1
|
Hunter-Barnett S, Viney M. Gut protozoa of wild rodents - a meta-analysis. Parasitology 2024:1-12. [PMID: 38714350 DOI: 10.1017/s0031182024000556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/09/2024]
Abstract
Protozoa are well-known inhabitants of the mammalian gut and so of the gut microbiome. While there has been extensive study of a number of species of gut protozoa in laboratory animals, particularly rodents, the biology of the gut protozoa of wild rodents is much less well-known. Here we have systematically searched the published literature to describe the gut protozoa of wild rodents, in total finding records of 44 genera of protozoa infecting 228 rodent host species. We then undertook meta-analyses that estimated the overall prevalence of gut protozoa in wild rodents to be 24%, with significant variation in prevalence among some host species. We investigated how host traits may affect protozoa prevalence, finding that for some host lifestyles some protozoa differed in their prevalence. This synthesis of existing data on wild rodent gut protozoa provides a better understanding of the biology of these common gut inhabitants and suggests directions for their future study.
Collapse
Affiliation(s)
- Simon Hunter-Barnett
- Department of Evolution, Ecology and Behaviour, University of Liverpool, Liverpool L69 7ZB, UK
| | - Mark Viney
- Department of Evolution, Ecology and Behaviour, University of Liverpool, Liverpool L69 7ZB, UK
| |
Collapse
|
2
|
Subrata SA, Yuda P, Artama WT, de-Garine Wichatitsky M, André A, Michaux J. Rusa deer microbiota: the importance of preliminary data analysis for meaningful diversity comparisons. Int Microbiol 2024:10.1007/s10123-024-00521-x. [PMID: 38589705 DOI: 10.1007/s10123-024-00521-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 03/26/2024] [Accepted: 04/01/2024] [Indexed: 04/10/2024]
Abstract
The microbiome is an important consideration for the conservation of endangered species. Studies provided evidence of the effect of behavior and habitat change on the microbiota of wild animals and reported various inferences. It indicates the complexity of factors influencing microbiota diversity, including incomplete sampling procedures. Data abnormality may arise due to the procedures warranting preliminary analysis, such as rarefaction, before downstream analysis. This present study demonstrated the effect of data rarefaction and aggregation on the comparison of wild rusa deer's gut microbial diversity. Eighty-five feces samples were collected from 11 deer populations inhabiting three national parks in Java and Bali islands. Using the Illumina Nova-Seq platform, fragments of 16s rRNA gene were sequenced, and raw data of 51,389 reads corresponding to 2 domains, 22 phyla, 45 classes, 83 orders, 182 families, and 460 genera of bacteria were obtained. Data rarefaction was applied at two different library sizes (minimum and fixed) and aggregation (11 populations into 3 research sites) to investigate its effect on the microbial diversity comparison. There are significant differences in alpha diversity between populations, but not research sites, at all library sizes of rarefaction. A similar finding is also found in beta diversity. Moreover, data rarefaction and aggregation result in different values of the diversity metrics. This present study shows that statistical analysis remains a substantial concern in microbiome studies applied to conservation biology. It suggests reporting a more detailed data normalization in microbiome studies as an inherent control of suboptimal sampling, particularly when involving feces.
Collapse
Affiliation(s)
- Sena A Subrata
- Faculty of Forestry, Universitas Gadjah Mada, Yogyakarta, Indonesia.
