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Raulo A, Bürkner PC, Finerty GE, Dale J, Hanski E, English HM, Lamberth C, Firth JA, Coulson T, Knowles SCL. Social and environmental transmission spread different sets of gut microbes in wild mice. Nat Ecol Evol 2024; 8:972-985. [PMID: 38689017 DOI: 10.1038/s41559-024-02381-0] [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: 08/09/2023] [Accepted: 03/01/2024] [Indexed: 05/02/2024]
Abstract
Gut microbes shape many aspects of organismal biology, yet how these key bacteria transmit among hosts in natural populations remains poorly understood. Recent work in mammals has emphasized either transmission through social contacts or indirect transmission through environmental contact, but the relative importance of different routes has not been directly assessed. Here we used a novel radio-frequency identification-based tracking system to collect long-term high-resolution data on social relationships, space use and microhabitat in a wild population of mice (Apodemus sylvaticus), while regularly characterizing their gut microbiota with 16S ribosomal RNA profiling. Through probabilistic modelling of the resulting data, we identify positive and statistically distinct signals of social and environmental transmission, captured by social networks and overlap in home ranges, respectively. Strikingly, microorganisms with distinct biological attributes drove these different transmission signals. While the social network effect on microbiota was driven by anaerobic bacteria, the effect of shared space was most influenced by aerotolerant spore-forming bacteria. These findings support the prediction that social contact is important for the transfer of microorganisms with low oxygen tolerance, while those that can tolerate oxygen or form spores may be able to transmit indirectly through the environment. Overall, these results suggest social and environmental transmission routes can spread biologically distinct members of the mammalian gut microbiota.
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Affiliation(s)
- Aura Raulo
- Department of Biology, University of Oxford, Oxford, UK.
- Department of Computing, University of Turku, Turku, Finland.
| | | | - Genevieve E Finerty
- Department of Biology, University of Oxford, Oxford, UK
- Department for the Ecology of Animal Societies, Max Planck Institute of Animal Behaviour, Constance, Germany
- Department of Biology, University of Konstanz, Constance, Germany
| | - Jarrah Dale
- Department of Biology, University of Oxford, Oxford, UK
| | | | - Holly M English
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Curt Lamberth
- Department of Biology, University of Oxford, Oxford, UK
| | - Josh A Firth
- Department of Biology, University of Oxford, Oxford, UK
- School of Biology, University of Leeds, Leeds, UK
| | - Tim Coulson
- Department of Biology, University of Oxford, Oxford, UK
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2
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Rimbach R, Pontzer H. Increased physical activity is not related to markers of cardiometabolic health in two lemur species. Am J Primatol 2024; 86:e23564. [PMID: 37839049 DOI: 10.1002/ajp.23564] [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: 08/08/2023] [Revised: 09/18/2023] [Accepted: 10/01/2023] [Indexed: 10/17/2023]
Abstract
Insufficient physical activity is a major risk factor for cardiometabolic disease (i.e., unhealthy weight gain, heart disease, and diabetes) in humans and may also negatively affect health of primates in human care. Effects of physical activity on energy expenditure and cardiometabolic health are virtually unstudied in nonhuman primates. We investigated physical activity and metabolic markers in 15 adult ring-tailed lemurs (Lemur catta) and 11 Coquerel's sifakas (Propithecus coquereli) at the Duke Lemur Center during a period of low activity in winter when the animals were housed in buildings (with outdoor access) and a period of high activity when individuals were free-ranging in large, outdoor, forested enclosures. We compared body mass, blood glucose, triglycerides, HDL- and LDL-cholesterol, physical activity via accelerometry, and total energy expenditure (TEE) via the doubly labeled water method (in ring-tailed lemurs only) between both conditions. Both species were more active and had a lower body mass in summer. Ring-tailed lemurs had a higher TEE and lower triglyceride levels in summer, whereas sifaka had higher triglyceride levels in summer. Individuals that increased their activity more, also lost more body mass. Individuals that lost more body mass, also had a positive change in HDL-cholesterol (i.e., higher values in summer). Changes in activity were not associated with changes in markers of metabolic health, body fat percentage and TEE (both unadjusted and adjusted for body composition). Older age was associated with lower activity in both species, and decreased glucose in ring-tailed lemurs, but was otherwise unrelated to metabolic markers and, for ring-tailed lemurs, adjusted TEE. Overall, body mass was lower during summer but the increase in physical activity did not strongly influence metabolic health or TEE in these populations.
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Affiliation(s)
- Rebecca Rimbach
- Evolutionary Anthropology, Duke University, Durham, North Carolina, USA
- Department of Behavioural Biology, University of Münster, Münster, Germany
- School of Animal, Plant & Environmental Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Herman Pontzer
- Evolutionary Anthropology, Duke University, Durham, North Carolina, USA
- Duke Global Health Institute, Duke University, Durham, North Carolina, USA
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3
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Dong Y, Li Y, Ge M, Takatsu T, Wang Z, Zhang X, Ding D, Xu Q. Distinct gut microbial communities and functional predictions in divergent ophiuroid species: host differentiation, ecological niches, and adaptation to cold-water habitats. Microbiol Spectr 2023; 11:e0207323. [PMID: 37889056 PMCID: PMC10715168 DOI: 10.1128/spectrum.02073-23] [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: 05/17/2023] [Accepted: 09/20/2023] [Indexed: 10/28/2023] Open
Abstract
IMPORTANCE Gastrointestinal microorganisms are critical to the survival and adaptation of hosts, and there are few studies on the differences and functions of gastrointestinal microbes in widely distributed species. This study investigated the gut microbes of two ophiuroid species (Ophiura sarsii and its subspecies O. sarsii vadicola) in cold-water habitats of the Northern Pacific Ocean. The results showed that a combination of host and environmental factors shapes the intestinal microbiota of ophiuroids. There was a high similarity in microbial communities between the two groups living in different regions, which may be related to their similar ecological niches. These microorganisms played a vital role in the ecological success of ophiuroids as the foundation for their adaptation to cold-water environments. This study revealed the complex relationship between hosts and their gut microbes, providing insights into the role they play in the adaptation and survival of marine species.
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Affiliation(s)
- Yue Dong
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, China
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
| | - Yixuan Li
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
- Department of Biology, Hong Kong Baptist University, Hong Kong SAR, China
| | - Meiling Ge
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, China
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
| | - Tetsuya Takatsu
- Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
| | - Zongling Wang
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
| | - Xuelei Zhang
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
| | - Dewen Ding
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
| | - Qinzeng Xu
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
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4
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Cao Y, Feng T, Wu Y, Xu Y, Du L, Wang T, Luo Y, Wang Y, Li Z, Xuan Z, Chen S, Yao N, Gao NL, Xiao Q, Huang K, Wang X, Cui K, Rehman SU, Tang X, Liu D, Han H, Li Y, Chen WH, Liu Q. The multi-kingdom microbiome of the goat gastrointestinal tract. MICROBIOME 2023; 11:219. [PMID: 37779211 PMCID: PMC10544373 DOI: 10.1186/s40168-023-01651-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 08/14/2023] [Indexed: 10/03/2023]
Abstract
BACKGROUND Goat is an important livestock worldwide, which plays an indispensable role in human life by providing meat, milk, fiber, and pelts. Despite recent significant advances in microbiome studies, a comprehensive survey on the goat microbiomes covering gastrointestinal tract (GIT) sites, developmental stages, feeding styles, and geographical factors is still unavailable. Here, we surveyed its multi-kingdom microbial communities using 497 samples from ten sites along the goat GIT. RESULTS We reconstructed a goat multi-kingdom microbiome catalog (GMMC) including 4004 bacterial, 71 archaeal, and 7204 viral genomes and annotated over 4,817,256 non-redundant protein-coding genes. We revealed patterns of feeding-driven microbial community dynamics along the goat GIT sites which were likely associated with gastrointestinal food digestion and absorption capabilities and disease risks, and identified an abundance of large intestine-enriched genera involved in plant fiber digestion. We quantified the effects of various factors affecting the distribution and abundance of methane-producing microbes including the GIT site, age, feeding style, and geography, and identified 68 virulent viruses targeting the methane producers via a comprehensive virus-bacterium/archaea interaction network. CONCLUSIONS Together, our GMMC catalog provides functional insights of the goat GIT microbiota through microbiome-host interactions and paves the way to microbial interventions for better goat and eco-environmental qualities. Video Abstract.
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Affiliation(s)
- Yanhong Cao
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, 528225, China
- Guangxi Vocational University of Agriculture, Nanning, Guangxi, 530007, China
| | - Tong Feng
- Department of Bioinformatics and Systems Biology, Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China.
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China.
| | - Yingjian Wu
- Department of Bioinformatics and Systems Biology, Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Yixue Xu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China
| | - Li Du
- Hainan Key Lab of Tropical Animal Reproduction and Breeding and Epidemic Disease Research, College of Animal Science and Technology, Hainan University, Haikou, 570000, Hainan, China
| | - Teng Wang
- Department of Bioinformatics and Systems Biology, Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Yuhong Luo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China
| | - Yan Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China
| | - Zhipeng Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China
| | - Zeyi Xuan
- Animal Husbandry Research Institute of Guangxi Zhuang Autonomous Region, Nanning, 530001, Guangxi, China
| | - Shaomei Chen
- Animal Husbandry Research Institute of Guangxi Zhuang Autonomous Region, Nanning, 530001, Guangxi, China
| | - Na Yao
- Animal Husbandry Research Institute of Guangxi Zhuang Autonomous Region, Nanning, 530001, Guangxi, China
| | - Na L Gao
- Department of Bioinformatics and Systems Biology, Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Qian Xiao
- Hainan Key Lab of Tropical Animal Reproduction and Breeding and Epidemic Disease Research, College of Animal Science and Technology, Hainan University, Haikou, 570000, Hainan, China
| | - Kongwei Huang
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, 528225, China
| | - Xiaobo Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China
| | - Kuiqing Cui
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, 528225, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China
| | - Saif Ur Rehman
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China
| | - Xiangfang Tang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Dewu Liu
- South China Agricultural University, Guangzhou, 510642, China
| | - Hongbing Han
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Ying Li
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, 528225, China
| | - Wei-Hua Chen
- Department of Bioinformatics and Systems Biology, Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China.
- Institution of Medical Artificial Intelligence, Binzhou Medical University, Yantai, 264003, China.
| | - Qingyou Liu
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, 528225, China.
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China.
