1
|
Zheng P, Gao W, Cong S, Leng L, Wang T, Shi L. High-Energy Supplemental Feeding Shifts Gut Microbiota Composition and Function in Red Deer ( Cervus elaphus). Animals (Basel) 2024; 14:1428. [PMID: 38791646 PMCID: PMC11117297 DOI: 10.3390/ani14101428] [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: 04/08/2024] [Revised: 05/02/2024] [Accepted: 05/07/2024] [Indexed: 05/26/2024] Open
Abstract
Winter supplemental feeding (SF) is commonly used to improve the survival of captive wildlife. To investigate the impact of winter supplementation on the gut microbiota of wildlife, we assessed changes in the gut microbiota of red deer (Cervus elaphus) during the supplementary and non-supplementary feeding (NSF) groups using 16S rRNA sequencing technology. We found no significant differences in the diversity of the gut microbiota between SF and NSF except for the Simpson's index. However, the relative abundance of Bacteroidetes, Lentisphaerae, and Proteobacteria in the gut microbiota was significantly higher during SF. Further, genera such as Intestinimonas, Rikenella, Lawsonibacter, Muribaculum, and Papillibacter were more abundant during SF. Beta diversity analysis showed significant differences between SF and NSF. The microbes detected during SF were primarily associated with lipid metabolism, whereas those detected during NSF were linked to fiber catabolism. High-energy feed affects the gut microbial composition and function in red deer. During SF, the gut microbes in red deer were enriched in microorganisms associated with butyrate and lipid metabolism, such as R. microfusus, M. intestinale, and Papillibacter cinnamivorans. These gut microbes may be involved in ameliorating obesity associated with high-energy diets. In summary, SF is a reasonable and effective management strategy.
Collapse
Affiliation(s)
- Peng Zheng
- College of Animal Sciences, Xinjiang Agricultural University, Urumqi 830052, China; (P.Z.); (W.G.)
- Key Laboratory of Ecological Adaptation and Evolution of Extreme Environment Biology in Xinjiang, College of Life Sciences, Xinjiang Agricultural University, Urumqi 830052, China; (L.L.); (T.W.)
| | - Weizhen Gao
- College of Animal Sciences, Xinjiang Agricultural University, Urumqi 830052, China; (P.Z.); (W.G.)
- Key Laboratory of Ecological Adaptation and Evolution of Extreme Environment Biology in Xinjiang, College of Life Sciences, Xinjiang Agricultural University, Urumqi 830052, China; (L.L.); (T.W.)
| | - Shaobo Cong
- Xinjiang Tianshan Wildlife Park, Urumqi 830039, China;
| | - Lin Leng
- Key Laboratory of Ecological Adaptation and Evolution of Extreme Environment Biology in Xinjiang, College of Life Sciences, Xinjiang Agricultural University, Urumqi 830052, China; (L.L.); (T.W.)
| | - Tao Wang
- Key Laboratory of Ecological Adaptation and Evolution of Extreme Environment Biology in Xinjiang, College of Life Sciences, Xinjiang Agricultural University, Urumqi 830052, China; (L.L.); (T.W.)
| | - Lei Shi
- College of Animal Sciences, Xinjiang Agricultural University, Urumqi 830052, China; (P.Z.); (W.G.)
- Key Laboratory of Ecological Adaptation and Evolution of Extreme Environment Biology in Xinjiang, College of Life Sciences, Xinjiang Agricultural University, Urumqi 830052, China; (L.L.); (T.W.)
| |
Collapse
|
2
|
Dick C, Larson WA, Karpan K, Baetscher DS, Shi Y, Sethi S, Fangue NA, Henderson MJ. Prey ration, temperature, and predator species influence digestion rates of prey DNA inferred from qPCR and metabarcoding. Mol Ecol Resour 2023. [PMID: 37555692 DOI: 10.1111/1755-0998.13849] [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: 12/22/2022] [Revised: 07/07/2023] [Accepted: 07/17/2023] [Indexed: 08/10/2023]
Abstract
Diet analysis is a vital tool for understanding trophic interactions and is frequently used to inform conservation and management. Molecular approaches can identify diet items that are impossible to distinguish using more traditional visual-based methods. Yet, our understanding of how different variables, such as predator species or prey ration size, influence molecular diet analysis is still incomplete. Here, we conducted a large feeding trial to assess the impact that ration size, predator species, and temperature had on digestion rates estimated with visual identification, qPCR, and metabarcoding. Our trial was conducted by feeding two rations of Chinook salmon (Oncorhynchus tshawytscha) to two piscivorous fish species (largemouth bass [Micropterus salmoides] and channel catfish [Ictalurus punctatus]) held at two different temperatures (15.5 and 18.5°C) and sacrificed at regular intervals up to 120 h from the time of ingestion to quantify the prey contents remaining in the digestive tract. We found that ration size, temperature, and predator species all influenced digestion rate, with some indication that ration size had the largest influence. DNA-based analyses were able to identify salmon smolt prey in predator gut samples for much longer than visual analysis (~12 h for visual analysis vs. ~72 h for molecular analyses). Our study provides evidence that modelling the persistence of prey DNA in predator guts for molecular diet analyses may be feasible using a small set of controlling variables for many fish systems.