| | - Pramana Yuda
- Faculty of Technobiology, Universitas Atma Jaya Yogyakarta, Yogyakarta, Indonesia
| | - Wayan T Artama
- Faculty of Veterinary Medicine, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | | | - Adrien André
- Conservation Genetics Unit, Department of Life Sciences, University of Liège, Liege, Belgium
| | - Johan Michaux
- Conservation Genetics Unit, Department of Life Sciences, University of Liège, Liege, Belgium
| |
Collapse
|
3
|
Gani M, Mohd-Ridwan AR, Sitam FT, Kamarudin Z, Selamat SS, Awang NMZ, Karuppannan KV, Md-Zain BM. Habitat shapes the gut microbiome diversity of Malayan tigers (Panthera tigris jacksoni) as revealed through metabarcoding 16S rRNA profiling. World J Microbiol Biotechnol 2024; 40:111. [PMID: 38416247 DOI: 10.1007/s11274-023-03868-x] [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: 10/17/2023] [Accepted: 12/06/2023] [Indexed: 02/29/2024]
Abstract
The gut microbiome refers to the microorganism community living within the digestive tract. The environment plays a crucial role in shaping the gut microbiome composition of animals. The gut microbiome influences the health and behavior of animals, including the critically endangered Malayan tiger (Panthera tigris jacksoni). However, the gut microbiome composition of Malayan tigers, especially those living in their natural habitats, remains poorly understood. To address this knowledge gap, we used next-generation sequencing DNA metabarcoding techniques to analyze the gut microbiome of wild Malayan tigers using fecal samples collected from their natural habitats and in captivity. Our aim was to determine the gut microbiota composition of the Malayan tiger, considering the different types of habitat environments. The results revealed a diverse microbial community within the gut microbiome of Malayan tigers. The prominent phyla that were observed included Firmicutes, Proteobacteria, Actinobacteriota, Fusobacteriota and Bacteroidota. Beta diversity analysis revealed significant differences in gut microbiome composition of Malayan tigers that inhabited oil palm plantations, in villages and protected areas. Diversity analysis also revealed significant difference in the gut microbiome between wild and captive Malayan tigers. However, the distinctions of gut microbiome between wild and captive alpha diversity did not yield significant differences. The differences in microbiome diversity resulted from the interplay of dietary intake and environmental factors. This information will facilitate the establishment of focused conservation approaches and enhance our understanding of the effect of microbiome composition on Malayan tiger health.
Collapse
Affiliation(s)
- Millawati Gani
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
- National Wildlife Forensic Laboratory (NWFL), Ex-Situ Conservation Division, Department of Wildlife and National Parks (PERHILITAN), KM 10 Jalan Cheras, 56100, Kuala Lumpur, Malaysia
| | - Abd Rahman Mohd-Ridwan
- Centre for Pre-University Studies, Universiti Malaysia Sarawak, 94300, Kota Samarahan, Sarawak, Malaysia
| | - Frankie Thomas Sitam
- National Wildlife Forensic Laboratory (NWFL), Ex-Situ Conservation Division, Department of Wildlife and National Parks (PERHILITAN), KM 10 Jalan Cheras, 56100, Kuala Lumpur, Malaysia
| | - Zubaidah Kamarudin
- National Wildlife Rescue Centre (NWRC), Department of Wildlife and National Parks (PERHILITAN), 35600, Sungkai, Perak, Malaysia
| | - Siti Suzana Selamat
- National Wildlife Rescue Centre (NWRC), Department of Wildlife and National Parks (PERHILITAN), 35600, Sungkai, Perak, Malaysia
| | - Nik Mohd Zamani Awang
- National Wildlife Rescue Centre (NWRC), Department of Wildlife and National Parks (PERHILITAN), 35600, Sungkai, Perak, Malaysia
| | - Kayal Vizi Karuppannan
- National Wildlife Forensic Laboratory (NWFL), Ex-Situ Conservation Division, Department of Wildlife and National Parks (PERHILITAN), KM 10 Jalan Cheras, 56100, Kuala Lumpur, Malaysia
| | - Badrul Munir Md-Zain
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia.
| |
Collapse
|
4
|
Lu Y, Chu S, Shi Z, You R, Chen H. Marked variations in diversity and functions of gut microbiota between wild and domestic stag beetle Dorcus Hopei Hopei. BMC Microbiol 2024; 24:24. [PMID: 38238710 PMCID: PMC10795464 DOI: 10.1186/s12866-023-03177-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 12/26/2023] [Indexed: 01/22/2024] Open
Abstract
BACKGROUND Although stag beetles are a popular saprophytic insect, their gut microbiome has been poorly studied. Here, 16 S rRNA gene sequencing was employed to reveal the gut microbiota composition and functional variations between wild and domestic Dorcus hopei hopei (Dhh) larval individuals. RESULTS The results indicated a significant difference between the wild and domestic Dhh gut microbiota., the domestic Dhh individuals contained more gut microbial taxa (e.g. genera Ralstonia and Methyloversatilis) with xenobiotic degrading functions. The wild Dhh possesses gut microbiota compositions (e.g. Turicibacter and Tyzzerella ) more appropriate for energy metabolism and potential growth. This study furthermore assigned all Dhh individuals by size into groups for data analysis; which indicated limited disparities between the gut microbiota of different-sized D. hopei hopei larvae. CONCLUSION The outcome of this study illustrated that there exists a significant discrepancy in gut microbiota composition between wild and domestic Dhh larvae. In addition, the assemblage of gut microbiome in Dhh was primarily attributed to environmental influences instead of individual differences such as developmental potential or size. These findings will provide a valuable theoretical foundation for the protection of wild saprophytic insects and the potential utilization of the insect-associated intestinal microbiome in the future.