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Roche CE, Montague MJ, Wang J, Dickey AN, Ruiz-Lambides A, Brent LJN, Platt ML, Horvath JE. Yearly variation coupled with social interactions shape the skin microbiome in free-ranging rhesus macaques. Microbiol Spectr 2023; 11:e0297423. [PMID: 37750731 PMCID: PMC10580906 DOI: 10.1128/spectrum.02974-23] [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: 08/04/2023] [Accepted: 08/07/2023] [Indexed: 09/27/2023] Open
Abstract
While skin microbes are known to mediate human health and disease, there has been minimal research on the interactions between skin microbiota, social behavior, and year-to-year effects in non-human primates-important animal models for translational biomedical research. To examine these relationships, we analyzed skin microbes from 78 rhesus macaques living on Cayo Santiago Island, Puerto Rico. We considered age, sex, and social group membership, and characterized social behavior by assessing dominance rank and patterns of grooming as compared to nonsocial behaviors. To measure the effects of a shifting environment, we sampled skin microbiota (based on sequence analysis of the 16S rRNA V4 region) and assessed weather across sampling periods between 2013 and 2015. We hypothesized that, first, monkeys with similar social behavior and/or in the same social group would possess similar skin microbial composition due, in part, to physical contact, and, second, microbial diversity would differ across sampling periods. We found significant phylum-level differences between social groups in the core microbiome as well as an association between total grooming rates and alpha diversity in the complete microbiome, but no association between microbial diversity and measures of rank or other nonsocial behaviors. We also identified alpha and beta diversity differences in microbiota and differential taxa abundance across two sampling periods. Our findings indicate that social dynamics interact with yearly environmental changes to shape the skin microbiota in rhesus macaques, with potential implications for understanding the factors affecting the microbiome in humans, which share many biological and social characteristics with these animals. IMPORTANCE Primate studies are valuable for translational and evolutionary insights into the human microbiome. The majority of primate microbiome studies focus on the gut, so less is known about the factors impacting the microbes on skin and how their links affect health and behavior. Here, we probe the impact of social interactions and the yearly environmental changes on food-provisioned, free-ranging monkeys living on a small island. We expected animals that lived together and groomed each other would have more similar microbes on their skin, but surprisingly found that the external environment was a stronger influence on skin microbiome composition. These findings have implications for our understanding of the human skin microbiome, including potential manipulations to improve health and treat disease.
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Affiliation(s)
| | - Michael J. Montague
- Department of Neuroscience, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - JiCi Wang
- Department of Neuroscience, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Allison N. Dickey
- Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina, USA
| | - Angelina Ruiz-Lambides
- Caribbean Primate Research Center, University of Puerto Rico, San Juan, Puerto Rico, USA
| | - Lauren J. N. Brent
- Centre for Research in Animal Behaviour, University of Exeter, Exeter, United Kingdom
| | - Michael L. Platt
- Department of Neuroscience, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Marketing Department, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Psychology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Julie E. Horvath
- North Carolina Museum of Natural Sciences, Raleigh, North Carolina, USA
- Department of Biological and Biomedical Sciences, North Carolina Central University, Durham, North Carolina, USA
- Department of Evolutionary Anthropology, Duke University, Durham, North Carolina, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, USA
- Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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6
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Lapid R, Motro Y, Craddock H, Khalfin B, King R, Bar-Gal GK, Moran-Gilad J. Fecal microbiota of the synanthropic golden jackal (Canis aureus). Anim Microbiome 2023; 5:37. [PMID: 37542305 PMCID: PMC10403885 DOI: 10.1186/s42523-023-00259-3] [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: 03/25/2023] [Accepted: 07/26/2023] [Indexed: 08/06/2023] Open
Abstract
The golden jackal (Canis aureus), is a medium canid carnivore widespread throughout the Mediterranean region and expanding into Europe. This species thrives near human settlements and is implicated in zoonoses such as rabies. This study explores for the first time, the golden jackal fecal microbiota. We analyzed 111 fecal samples of wild golden jackals using 16S rRNA amplicon sequencing the connection of the microbiome to animal characteristics, burden of pathogens and geographic and climate characteristics. We further compared the fecal microbiota of the golden jackal to the black-backed jackal and domestic dog. We found that the golden jackal fecal microbiota is dominated by the phyla Bacteroidota, Fusobacteriota and Firmicutes. The golden jackal fecal microbiota was associated with different variables, including geographic region, age-class, exposure to rabies oral vaccine, fecal parasites and toxoplasmosis. A remarkable variation in the relative abundance of different taxa was also found associated with different variables, such as age-class. Linear discriminant analysis effect size (LEfSe) analysis found abundance of specific taxons in each region, Megasphaera genus in group 1, Megamonas genus in group 2 and Bacteroides coprocola species in group 3. We also found a different composition between the fecal microbiota of the golden jackal, blacked-backed jackal and the domestic dog. Furthermore, LEfSe analysis found abundance of Fusobacterium and Bacteroides genera in the golden jackal, Clostridia class in blacked-backed jackal and Megamonas genus in domestic dog. The golden jackal fecal microbiota is influenced by multiple factors including host traits and pathogen burden. The characterization of the microbiota of this thriving species may aid in mapping its spread and proximity to human settlements. Moreover, understanding the jackal microbiota could inform the study of potential animal and human health risks and inform control measures.
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Affiliation(s)
- Roi Lapid
- The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, P.O.B. 12, 7610001, Rehovot, Israel
| | - Yair Motro
- Department of Health Policy and Management, School of Public Health, Faculty of Health Sciences, Ben-Gurion University of the Negev, 8410501, Beer-Sheva, Israel
| | - Hillary Craddock
- Department of Health Policy and Management, School of Public Health, Faculty of Health Sciences, Ben-Gurion University of the Negev, 8410501, Beer-Sheva, Israel
| | - Boris Khalfin
- Department of Health Policy and Management, School of Public Health, Faculty of Health Sciences, Ben-Gurion University of the Negev, 8410501, Beer-Sheva, Israel
| | - Roni King
- Science and Conservation Division, Israel Nature and Parks Authority, 3 Am Ve'Olamo St., 95463, Jerusalem, Israel
| | - Gila Kahila Bar-Gal
- The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, P.O.B. 12, 7610001, Rehovot, Israel
| | - Jacob Moran-Gilad
- Department of Health Policy and Management, School of Public Health, Faculty of Health Sciences, Ben-Gurion University of the Negev, 8410501, Beer-Sheva, Israel.
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7
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Corduneanu A, Wu-Chuang A, Maitre A, Obregon D, Sándor AD, Cabezas-Cruz A. Structural differences in the gut microbiome of bats using terrestrial vs. aquatic feeding resources. BMC Microbiol 2023; 23:93. [PMID: 37005589 PMCID: PMC10067309 DOI: 10.1186/s12866-023-02836-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 03/25/2023] [Indexed: 04/04/2023] Open
Abstract
Bat gut microbiomes are adapted to the specific diets of their hosts. Despite diet variation has been associated with differences in bat microbiome diversity, the influence of diet on microbial community assembly have not been fully elucidated. In the present study, we used available data on bat gut microbiome to characterize the microbial community assembly of five selected bat species (i.e., Miniopterus schreibersii, Myotis capaccinii, Myotis myotis, Myotis pilosus, and Myotis vivesi), using network analysis. These bat species with contrasting habitat and food preferences (i.e., My. capaccinii and My. pilosus can be piscivorous and/or insectivorous; Mi. schreibersii and My. myotis are exclusively insectivorous; while My. vivesi is a marine predator) offer an invaluable opportunity to test the impact of diet on bat gut microbiome assembly. The results showed that My. myotis showed the most complex network, with the highest number of nodes, while My. vivesi has the least complex structured microbiome, with lowest number of nodes in its network. No common nodes were observed in the networks of the five bat species, with My. myotis possessing the highest number of unique nodes. Only three bat species, My. myotis, My. pilosus and My. vivesi, presented a core microbiome and the distribution of local centrality measures of nodes was different in the five networks. Taxa removal followed by measurement of network connectivity revealed that My. myotis had the most robust network, while the network of My. vivesi presented the lowest tolerance to taxa removal. Prediction of metabolic pathways using PICRUSt2 revealed that Mi. schreibersii had significantly higher functional pathway's richness compared to the other bat species. Most of predicted pathways (82%, total 435) were shared between all bat species, while My. capaccinii, My. myotis and My. vivesi, but no Mi. schreibersii or My. pilosus, showed specific pathways. We concluded that despite similar feeding habits, microbial community assembly can differ between bat species. Other factors beyond diet may play a major role in bat microbial community assembly, with host ecology, sociality and overlap in roosts likely providing additional predictors governing gut microbiome of insectivorous bats.
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Affiliation(s)
- Alexandra Corduneanu
- Department of Animal Breeding and Animal Production, University of Agricultural Sciences and Veterinary Medicine of Cluj-Napoca, Cluj-Napoca, Romania
- Department of Parasitology and Parasitic Diseases, University of Agricultural Sciences and Veterinary Medicine, Cluj-Napoca-Napoca, Romania
| | - Alejandra Wu-Chuang
- UMR BIPAR, Laboratoire de Santé Animale, ANSES, INRAE, Ecole Nationale Vétérinaire d'Alfort, Maisons-Alfort, France
| | - Apolline Maitre
- UMR BIPAR, Laboratoire de Santé Animale, ANSES, INRAE, Ecole Nationale Vétérinaire d'Alfort, Maisons-Alfort, France
- INRAE, UR 0045 Laboratoire de Recherches Sur Le Développement de L'Elevage (SELMET-LRDE), 20250, Corte, France
- EA 7310, Laboratoire de Virologie, Université de Corse, Corte, France
| | - Dasiel Obregon
- School of Environmental Sciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Attila D Sándor
- Department of Parasitology and Parasitic Diseases, University of Agricultural Sciences and Veterinary Medicine, Cluj-Napoca-Napoca, Romania
- Department of Parasitology and Zoology, University of Veterinary Medicine, Budapest, Hungary
- ELKH-ÁTE Climate Change: New Blood-Sucking Parasites and Vector-Borne Pathogens Research Group, Budapest, Hungary
| | - Alejandro Cabezas-Cruz
- UMR BIPAR, Laboratoire de Santé Animale, ANSES, INRAE, Ecole Nationale Vétérinaire d'Alfort, Maisons-Alfort, France.
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8
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Zhang L, Yang Z, Yang F, Wang G, Zeng M, Zhang Z, Yang M, Wang Z, Li Z. Gut microbiota of two invasive fishes respond differently to temperature. Front Microbiol 2023; 14:1087777. [PMID: 37056740 PMCID: PMC10088563 DOI: 10.3389/fmicb.2023.1087777] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 03/13/2023] [Indexed: 03/30/2023] Open
Abstract
Temperature variation structures the composition and diversity of gut microbiomes in ectothermic animals, key regulators of host physiology, with potential benefit to host or lead to converse results (i.e., negative). So, the significance of either effect may largely depend on the length of time exposed to extreme temperatures and how rapidly the gut microbiota can be altered by change in temperature. However, the temporal effects of temperature on gut microbiota have rarely been clarified. To understand this issue, we exposed two juvenile fishes (Cyprinus carpio and Micropterus salmoides), which both ranked among the 100 worst invasive alien species in the world, to increased environmental temperature and sampled of the gut microbiota at multiple time points after exposure so as to determine when differences in these communities become detectable. Further, how temperature affects the composition and function of microbiota was examined by comparing predicted metagenomic profiles of gut microbiota between treatment groups at the final time point of the experiment. The gut microbiota of C. carpio was more plastic than those of M. salmoides. Specifically, communities of C. carpio were greatly altered by increased temperature within 1 week, while communities of M. salmoides exhibit no significant changes. Further, we identified 10 predicted bacterial functional pathways in C. carpio that were temperature-dependent, while none functional pathways in M. salmoides was found to be temperature-dependent. Thus, the gut microbiota of C. carpio was more sensitive to temperature changes and their functional pathways were significantly changed after temperature treatment. These results showed the gut microbiota of the two invasive fishes differ in response to temperature change, which may indicate that they differ in colonization modes. Broadly, we have confirmed that the increased short-term fluctuations in temperatures are always expected to alter the gut microbiota of ectothermic vertebrates when facing global climate change.