Collapse
Affiliation(s)
- Cory Dick
- California Cooperative Fish and Wildlife Research Unit, Department of Fisheries Biology, Humboldt State University, Arcata, California, USA
| | - Wesley A Larson
- Alaska Fisheries Science Center, Auke Bay Laboratories, National Oceanographic and Atmospheric Administration, National Marine Fisheries Service, Juneau, Alaska, USA
| | - Kirby Karpan
- Alaska Fisheries Science Center, Auke Bay Laboratories, National Oceanographic and Atmospheric Administration, National Marine Fisheries Service, Juneau, Alaska, USA
| | - Diana S Baetscher
- Alaska Fisheries Science Center, Auke Bay Laboratories, National Oceanographic and Atmospheric Administration, National Marine Fisheries Service, Juneau, Alaska, USA
| | - Yue Shi
- Wisconsin Cooperative Fishery Research Unit, College of Natural Resources, University of Wisconsin-Stevens Point, Stevens Point, Wisconsin, USA
| | - Suresh Sethi
- U.S. Geological Survey, New York Cooperative Fish and Wildlife Research Unit, Department of Natural Resources and the Environment, Cornell University, Ithaca, New York, USA
| | - Nann A Fangue
- Department of Wildlife, Fish and Conservation Biology, University of California Davis, Davis, California, USA
| | - Mark J Henderson
- U.S. Geological Survey, California Cooperative Fish and Wildlife Research Unit, Department of Fisheries Biology, Humboldt State University, Arcata, California, USA
| |
Collapse
|
3
|
Ooi V, McMichael L, Hunter ME, Takoukam Kamla A, Lanyon JM. A new DNA extraction method (HV-CTAB-PCI) for amplification of nuclear markers from open ocean-retrieved faeces of an herbivorous marine mammal, the dugong. PLoS One 2023; 18:e0278792. [PMID: 37285349 DOI: 10.1371/journal.pone.0278792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 04/27/2023] [Indexed: 06/09/2023] Open
Abstract
Non-invasively collected faecal samples are an alternative source of DNA to tissue samples, that may be used in genetic studies of wildlife when direct sampling of animals is difficult. Although several faecal DNA extraction methods exist, their efficacy varies between species. Previous attempts to amplify mitochondrial DNA (mtDNA) markers from faeces of wild dugongs (Dugong dugon) have met with limited success and nuclear markers (microsatellites) have been unsuccessful. This study aimed to establish a tool for sampling both mtDNA and nuclear DNA (nDNA) from dugong faeces by modifying approaches used in studies of other large herbivores. First, a streamlined, cost-effective DNA extraction method that enabled the amplification of both mitochondrial and nuclear markers from large quantities of dugong faeces was developed. Faecal DNA extracted using a new 'High Volume- Cetyltrimethyl Ammonium Bromide- Phenol-Chloroform-Isoamyl Alcohol' (HV-CTAB-PCI) method was found to achieve comparable amplification results to extraction of DNA from dugong skin. As most prevailing practices advocate sampling from the outer surface of a stool to maximise capture of sloughed intestinal cells, this study compared amplification success of mtDNA between the outer and inner layers of faeces, but no difference in amplification was found. Assessment of the impacts of faecal age or degradation on extraction, however, demonstrated that fresher faeces with shorter duration of environmental (seawater) exposure amplified both markers better than eroded scats. Using the HV-CTAB-PCI method, nuclear markers were successfully amplified for the first time from dugong faeces. The successful amplification of single nucleotide polymorphism (SNP) markers represents a proof-of-concept showing that DNA from dugong faeces can potentially be utilised in population genetic studies. This novel DNA extraction protocol offers a new tool that will facilitate genetic studies of dugongs and other large and cryptic marine herbivores in remote locations.