Collapse
Affiliation(s)
- Yikai Lu
- BASIS International School Hangzhou, Hangzhou, 310020, Zhejiang, China
| | - Siyuan Chu
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, Zhejiang, China
| | - Zhiyuan Shi
- BASIS International School Hangzhou, Hangzhou, 310020, Zhejiang, China
| | - Ruobing You
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, Zhejiang, China
| | - Haimin Chen
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, Zhejiang, China.
| |
Collapse
|
5
|
A microbial tale of farming, invasion and conservation: on the gut bacteria of European and American mink in Western Europe. Biol Invasions 2023. [DOI: 10.1007/s10530-023-03007-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
|
6
|
Cui X, Zhang Q, Zhang Q, Chen H, Liu G, Zhu L. The putative maintaining mechanism of gut bacterial ecosystem in giant pandas and its potential application in conservation. Evol Appl 2022; 16:36-47. [PMID: 36699119 PMCID: PMC9850007 DOI: 10.1111/eva.13494] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 09/02/2022] [Accepted: 10/06/2022] [Indexed: 01/01/2023] Open
Abstract
Animals living in captivity and the wild show differences in the internal structure of their gut microbiomes. Here, we performed a meta-analysis of the microbial data of about 494 fecal samples obtained from giant pandas (captive and wild giant pandas). Our results show that the modular structures and topological features of the captive giant panda gut microbiome differ from those of the wild populations. The co-occurrence network of wild giant pandas also contained more nodes and edges, indicating a higher complexity and stability compared to that of captive giant pandas. Keystone species analysis revealed the differences between geographically different wild populations, indicating the potential effect of geography on the internal modular structure. When combining all the giant panda samples for module analysis, we found that the abundant taxa (e.g., belonged to Flavobacterium, Herbaspirillum, and Escherichia-Shigella) usually acted as module hubs to stabilize the modular structure, while the rare taxa usually acted as connectors of different modules. We conclude that abundant and rare taxa play different roles in the gut bacterial ecosystem. The conservation of some key bacterial species is essential for promoting the development of the gut microbiome in pandas. The living environment of the giant pandas can influence the internal structure, topological features, and strength of interrelationships in the gut microbiome. This study provides new insights into the conservation and management of giant panda populations.
Collapse
Affiliation(s)
- Xinyuan Cui
- College of Life SciencesNanjing Normal UniversityNanjingChina
| | - Qinrong Zhang
- College of Life SciencesNanjing Normal UniversityNanjingChina
| | - Qunde Zhang
- College of Life SciencesNanjing Normal UniversityNanjingChina
| | - Hua Chen
- Mingke Biotechnology (Hangzhou) Co., Ltd.HangzhouChina
| | - Guoqi Liu
- Mingke Biotechnology (Hangzhou) Co., Ltd.HangzhouChina
| | - Lifeng Zhu
- College of Life SciencesNanjing Normal UniversityNanjingChina
| |
Collapse
|
7
|
Ramanan V, Mechery S, Sarkar IN. GenBank as a source to monitor and analyze Host-Microbiome data. Bioinformatics 2022; 38:4172-4177. [PMID: 35801940 PMCID: PMC9438952 DOI: 10.1093/bioinformatics/btac487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 06/08/2022] [Accepted: 07/07/2022] [Indexed: 12/24/2022] Open
Abstract
MOTIVATION Microbiome datasets are often constrained by sequencing limitations. GenBank is the largest collection of publicly available DNA sequences, which is maintained by the National Center of Biotechnology Information (NCBI). The metadata of GenBank records are a largely understudied resource and may be uniquely leveraged to access the sum of prior studies focused on microbiome composition. Here, we developed a computational pipeline to analyze GenBank metadata, containing data on hosts, microorganisms and their place of origin. This work provides the first opportunity to leverage the totality of GenBank to shed light on compositional data practices that shape how microbiome datasets are formed as well as examine host-microbiome relationships. RESULTS The collected dataset contains multiple kingdoms of microorganisms, consisting of bacteria, viruses, archaea, protozoa, fungi, and invertebrate parasites, and hosts of multiple taxonomical classes, including mammals, birds and fish. A human data subset of this dataset provides insights to gaps in current microbiome data collection, which is biased towards clinically relevant pathogens. Clustering and phylogenic analysis reveals the potential to use these data to model host taxonomy and evolution, revealing groupings formed by host diet, environment and coevolution. AVAILABILITY AND IMPLEMENTATION GenBank Host-Microbiome Pipeline is available at https://github.com/bcbi/genbank_holobiome. The GenBank loader is available at https://github.com/bcbi/genbank_loader. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Vivek Ramanan
- Center of Computational Molecular Biology Brown University, Providence, RI, USA
- Center for Biomedical Informatics Brown University, Providence, RI, USA
| | - Shanti Mechery