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Affiliation(s)
- Lixia Zhang
- Department of Ecology, College of Life Sciences, Henan Normal University, Xinxiang, China
- Puyang Field Scientific Observation and Research Station for Yellow River Wetland Ecosystem and The Observation and Research Field Station of Taihang Mountain Forest Ecosystems of Henan Province, Xinxiang, China
- *Correspondence: Lixia Zhang,
| | - Zi Yang
- Department of Ecology, College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Fan Yang
- Department of Ecology, College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Gege Wang
- Department of Ecology, College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Ming Zeng
- Jigongshan National Nature Reserve, Xinyang, China
| | | | - Mengxiao Yang
- Department of Ecology, College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Zhanqi Wang
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou, China
| | - Zhibing Li
- Department of Ecology, College of Life Sciences, Henan Normal University, Xinxiang, China
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9
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Chen Y, Lai Y, Zheng J, Liu Z, Nong D, Liang J, Li Y, Huang Z. Seasonal variations in the gut microbiota of white-headed black langur (Trachypithecus leucocephalus) in a limestone forest in Southwest Guangxi, China. Front Ecol Evol 2023. [DOI: 10.3389/fevo.2023.1126243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023] Open
Abstract
Investigating gut microbiota is important for understanding the physiological adaptation of animals to food availability changes in fragmented habitats and consequently providing new ideas for the conservation of endangered wild animals. In this study, we explored the gut microbiota of the endangered white-headed black langur (Trachypithecus leucocephalus), which is endemic to the limestone forests of Southwest Guangxi, China, to understand its adaptation strategies to seasonal changes in habitat using 16S rRNA sequencing. Our results revealed significant seasonal variations in the gut microbiota of white-headed black langurs. In particular, the alpha diversity was higher in the rainy season than in the dry season, and the beta diversity was significantly different between the two seasons. At the phylum level, the relative abundance of Firmicutes, Actinobacteriota, and Proteobacteria was higher in the dry season than that in the rainy season, whereas that of Bacteroidetes, Spirochaetota, and Cyanobacteria was significantly higher in the rainy season than that in the dry season. At the family level, Oscillospiraceae and Eggerthellaceae were more abundant in the dry season than in the rainy season, whereas Lachnospiraceae, Ruminococcaceae, and Monoglobaceae were more abundant in the rainy season than in the dry season. These results could have been obtained due to seasonal changes in the diet of langurs in response to food plant phenology. In addition, the neutral community model revealed that the gut microbiota assembly of these langurs was dominated by deterministic processes and was more significantly affected by ecological factors in the dry season than in the rainy season, which could be linked to the higher dependence of these langurs on mature leaves in the dry season. We concluded that the seasonal variations in the gut microbiota of white-headed black langurs occurred in response to food plant phenology in their habitat, highlighting the importance of microbiota in responding to fluctuating ecological factors and adapting to seasonal dietary changes.
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10
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The History of the Intestinal Microbiota and the Gut-Brain Axis. Pathogens 2022; 11:pathogens11121540. [PMID: 36558874 PMCID: PMC9786924 DOI: 10.3390/pathogens11121540] [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: 11/25/2022] [Revised: 12/02/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022] Open
Abstract
The gut-brain axis and the intestinal microbiota have been an area of an intensive research in the last few years. However, it is not a completely novel area of interest for physicians and scientists. From the earliest centuries, both professionals and patients turned their attention to the gastrointestinal system in order to find the root of physical and mental disturbances. The approach to the gut-brain axis and the therapeutic methods have changed alongside the development of different medical approaches to health and illness. They often reflected the social changes. The authors of this article aim to provide a brief history of the gut-brain axis and the intestinal microbiota in order to demonstrate how important the study of these systems is for both scientists and medical professionals, as well as for the general public. We analysed the publications accessible through PubMed regarding the microbiota and gut-brain axis history. If available, we accessed the original historical sources. We conclude that although the history of this science might be long, there are still many areas that need to be researched, analysed, and understood in future projects. The interest in the subject is not diminishing, but rather it has increased throughout the years.
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11
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Murillo T, Schneider D, Heistermann M, Daniel R, Fichtel C. Assessing the drivers of gut microbiome composition in wild redfronted lemurs via longitudinal metacommunity analysis. Sci Rep 2022; 12:21462. [PMID: 36509795 PMCID: PMC9744850 DOI: 10.1038/s41598-022-25733-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 12/05/2022] [Indexed: 12/15/2022] Open
Abstract
The gut microbiome influences host's immunity, development, and metabolism and participates in the gut-brain axis, thus impacting the health of the host. It is a dynamic community varying between individuals and within individuals at different time points. Hence, determining the factors causing this variability may elucidate their impact on host's health. However, understanding the drivers of variation has proven difficult particularly as multiple interactions occur simultaneously in the gut microbiome. We investigated the factors shaping the gut microbiome by applying the metacommunity concept where the gut microbiome is considered as a microbial community shaped by the interactions within the community, with the host and microbial communities outside the host, this through a longitudinal study in a wild primate. Focal behavioral data were collected for 1 year in four groups of redfronted lemurs to determine individual social and feeding behaviors. In addition, regular fecal samples were collected to assess bacteria, protozoa, and helminths through marker gene analysis and to measure fecal glucocorticoid metabolite (fGCM) concentrations to investigate the impact of physiological stress on the gut microbiome. Higher consumption of leaves and elevated fGCM concentrations correlated with higher alpha diversity, which also differed among groups. The major drivers of variation in beta diversity were group membership, precipitation and fGCM concentrations. We found positive and negative associations between bacterial genera and almost all studied factors. Correlations between bacterial indicator networks and social networks indicate transmission of bacteria between interacting individuals. We detected that processes occurring inside the gut environment are shaping the gut microbiome. Host associated factors such as, HPA axis, dietary changes, and fluctuations in water availability had a greater impact than interactions within the microbial community. The interplay with microbial communities outside the host also shape the gut microbiome through the exchange of bacteria through social relationships between individuals and the acquisition of microorganisms from environmental water sources.
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Affiliation(s)
- Tatiana Murillo
- grid.418215.b0000 0000 8502 7018Behavioral Ecology and Sociobiology Unit, German Primate Center, Göttingen, Germany ,grid.7450.60000 0001 2364 4210Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University of Göttingen, Göttingen, Germany ,grid.412889.e0000 0004 1937 0706Research Center for Tropical Diseases (CIET) and Faculty of Microbiology, University of Costa Rica, San José, Costa Rica
| | - Dominik Schneider
- grid.7450.60000 0001 2364 4210Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University of Göttingen, Göttingen, Germany
| | - Michael Heistermann
- grid.418215.b0000 0000 8502 7018Endocrinology Laboratory, German Primate Center, Göttingen, Germany
| | - Rolf Daniel
- grid.7450.60000 0001 2364 4210Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University of Göttingen, Göttingen, Germany
| | - Claudia Fichtel
- grid.418215.b0000 0000 8502 7018Behavioral Ecology and Sociobiology Unit, German Primate Center, Göttingen, Germany
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12
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Feng J, Zhu W, Jiang J, Zhao C, Sun Z, Jiang W, Luo Q, Zhao T. Reintroduction modifies the intraspecific variations of symbiotic microbes in captive bred Chinese giant salamander. Front Microbiol 2022; 13:1062604. [DOI: 10.3389/fmicb.2022.1062604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 11/14/2022] [Indexed: 12/04/2022] Open
Abstract
Microorganisms play as fundamental contributors to maintain hosts’ fitness, which can be shaped by external environment. Moreover, symbiotic microbiome also varied within species (e.g., between sexes and developmental stages). However, we still need more studies to quantify whether the intraspecific variation patterns of symbiotic microbes can be modified with the change of environment. The Chinese giant salamander (CGS; Andrias davidianus) is a Critically Endangered species. Despite quantitative captive bred individuals were released to rebuild wild populations, the effectiveness is limited. More importantly, no studies have revealed the adaptation of released CGSs to the complex field conditions. In the present study, we explored whether reintroduction can reshape the intraspecific variations of symbiotic microbiota in captive bred CGSs using high-throughput amplicon sequencing of the16S rRNA gene. We found no significant difference of symbiotic microbiome in captive bred males and females, but released males and females differed significantly in skin microbiome. Juveniles had higher diversity of microbial symbiont than adults in hatchery, but lower diversity in field. Moreover, dominant bacterial taxa differed between juveniles and adults in both hatchery and field. Importantly, this symbiotic microbiome variations within species can be modified (alpha and beta diversity, and community composition) when captive bred individuals were released to the field. Overall, we observed a lower alpha diversity and higher relative abundance of Chryseobacterium, Plesiomonas, and Acinetobacter in the bacterial community of captive bred individuals. Instead, higher alpha diversity of symbiotic microbiota and higher relative abundance of S24-7 and Lactobacillus was detected in released individuals. These modifications may associate with the change of living environment, as well as the specific behavior within CGSs (e.g., movement patterns and foraging activities). Future studies can incorporate other approaches (e.g., blood physiology) to better evaluate the growth and health of reintroduced CGSs.
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13
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Johnson KVA, Watson KK, Dunbar RIM, Burnet PWJ. Sociability in a non-captive macaque population is associated with beneficial gut bacteria. Front Microbiol 2022; 13:1032495. [PMID: 36439813 PMCID: PMC9691693 DOI: 10.3389/fmicb.2022.1032495] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 10/03/2022] [Indexed: 11/12/2022] Open
Abstract
The relationship between social behaviour and the microbiome is known to be reciprocal. Research in wild animal populations, particularly in primate social groups, has revealed the role that social interactions play in microbial transmission, whilst studies in laboratory animals have demonstrated that the gut microbiome can affect multiple aspects of behaviour, including social behaviour. Here we explore behavioural variation in a non-captive animal population with respect to the abundance of specific bacterial genera. Social behaviour based on grooming interactions is assessed in a population of rhesus macaques (Macaca mulatta), and combined with gut microbiome data. We focus our analyses on microbiome genera previously linked to sociability and autistic behaviours in rodents and humans. We show in this macaque population that some of these genera are also related to an individual's propensity to engage in social interactions. Interestingly, we find that several of the genera positively related to sociability, such as Faecalibacterium, are well known for their beneficial effects on health and their anti-inflammatory properties. In contrast, the genus Streptococcus, which includes pathogenic species, is more abundant in less sociable macaques. Our results indicate that microorganisms whose abundance varies with individual social behaviour also have functional links to host immune status. Overall, these findings highlight the connections between social behaviour, microbiome composition, and health in an animal population.