Collapse
Affiliation(s)
- Vicky Ooi
- School of Biological Sciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Lee McMichael
- School of Veterinary Science, The University of Queensland, Gatton, Queensland, Australia
| | - Margaret E Hunter
- U.S. Geological Survey, Wetland and Aquatic Research Center, Sirenia Project, Gainesville, Florida, United States of America
| | - Aristide Takoukam Kamla
- Aquatic Animal Health Program, College of Veterinary Medicine, University of Florida, Gainesville, Florida, United States of America
- African Marine Mammal Conservation Organization, Dizangue, Littoral, Cameroon
| | - Janet M Lanyon
- School of Biological Sciences, The University of Queensland, St Lucia, Queensland, Australia
| |
Collapse
|
4
|
Enabling pinniped conservation by means of non-invasive genetic population analysis. CONSERV GENET RESOUR 2021. [DOI: 10.1007/s12686-020-01182-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
5
|
Tighe AJ, Overby S, Thurman K, Gandola R, Fulanda B, Byrne J, Carlsson J. Investigating a simplified method for noninvasive genetic sampling in East African mammals using silica dried scat swabs. Ecol Evol 2020; 10:3330-3337. [PMID: 32273990 PMCID: PMC7141023 DOI: 10.1002/ece3.6115] [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: 10/04/2019] [Revised: 01/13/2020] [Accepted: 01/15/2020] [Indexed: 11/06/2022] Open
Abstract
Swabbing scat has proved to be an effective noninvasive method to collect DNA from mammals in the field. Previously, this method has relied on preservative liquids or freezing to preserve the DNA collected on swabs. In this study, we determine the effectiveness of using silica to simply dry the swab in field as an alternative way to prevent DNA degredation. Four species were included in the study; reticulated giraffe, impala, fringe-eared oryx, and lion. Swabs were taken at multiple time points for giraffe and impala scat samples, with the lion and oryx sampled opportunistically. Mitochondrial DNA was successfully amplified and sequenced from scat swabs from all species; however, effectiveness varied between species, with 81.8% amplification success rate from swabs taken from impala scat compared to 25% amplification success rate in giraffe. This variation in success rate was overcome by taking multiple swabs, thus increasing the probability of a successful amplification. The true merit of this method is in its simplicity and cheapness; no preservative liquids were required to be brought into the field, at no stage in the 2 weeks of field sampling were samples frozen, and no commercial kits were used for DNA extraction.
Collapse
Affiliation(s)
- Andrew J Tighe
- Area 52 Research Group School of Biology and Environmental Science/Earth Institute University College Dublin Dublin Ireland
- Fish Health Unit Marine Institute Oranmore Ireland
| | - Sarah Overby
- Area 52 Research Group School of Biology and Environmental Science/Earth Institute University College Dublin Dublin Ireland
- Interdisciplinary Research Structure for Biotechnology and Biomedicine (ERI BIOTECMED) University of Valencia Valencia Spain
| | - Kiera Thurman
- Area 52 Research Group School of Biology and Environmental Science/Earth Institute University College Dublin Dublin Ireland
| | - Robert Gandola
- Area 52 Research Group School of Biology and Environmental Science/Earth Institute University College Dublin Dublin Ireland
| | - Bernerd Fulanda
- Department of Biological Sciences Pwani University Kilifi Kenya
| | - John Byrne
- Area 52 Research Group School of Biology and Environmental Science/Earth Institute University College Dublin Dublin Ireland
| | - Jens Carlsson
- Area 52 Research Group School of Biology and Environmental Science/Earth Institute University College Dublin Dublin Ireland
| |
Collapse
|
6
|
Anabalón L, Encina‐Montoya F, Sánchez P, Solano J, Benavente F, Guiñez B, Olivares F, Oberti C, Vega R. High-resolution melting of the cytochrome B gene in fecal DNA: A powerful approach for fox species identification of the Lycalopex genus in Chile. Ecol Evol 2019; 9:7448-7454. [PMID: 31346415 PMCID: PMC6635928 DOI: 10.1002/ece3.5230] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 04/08/2019] [Accepted: 04/09/2019] [Indexed: 11/22/2022] Open
Abstract
Easy, economic, precise species authentication is currently necessary in many areas of research and diagnosis in molecular biology applied to conservation studies of endangered species. Here, we present a new method for the identification of three fox species of the Lycalopex genus in Chile. We developed an assay based on high-resolution melt analysis of the mitochondrial cytochrome B gene, allowing a simple, low cost, fast, and accurate species determination. To validate the assay applicability for noninvasive samples, we collected fecal samples in the Atacama Desert, finding unexpectedly one species outside of its known distribution range. We conclude that the assay has a potential to become a valuable tool for a standardized genetic monitoring of the Lycalopex species in Chile.