- Center for Biomedical Informatics Brown University, Providence, RI, USA
| | - Indra Neil Sarkar
- Center of Computational Molecular Biology Brown University, Providence, RI, USA
- Center for Biomedical Informatics Brown University, Providence, RI, USA
- Rhode Island Quality Institute, Providence, RI, USA
| |
Collapse
|
8
|
Koyasu H, Takahashi H, Yoneda M, Naba S, Sakawa N, Sasao I, Nagasawa M, Kikusui T. Correlations between behavior and hormone concentrations or gut microbiome imply that domestic cats (Felis silvestris catus) living in a group are not like ‘groupmates’. PLoS One 2022; 17:e0269589. [PMID: 35895662 PMCID: PMC9328509 DOI: 10.1371/journal.pone.0269589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 05/25/2022] [Indexed: 11/18/2022] Open
Abstract
Domestic cats (Felis silvestris catus) can live in high densities, although most feline species are solitary and exclusively territorial animals; it is possible that certain behavioral strategies enable this phenomenon. These behaviors are regulated by hormones and the gut microbiome, which, in turn, is influenced by domestication. Therefore, we investigated the relationships between the sociality, hormone concentrations, and gut microbiome of domestic cats by conducting three sets of experiments for each group of five cats and analyzing their behavior, hormone concentrations (cortisol, oxytocin, and testosterone), and their gut microbiomes. We observed that individuals with high cortisol and testosterone concentrations established less contact with others, and individuals with high oxytocin concentrations did not exhibit affiliative behaviors as much as expected. Additionally, the higher the frequency of contact among the individuals, the greater the similarity in gut microbiome; gut microbial composition was also related to behavioral patterns and cortisol secretion. Notably, individuals with low cortisol and testosterone concentrations were highly tolerant, making high-density living easy. Oxytocin usually functions in an affiliative manner within groups, but our results suggest that even if typically solitary and territorial animals live in high densities, their oxytocin functions are opposite to those of typically group-living animals.
Collapse
Affiliation(s)
- Hikari Koyasu
- Laboratory of Human-Animal Interaction and Reciprocity, Azabu University, Kanagawa, Japan
- * E-mail:
| | - Hironobu Takahashi
- Laboratory of Human-Animal Interaction and Reciprocity, Azabu University, Kanagawa, Japan
| | - Moeka Yoneda
- Laboratory of Human-Animal Interaction and Reciprocity, Azabu University, Kanagawa, Japan
| | - Syunpei Naba
- Laboratory of Human-Animal Interaction and Reciprocity, Azabu University, Kanagawa, Japan
| | - Natsumi Sakawa
- Laboratory of Human-Animal Interaction and Reciprocity, Azabu University, Kanagawa, Japan
| | - Ikuto Sasao
- Laboratory of Human-Animal Interaction and Reciprocity, Azabu University, Kanagawa, Japan
| | - Miho Nagasawa
- Laboratory of Human-Animal Interaction and Reciprocity, Azabu University, Kanagawa, Japan
| | - Takefumi Kikusui
- Laboratory of Human-Animal Interaction and Reciprocity, Azabu University, Kanagawa, Japan
| |
Collapse
|
9
|
Ang L, Vinderola G, Endo A, Kantanen J, Jingfeng C, Binetti A, Burns P, Qingmiao S, Suying D, Zujiang Y, Rios-Covian D, Mantziari A, Beasley S, Gomez-Gallego C, Gueimonde M, Salminen S. Gut Microbiome Characteristics in feral and domesticated horses from different geographic locations. Commun Biol 2022; 5:172. [PMID: 35217713 PMCID: PMC8881449 DOI: 10.1038/s42003-022-03116-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 02/01/2022] [Indexed: 12/12/2022] Open
Abstract
Domesticated horses live under different conditions compared with their extinct wild ancestors. While housed, medicated and kept on a restricted source of feed, the microbiota of domesticated horses is hypothesized to be altered. We assessed the fecal microbiome of 57 domestic and feral horses from different locations on three continents, observing geographical differences. A higher abundance of eukaryota (p < 0.05) and viruses (p < 0.05) and lower of archaea (p < 0.05) were found in feral animals when compared with domestic ones. The abundance of genes coding for microbe-produced enzymes involved in the metabolism of carbohydrates was significantly higher (p < 0.05) in feral animals regardless of the geographic origin. Differences in the fecal resistomes between both groups of animals were also noted. The domestic/captive horse microbiomes were enriched in genes conferring resistance to tetracycline, likely reflecting the use of this antibiotic in the management of these animals. Our data showed an impoverishment of the fecal microbiome in domestic horses with diet, antibiotic exposure and hygiene being likely drivers. The results offer a view of the intestinal microbiome of horses and the impact of domestication or captivity, which may uncover novel targets for modulating the microbiome of horses to enhance animal health and well-being. Li Ang et al. present an investigation of feral and domesticated horse gut microbiomes across three continents. Their results provide new insight into how changes in horse lifestyle are reflected in the resident gut microbiome.