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Affiliation(s)
- Katerina V.-A. Johnson
- Department of Psychiatry, University of Oxford, Oxford, United Kingdom,Department of Experimental Psychology, University of Oxford, Oxford, United Kingdom,*Correspondence: Katerina V.-A. Johnson,
| | - Karli K. Watson
- Institute of Cognitive Science, University of Colorado Boulder, Boulder, CO, United States
| | - Robin I. M. Dunbar
- Department of Experimental Psychology, University of Oxford, Oxford, United Kingdom
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14
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Urlacher SS, Kim EY, Luan T, Young LJ, Adjetey B. Minimally invasive biomarkers in human and non-human primate evolutionary biology: Tools for understanding variation and adaptation. Am J Hum Biol 2022; 34:e23811. [PMID: 36205445 PMCID: PMC9787651 DOI: 10.1002/ajhb.23811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 08/21/2022] [Accepted: 09/10/2022] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND The use of minimally invasive biomarkers (MIBs - physiological biomarkers obtained from minimally invasive sample types) has expanded rapidly in science and medicine over the past several decades. The MIB approach is a methodological strength in the field of human and non-human primate evolutionary biology (HEB). Among humans and our closest relatives, MIBs provide unique opportunities to document phenotypic variation and to operationalize evolutionary hypotheses. AIMS This paper overviews the use of MIBs in HEB. Our objectives are to (1) highlight key research topics which successfully implement MIBs, (2) identify promising yet under-investigated areas of MIB application, and (3) discuss current challenges in MIB research, with suggestions for advancing the field. DISCUSSION AND CONCLUSIONS A range of MIBs are used to investigate focal topics in HEB, including energetics and life history variation/evolution, developmental plasticity, and social status and dominance relationships. Nonetheless, we identify gaps in existing MIB research on traits such as physical growth and gut function that are central to the field. Several challenges remain for HEB research using MIBs, including the need for additional biomarkers and methods of assessment, robust validations, and approaches that are standardized across labs and research groups. Importantly, researchers must provide better support for adaptation and fitness effects in hypothesis testing (e.g., by obtaining complementary measures of energy expenditure, demonstrating redundancy of function, and performing lifetime/longitudinal analyses). We point to continued progress in the use of MIBs in HEB to better understand the past, present, and future of humans and our closest primate relatives.
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Affiliation(s)
- Samuel S. Urlacher
- Department of AnthropologyBaylor UniversityWacoTexasUSA
- Human Evolutionary Biology and Health LabBaylor UniversityWacoTexasUSA
- Child and Brain Development ProgramCIFARTorontoOntarioCanada
| | - Elizabeth Y. Kim
- Human Evolutionary Biology and Health LabBaylor UniversityWacoTexasUSA
- Department of BiologyBaylor UniversityWacoTexasUSA
| | - Tiffany Luan
- Human Evolutionary Biology and Health LabBaylor UniversityWacoTexasUSA
| | - Lauren J. Young
- Human Evolutionary Biology and Health LabBaylor UniversityWacoTexasUSA
| | - Brian Adjetey
- Human Evolutionary Biology and Health LabBaylor UniversityWacoTexasUSA
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15
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Pinacho-Guendulain B, Montiel-Castro AJ, Ramos-Fernández G, Pacheco-López G. Social complexity as a driving force of gut microbiota exchange among conspecific hosts in non-human primates. Front Integr Neurosci 2022; 16:876849. [PMID: 36110388 PMCID: PMC9468716 DOI: 10.3389/fnint.2022.876849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 05/16/2022] [Indexed: 11/13/2022] Open
Abstract
The emergent concept of the social microbiome implies a view of a highly connected biological world, in which microbial interchange across organisms may be influenced by social and ecological connections occurring at different levels of biological organization. We explore this idea reviewing evidence of whether increasing social complexity in primate societies is associated with both higher diversity and greater similarity in the composition of the gut microbiota. By proposing a series of predictions regarding such relationship, we evaluate the existence of a link between gut microbiota and primate social behavior. Overall, we find that enough empirical evidence already supports these predictions. Nonetheless, we conclude that studies with the necessary, sufficient, explicit, and available evidence are still scarce. Therefore, we reflect on the benefit of founding future analyses on the utility of social complexity as a theoretical framework.
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Affiliation(s)
- Braulio Pinacho-Guendulain
- Doctorado en Ciencias Biológicas y de la Salud, Universidad Autónoma Metropolitana (UAM), Ciudad de México, Mexico
| | - Augusto Jacobo Montiel-Castro
- Department of Health Sciences, Metropolitan Autonomous University (UAM), Lerma, Mexico
- *Correspondence: Augusto Jacobo Montiel-Castro,
| | - Gabriel Ramos-Fernández
- Institute for Research on Applied Mathematics and Systems (IIMAS), National Autonomous University of Mexico (UNAM), Mexico City, Mexico
- Center for Complexity Sciences, National Autonomous University of Mexico, Mexico City, Mexico
| | - Gustavo Pacheco-López
- Department of Health Sciences, Metropolitan Autonomous University (UAM), Lerma, Mexico
- Gustavo Pacheco-López,
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16
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Abstract
The gut microbiome has significant effects on healthy aging and aging-related diseases, whether in humans or nonhuman primates. However, little is known about the divergence and convergence of gut microbial diversity between humans and nonhuman primates during aging, which limits their applicability for studying the gut microbiome's role in human health and aging. Here, we performed 16S rRNA gene sequencing analysis for captive rhesus macaques (Macaca mulatta) and compared this data set with other freely available gut microbial data sets containing four human populations (Chinese, Japanese, Italian, and British) and two nonhuman primates (wild lemurs [Lemur catta] and wild chimpanzees [Pan troglodytes]). Based on the consistent V4 region of the 16S rRNA gene, beta diversity analysis suggested significantly separated gut microbial communities associated with host backgrounds of seven host groups, but within each group, significant gut microbial divergences were observed, and indicator bacterial genera were identified as associated with aging. We further discovered six common anti-inflammatory gut bacteria (Prevotellamassilia, Prevotella, Gemmiger, Coprococcus, Faecalibacterium, and Roseburia) that had butyrate-producing potentials suggested by pangenomic analysis and that showed similar dynamic changes in at least two selected host groups during aging, independent of distinct host backgrounds. Finally, we found striking age-related changes in 66 plasma metabolites in macaques. Two highly changed metabolites, hydroxyproline and leucine, enriched in adult macaques were significantly and positively correlated with Prevotella and Prevotellamassilia. Furthermore, genus-level pangenome analysis suggested that those six common indicator bacteria can synthesize leucine and arginine as hydroxyproline and proline precursors in both humans and macaques. IMPORTANCE This study provides the first comprehensive investigation of age patterning of gut microbiota of four human populations and three nonhuman primates and found that Prevotellamassilia, Prevotella, Gemmiger, Coprococcus, Faecalibacterium, and Roseburia may be common antiaging microbial markers in both humans and nonhuman primates due to their potential metabolic capabilities for host health benefits. Our results also provide key support for using macaques as animal models in studies of the gut microbiome's role during human aging.
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17
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Hickmott AJ, Boose KJ, Wakefield ML, Brand CM, Snodgrass JJ, Ting N, White FJ. A comparison of faecal glucocorticoid metabolite concentration and gut microbiota diversity in bonobos ( Pan paniscus). MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 35960548 DOI: 10.1099/mic.0.001226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Sex, age, diet, stress and social environment have all been shown to influence the gut microbiota. In several mammals, including humans, increased stress is related to decreasing gut microbial diversity and may differentially impact specific taxa. Recent evidence from gorillas shows faecal glucocorticoid metabolite concentration (FGMC) did not significantly explain gut microbial diversity, but it was significantly associated with the abundance of the family Anaerolineaceae. These patterns have yet to be examined in other primates, like bonobos (Pan paniscus). We compared FGMC to 16S rRNA amplicons for 202 bonobo faecal samples collected across 5 months to evaluate the impact of stress, measured with FGMC, on the gut microbiota. Alpha diversity measures (Chao's and Shannon's indexes) were not significantly related to FGMC. FGMC explained 0.80 % of the variation in beta diversity for Jensen-Shannon and 1.2% for weighted UniFrac but was not significant for unweighted UniFrac. We found that genus SHD-231, a member of the family Anaerolinaceae had a significant positive relationship with FGMC. These results suggest that bonobos are relatively similar to gorillas in alpha diversity and family Anaerolinaceae responses to FGMC, but different from gorillas in beta diversity. Members of the family Anaerolinaceae may be differentially affected by FGMC across great apes. FGMC appears to be context dependent and may be species-specific for alpha and beta diversity but this study provides an example of consistent change in two African apes. Thus, the relationship between physiological stress and the gut microbiome may be difficult to predict, even among closely related species.
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Affiliation(s)
- Alexana J Hickmott
- Department of Anthropology, University of Oregon, Eugene, OR 97403, USA.,Texas Biomedical Research Institute, San Antonio, TX 78227, USA.,Southwest National Primate Research Center, San Antonio, TX, USA
| | - Klaree J Boose
- Department of Anthropology, University of Oregon, Eugene, OR 97403, USA
| | - Monica L Wakefield
- Sociology, Anthropology, and Philosophy, Northern Kentucky University, Highland Heights, KY 41099, USA
| | - Colin M Brand
- Department of Epidemiology and Biostatistics, University of California, San Francisco, USA.,Bakar Computational Health Sciences Institute, University of California, San Francisco, USA
| | - J Josh Snodgrass
- Department of Anthropology, University of Oregon, Eugene, OR 97403, USA
| | - Nelson Ting
- Department of Anthropology, University of Oregon, Eugene, OR 97403, USA.,Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
| | - Frances J White
- Department of Anthropology, University of Oregon, Eugene, OR 97403, USA
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18
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Sadoughi B, Schneider D, Daniel R, Schülke O, Ostner J. Aging gut microbiota of wild macaques are equally diverse, less stable, but progressively personalized. MICROBIOME 2022; 10:95. [PMID: 35718778 PMCID: PMC9206754 DOI: 10.1186/s40168-022-01283-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 04/21/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Pronounced heterogeneity of age trajectories has been identified as a hallmark of the gut microbiota in humans and has been explained by marked changes in lifestyle and health condition. Comparatively, age-related personalization of microbiota is understudied in natural systems limiting our comprehension of patterns observed in humans from ecological and evolutionary perspectives. RESULTS Here, we tested age-related changes in the diversity, stability, and composition of the gut bacterial community using 16S rRNA gene sequencing with dense repeated sampling over three seasons in a cross-sectional age sample of adult female Assamese macaques (Macaca assamensis) living in their natural forest habitat. Gut bacterial composition exhibited a personal signature which became less stable as individuals aged. This lack of stability was not explained by differences in microbiota diversity but rather linked to an increase in the relative abundance of rare bacterial taxa. The lack of age-related changes in core taxa or convergence with age to a common state of the community hampered predicting gut bacterial composition of aged individuals. On the contrary, we found increasing personalization of the gut bacterial composition with age, indicating that composition in older individuals was increasingly divergent from the rest of the population. Reduced direct transmission of bacteria resulting from decreasing social activity may contribute to, but not be sufficient to explain, increasing personalization with age. CONCLUSIONS Together, our results challenge the assumption of a constant microbiota through adult life in a wild primate. Within the limits of this study, the fact that increasing personalization of the aging microbiota is not restricted to humans suggests the underlying process to be evolved instead of provoked only by modern lifestyle of and health care for the elderly. Video abstract.
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Affiliation(s)
- Baptiste Sadoughi
- Department of Behavioral Ecology, Johann-Friedrich-Blumenbach Institute for Zoology and Anthropology, Georg-August-University Göttingen, Kellnerweg 6, D-37077, Göttingen, Germany.
- Research Group Primate Social Evolution, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany.
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Germany.
