Waltzek
- College of Veterinary Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Leigh Owens
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, 4811, Qld, Australia
| | - Ellen Ariel
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, 4811, Qld, Australia
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