Collapse
Affiliation(s)
- Li Ang
- Health Management Centre, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Department of Henan Gene Hospital, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Department of Infection Disease, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Gabriel Vinderola
- Instituto de Lactología Industrial (INLAIN, UNL-CONICET), Facultad de Ingeniería Química, Universidad Nacional del Litoral, Santa Fe, Argentina
| | - Akihito Endo
- Department of Food, Aroma and Cosmetic Chemistry, Tokyo University of Agriculture, Hokkaido, Japan
| | - Juha Kantanen
- Production Systems, Natural Resources Institute Finland, Jokioinen, Finland
| | - Chen Jingfeng
- Health Management Centre, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ana Binetti
- Instituto de Lactología Industrial (INLAIN, UNL-CONICET), Facultad de Ingeniería Química, Universidad Nacional del Litoral, Santa Fe, Argentina
| | - Patricia Burns
- Instituto de Lactología Industrial (INLAIN, UNL-CONICET), Facultad de Ingeniería Química, Universidad Nacional del Litoral, Santa Fe, Argentina
| | - Shi Qingmiao
- Department of Henan Gene Hospital, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Department of Infection Disease, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ding Suying
- Health Management Centre, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yu Zujiang
- Department of Henan Gene Hospital, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Department of Infection Disease, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - David Rios-Covian
- Department and Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Asturias, Spain
| | - Anastasia Mantziari
- Functional Foods Forum, Faculty of Medicine, University of Turku, Turku, Finland
| | - Shea Beasley
- Functional Foods Forum, Faculty of Medicine, University of Turku, Turku, Finland
| | - Carlos Gomez-Gallego
- Functional Foods Forum, Faculty of Medicine, University of Turku, Turku, Finland.,Institute of Public Health and Nutrition, University of Eastern Finland, Kuopio, Finland
| | - Miguel Gueimonde
- Department and Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Asturias, Spain.
| | - Seppo Salminen
- Functional Foods Forum, Faculty of Medicine, University of Turku, Turku, Finland.
| |
Collapse
|
10
|
Chiang E, Deblois CL, Carey HV, Suen G. Characterization of captive and wild 13-lined ground squirrel cecal microbiotas using Illumina-based sequencing. Anim Microbiome 2022; 4:1. [PMID: 34980290 PMCID: PMC8722175 DOI: 10.1186/s42523-021-00154-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 12/12/2021] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Hibernating animals experience extreme changes in diet that make them useful systems for understanding host-microbial symbioses. However, most of our current knowledge about the hibernator gut microbiota is derived from studies using captive animals. Given that there are substantial differences between captive and wild environments, conclusions drawn from studies with captive hibernators may not reflect the gut microbiota's role in the physiology of wild animals. To address this, we used Illumina-based sequencing of the 16S rRNA gene to compare the bacterial cecal microbiotas of captive and wild 13-lined ground squirrels (TLGS) in the summer. As the first study to use Illumina-based technology to compare the microbiotas of an obligate rodent hibernator across the year, we also reported changes in captive TLGS microbiotas in summer, winter, and spring. RESULTS Wild TLGS microbiotas had greater richness and phylogenetic diversity with less variation in beta diversity when compared to captive microbiotas. Taxa identified as core operational taxonomic units (OTUs) and found to significantly contribute to differences in beta diversity were primarily in the families Lachnospiraceae and Ruminococcaceae. Captive TLGS microbiotas shared phyla and core OTUs across the year, but active season (summer and spring) microbiotas had different alpha and beta diversities than winter season microbiotas. CONCLUSIONS This is the first study to compare the microbiotas of captive and wild rodent hibernators. Our findings suggest that data from captive and wild ground squirrels should be interpreted separately due to their distinct microbiotas. Additionally, as the first study to compare seasonal microbiotas of obligate rodent hibernators using Illumina-based 16S rRNA sequencing, we reported changes in captive TLGS microbiotas that are consistent with previous work. Taken together, this study provides foundational information for improving the reproducibility and experimental design of future hibernation microbiota studies.