Collapse
Affiliation(s)
- Leonardo Anabalón
- Departamento de Ciencias Biológicas y QuímicasUniversidad Católica de TemucoTemucoChile
| | - Francisco Encina‐Montoya
- Departamento de Ciencias AmbientalesUniversidad Católica de TemucoTemucoChile
- Núcleo de Estudios AmbientalesUniversidad Católica de TemucoTemucoChile
| | - Pamela Sánchez
- Departamento de Ciencias AmbientalesUniversidad Católica de TemucoTemucoChile
| | - Jaime Solano
- Departamento de Ciencias Agropecuarias y AcuícolasUniversidad Católica de TemucoTemucoChile
| | - Felipe Benavente
- Facultad de Ciencias de la SaludUniversidad Católica de TemucoTemucoChile
| | | | | | - Carlos Oberti
- Departamento de Ciencias AmbientalesUniversidad Católica de TemucoTemucoChile
| | - Rolando Vega
- Departamento de Ciencias Agropecuarias y AcuícolasUniversidad Católica de TemucoTemucoChile
- Núcleo de Producción AlimentariaUniversidad Católica de TemucoTemucoChile
| |
Collapse
|
7
|
Alberts CC, Saranholi BH, Frei F, Galetti PM. Comparing hair-morphology and molecular methods to identify fecal samples from Neotropical felids. PLoS One 2017; 12:e0184073. [PMID: 28880947 PMCID: PMC5589158 DOI: 10.1371/journal.pone.0184073] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 08/17/2017] [Indexed: 11/19/2022] Open
Abstract
To avoid certain problems encountered with more-traditional and invasive methods in behavioral-ecology studies of mammalian predators, such as felids, molecular approaches have been employed to identify feces found in the field. However, this method requires a complete molecular biology laboratory, and usually also requires very fresh fecal samples to avoid DNA degradation. Both conditions are normally absent in the field. To address these difficulties, identification based on morphological characters (length, color, banding, scales and medullar patterns) of hairs found in feces could be employed as an alternative. In this study we constructed a morphological identification key for guard hairs of eight Neotropical felids (jaguar, oncilla, Geoffroy's cat, margay, ocelot, Pampas cat, puma and jaguarundi) and compared its efficiency to that of a molecular identification method, using the ATP6 region as a marker. For this molecular approach, we simulated some field conditions by postponing sample-conservation procedures. A blind test of the identification key obtained a nearly 70% overall success rate, which we considered equivalent to or better than the results of some molecular methods (probably due to DNA degradation) found in other studies. The jaguar, puma and jaguarundi could be unequivocally discriminated from any other Neotropical felid. On a scale ranging from inadequate to excellent, the key proved poor only for the margay, with only 30% of its hairs successfully identified using this key; and have intermediate success rates for the remaining species, the oncilla, Geoffroy's cat, ocelot and Pampas cat, were intermediate. Complementary information about the known distributions of felid populations may be necessary to substantially improve the results obtained with the key. Our own molecular results were even better, since all blind-tested samples were correctly identified. Part of these identifications were made from samples kept in suboptimal conditions, with some samples remaining outdoors for up to seven days, simulating conditions in the field. It appears that both methods can be used, depending on the available laboratory facilities and on the expected results.