- Leibniz ScienceCampus Primate Cognition, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany.
| | - Dominik Schneider
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Germany
| | - Rolf Daniel
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Germany
| | - Oliver Schülke
- Department of Behavioral Ecology, Johann-Friedrich-Blumenbach Institute for Zoology and Anthropology, Georg-August-University Göttingen, Kellnerweg 6, D-37077, Göttingen, Germany
- Research Group Primate Social Evolution, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
- Leibniz ScienceCampus Primate Cognition, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
| | - Julia Ostner
- Department of Behavioral Ecology, Johann-Friedrich-Blumenbach Institute for Zoology and Anthropology, Georg-August-University Göttingen, Kellnerweg 6, D-37077, Göttingen, Germany
- Research Group Primate Social Evolution, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
- Leibniz ScienceCampus Primate Cognition, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
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19
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Videvall E. Personalized microbiomes in social baboons. Nat Ecol Evol 2022; 6:849-850. [PMID: 35654894 DOI: 10.1038/s41559-022-01769-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Elin Videvall
- Department of Ecology, Evolution and Organismal Biology, Brown University, Providence, RI, USA. .,Institute at Brown for Environment and Society, Brown University, Providence, RI, USA. .,Animal Ecology, Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden.
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20
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Marsh KJ, Raulo AM, Brouard M, Troitsky T, English HM, Allen B, Raval R, Venkatesan S, Pedersen AB, Webster JP, Knowles SCL. Synchronous Seasonality in the Gut Microbiota of Wild Mouse Populations. Front Microbiol 2022; 13:809735. [PMID: 35547129 PMCID: PMC9083407 DOI: 10.3389/fmicb.2022.809735] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 03/08/2022] [Indexed: 12/03/2022] Open
Abstract
The gut microbiome performs many important functions in mammalian hosts, with community composition shaping its functional role. However, the factors that drive individual microbiota variation in wild animals and to what extent these are predictable or idiosyncratic across populations remains poorly understood. Here, we use a multi-population dataset from a common rodent species (the wood mouse, Apodemus sylvaticus), to test whether a consistent “core” gut microbiota is identifiable in this species, and to what extent the predictors of microbiota variation are consistent across populations. Between 2014 and 2018 we used capture-mark-recapture and 16S rRNA profiling to intensively monitor two wild wood mouse populations and their gut microbiota, as well as characterising the microbiota from a laboratory-housed colony of the same species. Although the microbiota was broadly similar at high taxonomic levels, the two wild populations did not share a single bacterial amplicon sequence variant (ASV), despite being only 50km apart. Meanwhile, the laboratory-housed colony shared many ASVs with one of the wild populations from which it is thought to have been founded decades ago. Despite not sharing any ASVs, the two wild populations shared a phylogenetically more similar microbiota than either did with the colony, and the factors predicting compositional variation in each wild population were remarkably similar. We identified a strong and consistent pattern of seasonal microbiota restructuring that occurred at both sites, in all years, and within individual mice. While the microbiota was highly individualised, some seasonal convergence occurred in late winter/early spring. These findings reveal highly repeatable seasonal gut microbiota dynamics in multiple populations of this species, despite different taxa being involved. This provides a platform for future work to understand the drivers and functional implications of such predictable seasonal microbiome restructuring, including whether it might provide the host with adaptive seasonal phenotypic plasticity.
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Affiliation(s)
- Kirsty J Marsh
- Department of Pathobiology and Population Sciences, The Royal Veterinary College, University of London, Hatfield, United Kingdom.,College of Life and Environmental Sciences, University of Exeter, Cornwall, United Kingdom
| | - Aura M Raulo
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Marc Brouard
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Tanya Troitsky
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Holly M English
- Department of Pathobiology and Population Sciences, The Royal Veterinary College, University of London, Hatfield, United Kingdom.,Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Bryony Allen
- Department of Life Sciences, Imperial College London, Silwood Park, Ascot, United Kingdom
| | - Rohan Raval
- Department of Life Sciences, Imperial College London, Silwood Park, Ascot, United Kingdom
| | - Saudamini Venkatesan
- Institute of Evolutionary Biology, School of Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Amy B Pedersen
- Institute of Evolutionary Biology, School of Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Joanne P Webster
- Department of Pathobiology and Population Sciences, The Royal Veterinary College, University of London, Hatfield, United Kingdom
| | - Sarah C L Knowles
- Department of Pathobiology and Population Sciences, The Royal Veterinary College, University of London, Hatfield, United Kingdom.,Department of Zoology, University of Oxford, Oxford, United Kingdom
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21
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Bornbusch SL, Greene LK, Rahobilalaina S, Calkins S, Rothman RS, Clarke TA, LaFleur M, Drea CM. Gut microbiota of ring-tailed lemurs (Lemur catta) vary across natural and captive populations and correlate with environmental microbiota. Anim Microbiome 2022; 4:29. [PMID: 35484581 PMCID: PMC9052671 DOI: 10.1186/s42523-022-00176-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 03/29/2022] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Inter-population variation in host-associated microbiota reflects differences in the hosts' environments, but this characterization is typically based on studies comparing few populations. The diversity of natural habitats and captivity conditions occupied by any given host species has not been captured in these comparisons. Moreover, intraspecific variation in gut microbiota, generally attributed to diet, may also stem from differential acquisition of environmental microbes-an understudied mechanism by which host microbiomes are directly shaped by environmental microbes. To more comprehensively characterize gut microbiota in an ecologically flexible host, the ring-tailed lemur (Lemur catta; n = 209), while also investigating the role of environmental acquisition, we used 16S rRNA sequencing of lemur gut and soil microbiota sampled from up to 13 settings, eight in the wilderness of Madagascar and five in captivity in Madagascar or the U.S. Based on matched fecal and soil samples, we used microbial source tracking to examine covariation between the two types of consortia. RESULTS The diversity of lemur gut microbes varied markedly within and between settings. Microbial diversity was not consistently greater in wild than in captive lemurs, indicating that this metric is not necessarily an indicator of host habitat or environmental condition. Variation in microbial composition was inconsistent both with a single, representative gut community for wild conspecifics and with a universal 'signal of captivity' that homogenizes the gut consortia of captive animals. Despite the similar, commercial diets of captive lemurs on both continents, lemur gut microbiomes within Madagascar were compositionally most similar, suggesting that non-dietary factors govern some of the variability. In particular, soil microbial communities varied across geographic locations, with the few samples from different continents being the most distinct, and there was significant and context-specific covariation between gut and soil microbiota. CONCLUSIONS As one of the broadest, single-species investigations of primate microbiota, our study highlights that gut consortia are sensitive to multiple scales of environmental differences. This finding begs a reevaluation of the simple 'captive vs. wild' dichotomy. Beyond the important implications for animal care, health, and conservation, our finding that environmental acquisition may mediate aspects of host-associated consortia further expands the framework for how host-associated and environmental microbes interact across different microbial landscapes.
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Affiliation(s)
- Sally L. Bornbusch
- Department of Evolutionary Anthropology, Duke University, Durham, NC USA
| | | | | | - Samantha Calkins
- Department of Psychology, Program in Animal Behavior and Conservation, Hunter College, New York, NY USA
| | - Ryan S. Rothman
- Institute for the Conservation of Tropical Environments, Interdepartmental Doctoral Program in Anthropological Sciences, Stony Brook University, Stony Brook, NY USA
| | - Tara A. Clarke
- Department of Sociology and Anthropology, North Carolina State University, Raleigh, NC USA
| | - Marni LaFleur
- Department of Anthropology, University of San Diego, 5998 Alcala Park, San Diego, CA USA
| | - Christine M. Drea
- Department of Evolutionary Anthropology, Duke University, Durham, NC USA
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22
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Donohue ME, Rowe AK, Kowalewski E, Hert ZL, Karrick CE, Randriamanandaza LJ, Zakamanana F, Nomenjanahary S, Andriamalala RY, Everson KM, Law AD, Moe L, Wright PC, Weisrock DW. Significant effects of host dietary guild and phylogeny in wild lemur gut microbiomes. ISME COMMUNICATIONS 2022; 2:33. [PMID: 37938265 PMCID: PMC9723590 DOI: 10.1038/s43705-022-00115-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 02/23/2022] [Accepted: 03/07/2022] [Indexed: 04/27/2023]
Abstract
Mammals harbor diverse gut microbiomes (GMs) that perform critical functions for host health and fitness. Identifying factors associated with GM variation can help illuminate the role of microbial symbionts in mediating host ecological interactions and evolutionary processes, including diversification and adaptation. Many mammals demonstrate phylosymbiosis-a pattern in which more closely-related species harbor more similar GMs-while others show overwhelming influences of diet and habitat. Here, we generated 16S rRNA sequence data from fecal samples of 15 species of wild lemurs across southern Madagascar to (1) test a hypothesis of phylosymbiosis, and (2) test trait correlations between dietary guild, habitat, and GM diversity. Our results provide strong evidence of phylosymbiosis, though some closely-related species with substantial ecological niche overlap exhibited greater GM similarity than expected under Brownian motion. Phylogenetic regressions also showed a significant correlation between dietary guild and UniFrac diversity, but not Bray-Curtis or Jaccard. This discrepancy between beta diversity metrics suggests that older microbial clades have stronger associations with diet than younger clades, as UniFrac weights older clades more heavily. We conclude that GM diversity is predominantly shaped by host phylogeny, and that microbes associated with diet were likely acquired before evolutionary radiations within the lemur families examined.
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Affiliation(s)
- Mariah E Donohue
- Department of Biology, University of Kentucky, Lexington, KY, USA.
| | - Amanda K Rowe
- Interdepartmental Doctoral Program in Anthropological Sciences, Stony Brook University, Stony Brook, New York, NY, USA
| | - Eric Kowalewski
- Department of Biology, University of Kentucky, Lexington, KY, USA
| | - Zoe L Hert
- Department of Biology, University of Kentucky, Lexington, KY, USA
| | - Carly E Karrick
- Department of Biology, University of Kentucky, Lexington, KY, USA
| | | | | | - Stela Nomenjanahary
- Anthropobiologie et Développement Durable, Université Antananarivo, Antananarivo, Madagascar
| | - Rostant Y Andriamalala
- Anthropobiologie et Développement Durable, Université Antananarivo, Antananarivo, Madagascar
| | | | - Audrey D Law
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, USA
| | - Luke Moe
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, USA
| | - Patricia C Wright
- Centre ValBio Research Station, Ranomafana, Madagascar
- Department of Anthropology, Stony Brook University, Stony Brook, New York, NY, USA
| | - David W Weisrock
- Department of Biology, University of Kentucky, Lexington, KY, USA
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23
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Rudolph K, Schneider D, Fichtel C, Daniel R, Heistermann M, Kappeler PM. Drivers of gut microbiome variation within and between groups of a wild Malagasy primate. MICROBIOME 2022; 10:28. [PMID: 35139921 PMCID: PMC8827170 DOI: 10.1186/s40168-021-01223-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 12/20/2021] [Indexed: 05/12/2023]
Abstract
BACKGROUND Various aspects of sociality can benefit individuals' health. The host social environment and its relative contributions to the host-microbiome relationship have emerged as key topics in microbial research. Yet, understanding the mechanisms that lead to structural variation in the social microbiome, the collective microbial metacommunity of an animal's social network, remains difficult since multiple processes operate simultaneously within and among animal social networks. Here, we examined the potential drivers of the convergence of the gut microbiome on multiple scales among and within seven neighbouring groups of wild Verreaux's sifakas (Propithecus verreauxi) - a folivorous primate of Madagascar. RESULTS Over four field seasons, we collected 519 faecal samples of 41 animals and determined gut communities via 16S and 18S rRNA gene amplicon analyses. First, we examined whether group members share more similar gut microbiota and if diet, home range overlap, or habitat similarity drive between-group variation in gut communities, accounting for seasonality. Next, we examined within-group variation in gut microbiota by examining the potential effects of social contact rates, male rank, and maternal relatedness. To explore the host intrinsic effects on the gut community structure, we investigated age, sex, faecal glucocorticoid metabolites, and female reproductive state. We found that group members share more similar gut microbiota and differ in alpha diversity, while none of the environmental predictors explained the patterns of between-group variation. Maternal relatedness played an important role in within-group microbial homogeneity and may also explain why adult group members shared the least similar gut microbiota. Also, dominant males differed in their bacterial composition from their group mates, which might be driven by rank-related differences in physiology and scent-marking behaviours. Links to sex, female reproductive state, or faecal glucocorticoid metabolites were not detected. CONCLUSIONS Environmental factors define the general set-up of population-specific gut microbiota, but intrinsic and social factors have a stronger impact on gut microbiome variation in this primate species. Video abstract.