Collapse
Affiliation(s)
- Edna Chiang
- Microbiology Doctoral Training Program, Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Courtney L. Deblois
- Microbiology Doctoral Training Program, Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Hannah V. Carey
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Garret Suen
- Present Address: Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706 USA
| |
Collapse
|
11
|
Diaz J, Reese AT. Possibilities and limits for using the gut microbiome to improve captive animal health. Anim Microbiome 2021; 3:89. [PMID: 34965885 PMCID: PMC8715647 DOI: 10.1186/s42523-021-00155-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 12/18/2021] [Indexed: 12/13/2022] Open
Abstract
Because of its potential to modulate host health, the gut microbiome of captive animals has become an increasingly important area of research. In this paper, we review the current literature comparing the gut microbiomes of wild and captive animals, as well as experiments tracking the microbiome when animals are moved between wild and captive environments. As a whole, these studies report highly idiosyncratic results with significant differences in the effect of captivity on the gut microbiome between host species. While a few studies have analyzed the functional capacity of captive microbiomes, there has been little research directly addressing the health consequences of captive microbiomes. Therefore, the current body of literature cannot broadly answer what costs, if any, arise from having a captive microbiome in captivity. Addressing this outstanding question will be critical to determining whether it is worth pursuing microbial manipulations as a conservation tool. To stimulate the next wave of research which can tie the captive microbiome to functional and health impacts, we outline a wide range of tools that can be used to manipulate the microbiome in captivity and suggest a variety of methods for measuring the impact of such manipulation preceding therapeutic use. Altogether, we caution researchers against generalizing results between host species given the variability in gut community responses to captivity and highlight the need to understand what role the gut microbiome plays in captive animal health before putting microbiome manipulations broadly into practice.
Collapse
Affiliation(s)
- Jessica Diaz
- Section of Ecology, Behavior, and Evolution, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Aspen T Reese
- Section of Ecology, Behavior, and Evolution, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
- Center for Microbiome Innovation, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
| |
Collapse
|
12
|
Wildlife symbiotic bacteria are indicators of the health status of the host and its ecosystem. Appl Environ Microbiol 2021; 88:e0138521. [PMID: 34669453 PMCID: PMC8752132 DOI: 10.1128/aem.01385-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Lactic acid bacteria (LAB) are gut symbionts that can be used as a model to understand the host-microbiota crosstalk under unpredictable environmental conditions such as wildlife ecosystems. The aim of this study was to determine whether viable LAB can be informative of the health status of wild boar populations. We monitored the genotype and phenotype of LAB based on markers that included safety and phylogenetic origin, antibacterial activity and immunomodulatory properties. A LAB profile dominated by lactobacilli appears to stimulate protective immune responses and relates to strains widely used as probiotics, resulting in a potentially healthy wildlife population whereas microbiota overpopulated by enterococci was observed in a hostile environment. These enterococci were closely related to pathogenic strains that have developed mechanisms to evade innate immune system, posing a potential risk for the host health. Furthermore, our LAB isolates displayed antibacterial properties in a species-dependent manner. Nearly all of them were able to inhibit bacterial pathogens, raising the possibility of using them as a la carte antibiotic alternative in the unexplored field of wildlife disease mitigation. Our study highlights that microbiological characterization of LAB is a useful indicator of wildlife health status and the ecological origin from which they derive. Significance Statement The wildlife symbiotic microbiota is an important component to the greater for greater diversity and functionality of their bacterial populations, influencing the host health and adaptability to its ecosystem. Although many microbes are partly responsible for the development of multiple physiological processes, only certain bacterial groups such as lactic acid bacteria (LAB) have the capacity to overpopulate the gut, promoting health (or disease) when specific genetic and environmental conditions are present. LAB have been exploited in many ways due to their probiotic properties, in particular lactobacilli, however their relationship with wildlife gut-associated microbiota hosts remains to be elucidated. On the other hand, it is unclear whether LAB such as enterococci, which have been associated with detrimental health effects, could lead to disease. These important questions have not been properly addressed in the field of wildlife, and therefore, should be clearly attained.