Collapse
Affiliation(s)
- Carlos C. Alberts
- LEvEtho (Laboratory of Evolution and Ethology), Faculdade de Ciências e Letras de Assis, Universidade Estadual Paulista, Assis, State of São Paulo, Brazil
| | - Bruno H. Saranholi
- LabBMC (Laboratório de Biodiversidade Molecular e Conservação), Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, State of São Paulo, Brazil
| | - Fernando Frei
- LEA (Laboratório de Estatística Aplicada), Faculdade de Ciências e Letras de Assis, Universidade Estadual Paulista, Assis, State of São Paulo, Brazil
| | - Pedro M. Galetti
- LabBMC (Laboratório de Biodiversidade Molecular e Conservação), Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, State of São Paulo, Brazil
| |
Collapse
|
8
|
Zhu Y, Liu HY, Yang HQ, Li YD, Zhang HM. Factors affecting genotyping success in giant panda fecal samples. PeerJ 2017; 5:e3358. [PMID: 28560107 PMCID: PMC5444362 DOI: 10.7717/peerj.3358] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 04/26/2017] [Indexed: 11/28/2022] Open
Abstract
Fecal samples play an important role in giant panda conservation studies. Optimal preservation conditions and choice of microsatellites for giant panda fecal samples have not been established. In this study, we evaluated the effect of four factors (namely, storage type (ethanol (EtOH), EtOH −20 °C, 2-step storage medium, DMSO/EDTA/Tris/salt buffer (DETs) and frozen at −20 °C), storage time (one, three and six months), fragment length, and repeat motif of microsatellite loci) on the success rate of microsatellite amplification, allelic dropout (ADO) and false allele (FA) rates from giant panda fecal samples. Amplification success and ADO rates differed between the storage types. Freezing was inferior to the other four storage methods based on the lowest average amplification success and the highest ADO rates (P < 0.05). The highest microsatellite amplification success was obtained from either EtOH or the 2-step storage medium at three storage time points. Storage time had a negative effect on the average amplification of microsatellites and samples stored in EtOH and the 2-step storage medium were more stable than the other three storage types. We only detected the effect of repeat motif on ADO and FA rates. The lower ADO and FA rates were obtained from tri- and tetra-nucleotide loci. We suggest that freezing should not be used for giant panda fecal preservation in microsatellite studies, and EtOH and the 2-step storage medium should be chosen on priority for long-term storage. We recommend candidate microsatellite loci with longer repeat motif to ensure greater genotyping success for giant panda fecal studies.
Collapse
Affiliation(s)
- Ying Zhu
- Sichuan Nature Resources Science Academy, Chengdu, Sichuan, China.,Sichuan Province Laboratory for Natural Resources Protection and Sustainable Utilization, Chengdu, Sichuan, China
| | - Hong-Yi Liu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Hai-Qiong Yang
- Sichuan Nature Resources Science Academy, Chengdu, Sichuan, China.,Sichuan Province Laboratory for Natural Resources Protection and Sustainable Utilization, Chengdu, Sichuan, China
| | - Yu-Dong Li
- Sichuan Nature Resources Science Academy, Chengdu, Sichuan, China.,Sichuan Province Laboratory for Natural Resources Protection and Sustainable Utilization, Chengdu, Sichuan, China
| | - He-Min Zhang
- Sichuan Province Laboratory for Natural Resources Protection and Sustainable Utilization, Chengdu, Sichuan, China.,China Conservation and Research Center for the Giant Panda, Dujiangyan, Sichuan, China
| |
Collapse
|
9
|
Zhang W, Yang S, Zhao H, Huang L. Using the ITS2 sequence-structure as a DNA mini-barcode: A case study in authenticating the traditional medicine“Fang Feng”. BIOCHEM SYST ECOL 2016. [DOI: 10.1016/j.bse.2016.10.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
10
|
Goodman I, Shahar N, Bar-Gal GK, Saltz D, Bar-David S. Evaluation of noninvasive genetic methods for Nubian ibex. CONSERV GENET RESOUR 2016. [DOI: 10.1007/s12686-016-0642-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
11
|
Miles KA, Holtz MN, Lounsberry ZT, Sacks BN. A paired comparison of scat-collecting versus scat-swabbing methods for noninvasive recovery of mesocarnivore DNA from an arid environment. WILDLIFE SOC B 2015. [DOI: 10.1002/wsb.600] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Kathleen A. Miles
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory; University of California, Davis; 1 Shields Avenue Davis CA 95616 USA
| | - Michelle N. Holtz
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory; University of California, Davis; 1 Shields Avenue Davis CA 95616 USA
| | - Zachary T. Lounsberry
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory; University of California, Davis; 1 Shields Avenue Davis CA 95616 USA
| | - Benjamin N. Sacks
- Department of Population Health and Reproduction and Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory; University of California, Davis; 1 Shields Avenue Davis CA 95616 USA
| |
Collapse
|
12
|
Ramón-Laca A, Soriano L, Gleeson D, Godoy JA. A simple and effective method for obtaining mammal DNA from faeces. WILDLIFE BIOLOGY 2015. [DOI: 10.2981/wlb.00096] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
|