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Affiliation(s)
- Katja Rudolph
- Behavioral Ecology & Sociobiology Unit, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, 37077, Göttingen, Germany.
- Department of Sociobiology/Anthropology, Johann-Friedrich-Blumenbach Institute of Zoology and Anthropology, Georg-August University Göttingen, Kellnerweg 6, 37077, Göttingen, Germany.
- Leibniz Science Campus "Primate Cognition", Göttingen, Germany.
| | - Dominik Schneider
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University Göttingen, Grisebachstraße 8, 37077, Göttingen, Germany
| | - Claudia Fichtel
- Behavioral Ecology & Sociobiology Unit, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, 37077, Göttingen, Germany
- Leibniz Science Campus "Primate Cognition", Göttingen, Germany
| | - Rolf Daniel
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University Göttingen, Grisebachstraße 8, 37077, Göttingen, Germany
| | - Michael Heistermann
- Endocrinology Laboratory, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, 37077, Göttingen, Germany
| | - Peter M Kappeler
- Behavioral Ecology & Sociobiology Unit, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, 37077, Göttingen, Germany
- Department of Sociobiology/Anthropology, Johann-Friedrich-Blumenbach Institute of Zoology and Anthropology, Georg-August University Göttingen, Kellnerweg 6, 37077, Göttingen, Germany
- Leibniz Science Campus "Primate Cognition", Göttingen, Germany
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24
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Pannoni SB, Proffitt KM, Holben WE. Non-invasive monitoring of multiple wildlife health factors by fecal microbiome analysis. Ecol Evol 2022; 12:e8564. [PMID: 35154651 PMCID: PMC8826075 DOI: 10.1002/ece3.8564] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 12/16/2021] [Accepted: 12/23/2021] [Indexed: 01/04/2023] Open
Abstract
Fecal microbial biomarkers represent a less invasive alternative for acquiring information on wildlife populations than many traditional sampling methodologies. Our goal was to evaluate linkages between fecal microbiome communities in Rocky Mountain elk (Cervus canadensis) and four host factors including sex, age, population, and physical condition (body-fat). We paired a feature-selection algorithm with an LDA-classifier trained on elk differential bacterial abundance (16S-rRNA amplicon survey) to predict host health factors from 104 elk microbiomes across four elk populations. We validated the accuracy of the various classifier predictions with leave-one-out cross-validation using known measurements. We demonstrate that the elk fecal microbiome can predict the four host factors tested. Our results show that elk microbiomes respond to both the strong extrinsic factor of biogeography and simultaneously occurring, but more subtle, intrinsic forces of individual body-fat, sex, and age-class. Thus, we have developed and described herein a generalizable approach to disentangle microbiome responses attributed to multiple host factors of varying strength from the same bacterial sequence data set. Wildlife conservation and management presents many challenges, but we demonstrate that non-invasive microbiome surveys from scat samples can provide alternative options for wildlife population monitoring. We believe that, with further validation, this method could be broadly applicable in other species and potentially predict other measurements. Our study can help guide the future development of microbiome-based monitoring of wildlife populations and supports hypothetical expectations found in host-microbiome theory.
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Affiliation(s)
- Samuel B. Pannoni
- Franke College of Forestry and ConservationUniversity of MontanaMissoulaMontanaUSA
| | | | - William E. Holben
- Cellular, Molecular and Microbial Biology ProgramUniversity of MontanaMissoulaMontanaUSA
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25
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Distinct gut microbiomes in two polar bear subpopulations inhabiting different sea ice ecoregions. Sci Rep 2022; 12:522. [PMID: 35017585 PMCID: PMC8752607 DOI: 10.1038/s41598-021-04340-2] [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] [Received: 07/29/2021] [Accepted: 12/13/2021] [Indexed: 11/09/2022] Open
Abstract
Gut microbiomes were analyzed by 16S rRNA gene metabarcoding for polar bears (Ursus maritimus) from the southern Beaufort Sea (SB), where sea ice loss has led to increased use of land-based food resources by bears, and from East Greenland (EG), where persistent sea ice has allowed hunting of ice-associated prey nearly year-round. SB polar bears showed a higher number of total (940 vs. 742) and unique (387 vs. 189) amplicon sequence variants and higher inter-individual variation compared to EG polar bears. Gut microbiome composition differed significantly between the two subpopulations and among sex/age classes, likely driven by diet variation and ontogenetic shifts in the gut microbiome. Dietary tracer analysis using fatty acid signatures for SB polar bears showed that diet explained more intrapopulation variation in gut microbiome composition and diversity than other tested variables, i.e., sex/age class, body condition, and capture year. Substantial differences in the SB gut microbiome relative to EG polar bears, and associations between SB gut microbiome and diet, suggest that the shifting foraging habits of SB polar bears tied to sea ice loss may be altering their gut microbiome, with potential consequences for nutrition and physiology.
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26
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McManus N, Holmes SM, Louis EE, Johnson SE, Baden AL, Amato KR. The gut microbiome as an indicator of habitat disturbance in a Critically Endangered lemur. BMC Ecol Evol 2021; 21:222. [PMID: 34915861 PMCID: PMC8680155 DOI: 10.1186/s12862-021-01945-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 11/23/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Habitat disturbance affects the biology and health of animals globally. Understanding the factors that contribute to the differential responses of animals to habitat disturbance is critical for conservation. The gut microbiota represents a potential pathway through which host responses to habitat disturbance might be mediated. However, a lack of quantitative environmental data in many gut microbiome (GM) studies of wild animals limits our ability to pinpoint mechanisms through which habitat disturbance affects the GM. Here, we examine the impact of anthropogenic habitat disturbance on the diet and GM of the Critically Endangered black-and-white ruffed lemur (Varecia variegata editorum). We collected fecal samples and behavioral data from Varecia occupying habitats qualitatively categorized as primary forest, moderately disturbed forest, and heavily disturbed forest. RESULTS Varecia diet and GM composition differed substantially across sites. Dietary richness predicted GM richness across sites, and overall GM composition was strongly correlated to diet composition. Additionally, the consumption of three specific food items positively correlated to the relative abundances of five microbial strains and one microbial genus across sites. However, diet did not explain all of the GM variation in our dataset, and differences in the GM were detected that were not correlated with diet, as measured. CONCLUSIONS Our data suggest that diet is an important influence on the Varecia GM across habitats and thus could be leveraged in novel conservation efforts in the future. However, other factors such as contact with humans should also be accounted for. Overall, we demonstrate that quantitative data describing host habitats must be paired with GM data to better target the specific mechanisms through which environmental change affects the GM.
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Affiliation(s)
- Nicolette McManus
- Department of Anthropology, Northwestern University, Evanston, IL, 60208, USA
| | - Sheila M Holmes
- Department of Anthropology and Archaeology, University of Calgary, Calgary, AB, T2N 1N4, Canada
- Department of Wildlife, Fish and Environmental Studies, Swedish University of Agricultural Sciences, 90183, Umeå, Sweden
| | - Edward E Louis
- Grewcock Center for Conservation and Research, Omaha's Henry Doorly Zoo, Omaha, NE, 68107, USA
| | - Steig E Johnson
- Department of Anthropology and Archaeology, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Andrea L Baden
- Department of Anthropology, Hunter College of the City University of New York, New York, NY, 10065, USA.
- Department of Anthropology, The Graduate Center of the City University of New York, New York, NY, USA.
- The New York Consortium in Evolutionary Primatology (NYCEP), New York, USA.
| | - Katherine R Amato
- Department of Anthropology, Northwestern University, Evanston, IL, 60208, USA.
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27
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Sun G, Yang X, Wei Q, Xia T, Zhang L, Wang X, Zhang H. Characterization of gut microbiota in captive Himalayan tahr (Hemitragus jemlahicus) and the limited effect of sex on intestinal microorganisms of tahrs. THE EUROPEAN ZOOLOGICAL JOURNAL 2021. [DOI: 10.1080/24750263.2021.1994045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Affiliation(s)
- G. Sun
- College of Life Science, Qufu Normal University, Qufu, China
| | - X. Yang
- College of Life Science, Qufu Normal University, Qufu, China
| | - Q. Wei
- College of Life Science, Qufu Normal University, Qufu, China
| | - T. Xia
- College of Life Science, Qufu Normal University, Qufu, China
| | - L. Zhang
- College of Life Science, Qufu Normal University, Qufu, China
| | - X. Wang
- College of Life Science, Qufu Normal University, Qufu, China
| | - H. Zhang
- College of Life Science, Qufu Normal University, Qufu, China
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28
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Cui Z, Holmes AJ, Zhang W, Hu D, Shao Q, Wang Z, Lu J, Raubenheimer D. Seasonal diet and microbiome shifts in wild rhesus macaques are better correlated at the level of nutrient components than food items. Integr Zool 2021; 17:1147-1161. [PMID: 34767280 DOI: 10.1111/1749-4877.12601] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Food supply is one of the major drivers of animal behavior, and the gut microbiome is an important mediator between food supply and its effects on physiology. However, predicting the outcome of diet change on microbiome and consequences for the animal has proven extremely challenging. We propose this reflects processes occurring at different scales. Inadequate accounting for the multi-level complexity of nutrition (nutrients, foods, diets) obscures the diet influence on microbiome and subsequently animal. Here, we present a detailed year-round, multi-level analysis of diet and microbiome changes in a wild population of a temperate primate, the rhesus macaque (Macaca mulatta). Total daily food and nutrient intake of 6 male and 6 female macaques was monitored in each of the 4 seasons (total 120 days observations). For each individual, we found significant variation in the microbiome between all 4 seasons. This response was more strongly correlated with changes in macronutrient intake than with food items and much of the response could be explained at the level of 6 ecological guilds-sets of taxa sharing similar responses to nutrient intake. We conclude that study of diet, microbiome, and animal performance in ecology will more effectively identify patterns if diet is recorded at the level of nutrient intake. Although microbiome response to diet does show variation in species-level taxa in response to food items, there is greater commonality in response at the level of guilds. A goal for microbiome researchers should be to identify genes encoding microbial attributes that can define such guilds.