Collapse
|
13
|
Sun G, Xia T, Wei Q, Dong Y, Zhao C, Yang X, Zhang L, Wang X, Sha W, Zhang H. Analysis of gut microbiota in three species belonging to different genera ( Hemitragus, Pseudois, and Ovis) from the subfamily Caprinae in the absence of environmental variance. Ecol Evol 2021; 11:12129-12140. [PMID: 34522365 PMCID: PMC8427585 DOI: 10.1002/ece3.7976] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 06/28/2021] [Accepted: 07/13/2021] [Indexed: 12/29/2022] Open
Abstract
This study aimed to identify the effects of host species on the gut microbial flora in three species (Hemitragus jemlahicus, Pseudois nayaur, and Ovis orientalis) from the subfamily Caprinae, by excluding the impact of environment factors. We investigated the differences in intestinal flora of three species belonging to Caprinae, which were raised in identical conditions. Fecal samples were collected from tahr, mouflon, and bharal, and the V3-V4 region of the 16S ribosomal RNA gene was analyzed by high-throughput sequencing. The analysis of 16S rRNA gene sequences reveals that fecal samples were mainly composed of four phyla: Firmicutes, Bacteroidetes, Spirochaetes, and Proteobacteria. The most abundant phyla included Firmicutes and Bacteroidetes accounting for >90% of the bacteria, and a higher Firmicutes/Bacteroidetes ratio was observed in tahrs. Moreover, significant differences existed at multiple levels of classifications in the relative abundance of intestinal flora, differing greatly between species. Phylogenetic analyses based on 16S rRNA gene indicated that mouflon is closely related to bharal, and it is inconsistent with previous reports in the species evolutionary relationships. In this study, we demonstrated that the gut microbiota in tahr had a stronger ability to absorb and store energy from the diet compared with mouflon and bharal, and the characteristics of host-microbiome interactions were not significant.
Collapse
Affiliation(s)
- Guolei Sun
- College of Life ScienceQufu Normal UniversityQufuChina
| | - Tian Xia
- College of Life ScienceQufu Normal UniversityQufuChina
| | - Qinguo Wei
- College of Life ScienceQufu Normal UniversityQufuChina
| | - Yuehuan Dong
- College of Life ScienceQufu Normal UniversityQufuChina
| | - Chao Zhao
- College of Life ScienceQufu Normal UniversityQufuChina
| | - Xiufeng Yang
- College of Life ScienceQufu Normal UniversityQufuChina
| | - Lei Zhang
- College of Life ScienceQufu Normal UniversityQufuChina
| | - Xibao Wang
- College of Life ScienceQufu Normal UniversityQufuChina
| | - Weilai Sha
- College of Life ScienceQufu Normal UniversityQufuChina
| | - Honghai Zhang
- College of Life ScienceQufu Normal UniversityQufuChina
| |
Collapse
|
14
|
Alterations in gut microbiota linked to provenance, sex, and chronic wasting disease in white-tailed deer (Odocoileus virginianus). Sci Rep 2021; 11:13218. [PMID: 34168170 PMCID: PMC8225879 DOI: 10.1038/s41598-021-89896-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 05/04/2021] [Indexed: 01/04/2023] Open
Abstract
Chronic wasting disease (CWD) is a fatal, contagious, neurodegenerative prion disease affecting both free-ranging and captive cervid species. CWD is spread via direct or indirect contact or oral ingestion of prions. In the gastrointestinal tract, prions enter the body through microfold cells (M-cells), and the abundance of these cells can be influenced by the gut microbiota. To explore potential links between the gut microbiota and CWD, we collected fecal samples from farmed and free-ranging white-tailed deer (Odocoileus virginianus) around the Midwest, USA. Farmed deer originated from farms that were depopulated due to CWD. Free-ranging deer were sampled during annual deer harvests. All farmed deer were tested for CWD via ELISA and IHC, and we used 16S rRNA gene sequencing to characterize the gut microbiota. We report significant differences in gut microbiota by provenance (Farm 1, Farm 2, Free-ranging), sex, and CWD status. CWD-positive deer from Farm 1 and 2 had increased abundances of Akkermansia, Lachnospireacea UCG-010, and RF39 taxa. Overall, differences by provenance and sex appear to be driven by diet, while differences by CWD status may be linked to CWD pathogenesis.
Collapse
|
15
|
Quiroga-González C, Cardenas LAC, Ramírez M, Reyes A, González C, Stevenson PR. Monitoring the variation in the gut microbiota of captive woolly monkeys related to changes in diet during a reintroduction process. Sci Rep 2021; 11:6522. [PMID: 33753830 PMCID: PMC7985493 DOI: 10.1038/s41598-021-85990-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 02/04/2021] [Indexed: 01/31/2023] Open
Abstract
Microbiome is known to play an important role in the health of organisms and different factors such as diet have been associated with modifications in microbial communities. Differences in the microbiota composition of wild and captive animals has been evaluated; however, variation during a reintroduction process in primates has never been reported. Our aim was to identify changes in the bacterial composition of three individuals of reintroduced woolly monkeys (Lagothrix lagothricha) and the variables associated with such changes. Fecal samples were collected and the V4 region of the 16S rRNA gene was sequenced to determine gut microbial composition and functionality. Individual samples from released individuals showed a higher microbial diversity after being released compared to before liberation, associated with changes in their diet. Beta diversity and functionality analysis showed separation of samples from released and captive conditions and the major factor of variation was the moment of liberation. This study shows that intestinal microbiota varies depending on site conditions and is mainly associated with diet diversity. The intake of food from wild origin by released primates may promote a positive effect on gut microbiota, improving health, and potentially increasing success in reintroduction processes.
Collapse
Affiliation(s)
- Camilo Quiroga-González
- Laboratorio de Ecología de Bosques Tropicales y Primatología (LEBTYP), Departamento de Ciencias Biológicas, Facultad de Ciencias, Universidad de Los Andes, Bogotá, Colombia.
| | - Luis Alberto Chica Cardenas
- Grupo de Investigación en Biología Computacional y Ecología Microbiana (BCEM), Max Planck Tandem Research Group in Computational Biology, Universidad de Los Andes, Bogotá, Colombia
| | - Mónica Ramírez
- Laboratorio de Ecología de Bosques Tropicales y Primatología (LEBTYP), Departamento de Ciencias Biológicas, Facultad de Ciencias, Universidad de Los Andes, Bogotá, Colombia
| | - Alejandro Reyes
- Grupo de Investigación en Biología Computacional y Ecología Microbiana (BCEM), Max Planck Tandem Research Group in Computational Biology, Universidad de Los Andes, Bogotá, Colombia.
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, Saint Louis, MO, USA.
| | - Camila González
- Centro de Investigaciones en Microbiología y Parasitología Tropical (CIMPAT), Departamento de Ciencias Biológicas, Facultad de Ciencias, Universidad de Los Andes, Bogotá, Colombia
| | - Pablo R Stevenson
- Laboratorio de Ecología de Bosques Tropicales y Primatología (LEBTYP), Departamento de Ciencias Biológicas, Facultad de Ciencias, Universidad de Los Andes, Bogotá, Colombia
| |
Collapse
|
16
|
Ning Y, Qi J, Dobbins MT, Liang X, Wang J, Chen S, Ma J, Jiang G. Comparative Analysis of Microbial Community Structure and Function in the Gut of Wild and Captive Amur Tiger. Front Microbiol 2020; 11:1665. [PMID: 32793154 PMCID: PMC7393233 DOI: 10.3389/fmicb.2020.01665] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 06/25/2020] [Indexed: 12/15/2022] Open
Abstract
It has been well acknowledged that the gut microbiome is important for host health, composition changes in these microbial communities might increase susceptibility to infections and reduce adaptability to environment. Reintroduction, as an effective strategy for wild population recovery and genetic diversity maintenance for endangered populations, usually takes captive populations as rewilding resource. While, little is known about the compositional and functional differences of gut microbiota between captive and wild populations, especially for large carnivores, like Amur tiger. 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 variations of gut microbiota communities between captive and wild Amur tiger populations based on total 35 fecal samples (13 from captive tigers and 22 from wild tigers). Our results showed that captive Amur tigers have higher alpha diversity in gut microbiota, but that the average unweighted UniFrac distance of bacterial taxa among wild Amur tigers was much larger. The function differences involve most aspects of the body functions, especially for metabolism, environmental information processing, cellular processes, and organismal systems. It was indicated that the diet habit and environment difference between captive and wild populations lead to composition differences of gut microbiota and then resulted in significant differences in functions. These contrasts of functional and compositional variations in gut microbiota between wild and captive Amur tigers are essential insights for guiding conservation management and policy decision-making, and call for more attention on the influence of gut microbiota on the ability of captive animals to survive in the wild.
Collapse
Affiliation(s)
- Yao Ning
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
| | - Jinzhe Qi
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China.,Department of Wildlife, Fish, and Conservation, University of California, Davis, Davis, CA, United States
| | - Michael T Dobbins
- Department of Wildlife, Fish, and Conservation, University of California, Davis, Davis, CA, United States
| | - Xin Liang
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
| | - Jingxuan Wang
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
| | - Shiyu Chen
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
| | - Jianzhang Ma
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
| | - Guangshun Jiang
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
| |
Collapse
|