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Affiliation(s)
- Zhenwei Cui
- Centre for Nutritional Ecology, Centre for Sport Nutrition and Health, Zhengzhou University, Zhengzhou, China.,School of Life Sciences, Institute of Biodiversity and Ecology, Zhengzhou University, Zhengzhou, China.,School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Andrew J Holmes
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Wenjuan Zhang
- School of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Dalong Hu
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Qi Shao
- School of Life Sciences, Institute of Biodiversity and Ecology, Zhengzhou University, Zhengzhou, China
| | - Zhenlong Wang
- School of Life Sciences, Institute of Biodiversity and Ecology, Zhengzhou University, Zhengzhou, China
| | - Jiqi Lu
- School of Life Sciences, Institute of Biodiversity and Ecology, Zhengzhou University, Zhengzhou, China
| | - David Raubenheimer
- Centre for Nutritional Ecology, Centre for Sport Nutrition and Health, Zhengzhou University, Zhengzhou, China.,Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
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29
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Leech T, McDowall L, Hopkins KP, Sait SM, Harrison XA, Bretman A. Social environment drives sex and age-specific variation in Drosophila melanogaster microbiome composition and predicted function. Mol Ecol 2021; 30:5831-5843. [PMID: 34494339 DOI: 10.1111/mec.16149] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Revised: 08/05/2021] [Accepted: 08/20/2021] [Indexed: 12/25/2022]
Abstract
Social environments influence multiple traits of individuals including immunity, stress and ageing, often in sex-specific ways. The composition of the microbiome (the assemblage of symbiotic microorganisms within a host) is determined by environmental factors and the host's immune, endocrine and neural systems. The social environment could alter host microbiomes extrinsically by affecting transmission between individuals, probably promoting homogeneity in the microbiome of social partners. Alternatively, intrinsic effects arising from interactions between the microbiome and host physiology (the microbiota-gut-brain axis) could translate social stress into dysbiotic microbiomes, with consequences for host health. We investigated how manipulating social environments during larval and adult life-stages altered the microbiome composition of Drosophila melanogaster fruit flies. We used social contexts that particularly alter the development and lifespan of males, predicting that any intrinsic social effects on the microbiome would therefore be sex-specific. The presence of adult males during the larval stage significantly altered the microbiome of pupae of both sexes. In adults, same-sex grouping increased bacterial diversity in both sexes. Importantly, the microbiome community structure of males was more sensitive to social contact at older ages, an effect partially mitigated by housing focal males with young rather than coaged groups. Functional analyses suggest that these microbiome changes impact ageing and immune responses. This is consistent with the hypothesis that the substantial effects of the social environment on individual health are mediated through intrinsic effects on the microbiome, and provides a model for understanding the mechanistic basis of the microbiota-gut-brain axis.
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Affiliation(s)
- Thomas Leech
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK.,Max Planck Institute for Biology of Ageing, Köln, Germany
| | - Laurin McDowall
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK.,School of Life Sciences, University of Dundee, Dundee, UK
| | - Kevin P Hopkins
- Institute of Zoology, Zoological Society of London, London, UK
| | - Steven M Sait
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Xavier A Harrison
- Institute of Zoology, Zoological Society of London, London, UK.,Centre for Ecology & Conservation, University of Exeter, Penryn, UK
| | - Amanda Bretman
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
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30
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Correa F, Torti V, Spiezio C, Checcucci A, Modesto M, Borruso L, Cavani L, Mimmo T, Cesco S, Luise D, Randrianarison RM, Gamba M, Rarojoson NJ, Sanguinetti M, Di Vito M, Bugli F, Mattarelli P, Trevisi P, Giacoma C, Sandri C. Disentangling the Possible Drivers of Indri indri Microbiome: A Threatened Lemur Species of Madagascar. Front Microbiol 2021; 12:668274. [PMID: 34421838 PMCID: PMC8378179 DOI: 10.3389/fmicb.2021.668274] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 07/08/2021] [Indexed: 01/04/2023] Open
Abstract
Research on the gut microbiome may help with increasing our understanding of primate health with species' ecology, evolution, and behavior. In particular, microbiome-related information has the potential to clarify ecology issues, providing knowledge in support of wild primates conservation and their associated habitats. Indri (Indri indri) is the largest extant living lemur of Madagascar. This species is classified as "critically endangered" by the IUCN Red List of Threatened Species, representing one of the world's 25 most endangered primates. Indris diet is mainly folivorous, but these primates frequently and voluntarily engage in geophagy. Indris have never been successfully bred under human care, suggesting that some behavioral and/or ecological factors are still not considered from the ex situ conservation protocols. Here, we explored gut microbiome composition of 18 indris belonging to 5 different family groups. The most represented phyla were Proteobacteria 40.1 ± 9.5%, Bacteroidetes 28.7 ± 2.8%, Synergistetes 16.7 ± 4.5%, and Firmicutes 11.1 ± 1.9%. Further, our results revealed that bacterial alpha and beta diversity were influenced by indri family group and sex. In addition, we investigated the chemical composition of geophagic soil to explore the possible ecological value of soil as a nutrient supply. The quite acidic pH and high levels of secondary oxide-hydroxides of the soils could play a role in the folivorous diet's gut detoxification activity. In addition, the high contents of iron and manganese found the soils could act as micronutrients in the indris' diet. Nevertheless, the concentration of a few elements (i.e., calcium, sulfur, boron, nickel, sodium, and chromium) was higher in non-geophagic than in geophagic soils. In conclusion, the data presented herein provide a baseline for outlining some possible drivers responsible for the gut microbiome diversity in indris, thus laying the foundations for developing further strategies involved in indris' conservation.
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Affiliation(s)
- Federico Correa
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Valeria Torti
- Department of Life Sciences and Systems Biology, University of Torino, Turin, Italy
| | - Caterina Spiezio
- Department of Animal Health Care and Management, Parco Natura Viva – Garda Zoological Park, Verona, Italy
| | - Alice Checcucci
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Monica Modesto
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Luigimaria Borruso
- Faculty of Science and Technology, Free University of Bolzano-Bozen, Bolzano, Italy
| | - Luciano Cavani
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Tanja Mimmo
- Faculty of Science and Technology, Free University of Bolzano-Bozen, Bolzano, Italy
| | - Stefano Cesco
- Faculty of Science and Technology, Free University of Bolzano-Bozen, Bolzano, Italy
| | - Diana Luise
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Rose M. Randrianarison
- Groupe d’Étude et de Recherche sur les Primates de Madagascar, Antananarivo, Madagascar
- Mention d’Anthropobiologie et de Deìveloppement Durable, Université de Antananarivo, Antananarivo, Madagascar
| | - Marco Gamba
- Department of Life Sciences and Systems Biology, University of Torino, Turin, Italy
| | | | - Maurizio Sanguinetti
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Rome, Italy
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Maura Di Vito
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Francesca Bugli
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Rome, Italy
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Paola Mattarelli
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Paolo Trevisi
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Cristina Giacoma
- Department of Life Sciences and Systems Biology, University of Torino, Turin, Italy
| | - Camillo Sandri
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
- Department of Animal Health Care and Management, Parco Natura Viva – Garda Zoological Park, Verona, Italy
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31
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Grieneisen L, Dasari M, Gould TJ, Björk JR, Grenier JC, Yotova V, Jansen D, Gottel N, Gordon JB, Learn NH, Gesquiere LR, Wango TL, Mututua RS, Warutere JK, Siodi L, Gilbert JA, Barreiro LB, Alberts SC, Tung J, Archie EA, Blekhman R. Gut microbiome heritability is nearly universal but environmentally contingent. Science 2021; 373:181-186. [PMID: 34244407 DOI: 10.1126/science.aba5483] [Citation(s) in RCA: 93] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 01/25/2021] [Accepted: 05/17/2021] [Indexed: 12/31/2022]
Abstract
Relatives have more similar gut microbiomes than nonrelatives, but the degree to which this similarity results from shared genotypes versus shared environments has been controversial. Here, we leveraged 16,234 gut microbiome profiles, collected over 14 years from 585 wild baboons, to reveal that host genetic effects on the gut microbiome are nearly universal. Controlling for diet, age, and socioecological variation, 97% of microbiome phenotypes were significantly heritable, including several reported as heritable in humans. Heritability was typically low (mean = 0.068) but was systematically greater in the dry season, with low diet diversity, and in older hosts. We show that longitudinal profiles and large sample sizes are crucial to quantifying microbiome heritability, and indicate scope for selection on microbiome characteristics as a host phenotype.
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Affiliation(s)
- Laura Grieneisen
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Mauna Dasari
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Trevor J Gould
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Johannes R Björk
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Jean-Christophe Grenier
- Department of Genetics, CHU Sainte Justine Research Center, Montréal, Quebec H3T 1C5, Canada.,Research Center, Montreal Heart Institute, Montréal, Quebec H1T 1C8, Canada
| | - Vania Yotova
- Department of Genetics, CHU Sainte Justine Research Center, Montréal, Quebec H3T 1C5, Canada
| | - David Jansen
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Neil Gottel
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093
| | - Jacob B Gordon
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Niki H Learn
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
| | | | - Tim L Wango
- Amboseli Baboon Research Project, Amboseli National Park, Kenya.,The Department of Veterinary Anatomy and Animal Physiology, University of Nairobi, Kenya
| | | | | | - Long'ida Siodi
- Amboseli Baboon Research Project, Amboseli National Park, Kenya
| | - Jack A Gilbert
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093
| | - Luis B Barreiro
- Department of Genetics, CHU Sainte Justine Research Center, Montréal, Quebec H3T 1C5, Canada.,Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Susan C Alberts
- Department of Biology, Duke University, Durham, NC 27708, USA.,Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA.,Duke Population Research Institute, Duke University, Durham, NC 27708, USA
| | - Jenny Tung
- Department of Biology, Duke University, Durham, NC 27708, USA. .,Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA.,Duke Population Research Institute, Duke University, Durham, NC 27708, USA.,Canadian Institute for Advanced Research, Toronto, Ontario M5G 1M1, Canada
| | - Elizabeth A Archie
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA.
| | - Ran Blekhman
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA. .,Department of Ecology, Evolution, and Behavior, University of Minnesota, Minneapolis, MN 55455, USA
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32
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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: 68] [Impact Index Per Article: 22.7] [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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33
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Janiak MC, Montague MJ, Villamil CI, Stock MK, Trujillo AE, DePasquale AN, Orkin JD, Bauman Surratt SE, Gonzalez O, Platt ML, Martínez MI, Antón SC, Dominguez-Bello MG, Melin AD, Higham JP. Age and sex-associated variation in the multi-site microbiome of an entire social group of free-ranging rhesus macaques. MICROBIOME 2021; 9:68. [PMID: 33752735 PMCID: PMC7986251 DOI: 10.1186/s40168-021-01009-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 02/02/2021] [Indexed: 05/07/2023]
Abstract
BACKGROUND An individual's microbiome changes over the course of its lifetime, especially during infancy, and again in old age. Confounding factors such as diet and healthcare make it difficult to disentangle the interactions between age, health, and microbial changes in humans. Animal models present an excellent opportunity to study age- and sex-linked variation in the microbiome, but captivity is known to influence animal microbial abundance and composition, while studies of free-ranging animals are typically limited to studies of the fecal microbiome using samples collected non-invasively. Here, we analyze a large dataset of oral, rectal, and genital swabs collected from 105 free-ranging rhesus macaques (Macaca mulatta, aged 1 month-26 years), comprising one entire social group, from the island of Cayo Santiago, Puerto Rico. We sequenced 16S V4 rRNA amplicons for all samples. RESULTS Infant gut microbial communities had significantly higher relative abundances of Bifidobacterium and Bacteroides and lower abundances of Ruminococcus, Fibrobacter, and Treponema compared to older age groups, consistent with a diet high in milk rather than solid foods. The genital microbiome varied widely between males and females in beta-diversity, taxonomic composition, and predicted functional profiles. Interestingly, only penile, but not vaginal, microbiomes exhibited distinct age-related changes in microbial beta-diversity, taxonomic composition, and predicted functions. Oral microbiome composition was associated with age, and was most distinctive between infants and other age classes. CONCLUSIONS Across all three body regions, with notable exceptions in the penile microbiome, while infants were distinctly different from other age groups, microbiomes of adults were relatively invariant, even in advanced age. While vaginal microbiomes were exceptionally stable, penile microbiomes were quite variable, especially at the onset of reproductive age. Relative invariance among adults, including elderly individuals, is contrary to findings in humans and mice. We discuss potential explanations for this observation, including that age-related microbiome variation seen in humans may be related to changes in diet and lifestyle. Video abstract.
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Affiliation(s)
- Mareike C Janiak
- Department of Anthropology and Archaeology, University of Calgary, Alberta, Canada.
- Alberta Children's Hospital Research Institute, Alberta, Canada.
- Department of Anthropology, New York University, New York, USA.
- School of Science, Engineering and Environment, University of Salford, Salford, UK.
| | - Michael J Montague
- Department of Neuroscience, University of Pennsylvania, Philadelphia, PA, USA
| | - Catalina I Villamil
- School of Chiropractic, Universidad Central del Caribe, Bayamón, Puerto Rico
| | - Michala K Stock
- Department of Sociology and Anthropology, Metropolitan State University of Denver, Denver, CO, USA
| | - Amber E Trujillo
- Department of Anthropology, New York University, New York, USA
- New York Consortium in Evolutionary Primatology, New York, NY, USA
| | - Allegra N DePasquale
- Department of Anthropology and Archaeology, University of Calgary, Alberta, Canada
| | - Joseph D Orkin
- Institut de Biologia Evolutiva, Universitat Pompeu Fabra-CSIC, Barcelona, Spain
| | | | - Olga Gonzalez
- Disease Intervention and Prevention, Southwest National Primate Research Center, San Antonio, TX, USA
| | - Michael L Platt
- Department of Neuroscience, University of Pennsylvania, Philadelphia, PA, USA
| | - Melween I Martínez
- Caribbean Primate Research Center, University of Puerto Rico, San Juan, Puerto Rico
| | - Susan C Antón
- Department of Anthropology, New York University, New York, USA
- New York Consortium in Evolutionary Primatology, New York, NY, USA
| | - Maria Gloria Dominguez-Bello
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, USA
- Department of Anthropology, Rutgers University, New Brunswick, NJ, USA
| | - Amanda D Melin
- Department of Anthropology and Archaeology, University of Calgary, Alberta, Canada
- Alberta Children's Hospital Research Institute, Alberta, Canada
- Department of Medical Genetics, University of Calgary, Alberta, Canada
| | - James P Higham
- Department of Anthropology, New York University, New York, USA
- New York Consortium in Evolutionary Primatology, New York, NY, USA
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34
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Raulo A, Allen BE, Troitsky T, Husby A, Firth JA, Coulson T, Knowles SCL. Social networks strongly predict the gut microbiota of wild mice. ISME JOURNAL 2021; 15:2601-2613. [PMID: 33731838 PMCID: PMC8397773 DOI: 10.1038/s41396-021-00949-3] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 02/02/2021] [Accepted: 02/19/2021] [Indexed: 02/06/2023]
Abstract
The mammalian gut teems with microbes, yet how hosts acquire these symbionts remains poorly understood. Research in primates suggests that microbes can be picked up via social contact, but the role of social interactions in non-group-living species remains underexplored. Here, we use a passive tracking system to collect high resolution spatiotemporal activity data from wild mice (Apodemus sylvaticus). Social network analysis revealed social association strength to be the strongest predictor of microbiota similarity among individuals, controlling for factors including spatial proximity and kinship, which had far smaller or nonsignificant effects. This social effect was limited to interactions involving males (male-male and male-female), implicating sex-dependent behaviours as driving processes. Social network position also predicted microbiota richness, with well-connected individuals having the most diverse microbiotas. Overall, these findings suggest social contact provides a key transmission pathway for gut symbionts even in relatively asocial mammals, that strongly shapes the adult gut microbiota. This work underlines the potential for individuals to pick up beneficial symbionts as well as pathogens from social interactions.
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Affiliation(s)
- Aura Raulo
- Department of Zoology, University of Oxford, Oxford, UK.
| | - Bryony E Allen
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK.,Institute of Zoology, Zoological Society of London, Regents Park, London, UK
| | - Tanya Troitsky
- Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Arild Husby
- Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - Josh A Firth
- Department of Zoology, University of Oxford, Oxford, UK
| | - Tim Coulson
- Department of Zoology, University of Oxford, Oxford, UK
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35
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Maraci Ö, Antonatou-Papaioannou A, Jünemann S, Castillo-Gutiérrez O, Busche T, Kalinowski J, Caspers BA. The Gut Microbial Composition Is Species-Specific and Individual-Specific in Two Species of Estrildid Finches, the Bengalese Finch and the Zebra Finch. Front Microbiol 2021; 12:619141. [PMID: 33679641 PMCID: PMC7933042 DOI: 10.3389/fmicb.2021.619141] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 01/25/2021] [Indexed: 12/29/2022] Open
Abstract
Microbial communities residing in the gastrointestinal tracts of animals have profound impacts on the physiological processes of their hosts. In humans, host-specific and environmental factors likely interact together to shape gut microbial communities, resulting in remarkable inter-individual differences. However, we still lack a full understanding of to what extent microbes are individual-specific and controlled by host-specific factors across different animal taxa. Here, we document the gut microbial characteristics in two estrildid finch species, the Bengalese finch (Lonchura striata domestica) and the zebra finch (Taeniopygia guttata) to investigate between-species and within-species differences. We collected fecal samples from breeding pairs that were housed under strictly controlled environmental and dietary conditions. All individuals were sampled at five different time points over a range of 120 days covering different stages of the reproductive cycle. We found significant species-specific differences in gut microbial assemblages. Over a period of 3 months, individuals exhibited unique, individual-specific microbial profiles. Although we found a strong individual signature in both sexes, within-individual variation in microbial communities was larger in males of both species. Furthermore, breeding pairs had more similar microbial profiles, compared to randomly chosen males and females. Our study conclusively shows that host-specific factors contribute structuring of gut microbiota.
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Affiliation(s)
- Öncü Maraci
- Department of Behavioural Ecology, Bielefeld University, Bielefeld, Germany
| | - Anna Antonatou-Papaioannou
- Evolutionary Biology, Bielefeld University, Bielefeld, Germany
- Institute of Biology-Zoology, Freie Universität Berlin, Berlin, Germany
| | - Sebastian Jünemann
- Faculty of Technology, Bielefeld University, Bielefeld, Germany
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Omar Castillo-Gutiérrez
- Faculty of Technology, Bielefeld University, Bielefeld, Germany
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Tobias Busche
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Jörn Kalinowski
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Barbara A. Caspers
- Department of Behavioural Ecology, Bielefeld University, Bielefeld, Germany
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36
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Baniel A, Amato KR, Beehner JC, Bergman TJ, Mercer A, Perlman RF, Petrullo L, Reitsema L, Sams S, Lu A, Snyder-Mackler N. Seasonal shifts in the gut microbiome indicate plastic responses to diet in wild geladas. MICROBIOME 2021; 9:26. [PMID: 33485388 PMCID: PMC7828014 DOI: 10.1186/s40168-020-00977-9] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 12/07/2020] [Indexed: 05/22/2023]
Abstract
BACKGROUND Adaptive shifts in gut microbiome composition are one route by which animals adapt to seasonal changes in food availability and diet. However, outside of dietary shifts, other potential environmental drivers of gut microbial composition have rarely been investigated, particularly in organisms living in their natural environments. RESULTS Here, we generated the largest wild nonhuman primate gut microbiome dataset to date to identify the environmental drivers of gut microbial diversity and function in 758 samples collected from wild Ethiopian geladas (Theropithecus gelada). Because geladas live in a cold, high-altitude environment and have a low-quality grass-based diet, they face extreme thermoregulatory and energetic constraints. We tested how proxies of food availability (rainfall) and thermoregulatory stress (temperature) predicted gut microbiome composition of geladas. The gelada gut microbiome composition covaried with rainfall and temperature in a pattern that suggests distinct responses to dietary and thermoregulatory challenges. Microbial changes were driven by differences in the main components of the diet across seasons: in rainier periods, the gut was dominated by cellulolytic/fermentative bacteria that specialized in digesting grass, while during dry periods the gut was dominated by bacteria that break down starches found in underground plant parts. Temperature had a comparatively smaller, but detectable, effect on the gut microbiome. During cold and dry periods, bacterial genes involved in energy, amino acid, and lipid metabolism increased, suggesting a stimulation of fermentation activity in the gut when thermoregulatory and nutritional stress co-occurred, and potentially helping geladas to maintain energy balance during challenging periods. CONCLUSION Together, these results shed light on the extent to which gut microbiota plasticity provides dietary and metabolic flexibility to the host, and might be a key factor to thriving in changing environments. On a longer evolutionary timescale, such metabolic flexibility provided by the gut microbiome may have also allowed members of Theropithecus to adopt a specialized diet, and colonize new high-altitude grassland habitats in East Africa. Video abstract.
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Affiliation(s)
- Alice Baniel
- Department of Anthropology, Stony Brook University, Stony Brook, NY, 11794, USA.
| | - Katherine R Amato
- Department of Anthropology, Northwestern University, Evanston, IL, 60208, USA
| | - Jacinta C Beehner
- Department of Psychology, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Anthropology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Thore J Bergman
- Department of Psychology, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Arianne Mercer
- Department of Psychology, University of Washington, Seattle, WA, 98195, USA
| | - Rachel F Perlman
- Interdepartmental Doctoral Program in Anthropological Sciences, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Lauren Petrullo
- Interdepartmental Doctoral Program in Anthropological Sciences, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Laurie Reitsema
- Department of Anthropology, University of Georgia, Athens, GA, 30602, USA
| | - Sierra Sams
- Department of Psychology, University of Washington, Seattle, WA, 98195, USA
| | - Amy Lu
- Department of Anthropology, Stony Brook University, Stony Brook, NY, 11794, USA.
| | - Noah Snyder-Mackler
- Department of Psychology, University of Washington, Seattle, WA, 98195, USA.
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, 85281, USA.
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA.
- Department of Biology, University of Washington, Seattle, WA, 98195, USA.
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37
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Li H, Chen J, Ren X, Yang C, Liu S, Bai X, Shan S, Dong X. Gut Microbiota Composition Changes in Constipated Women of Reproductive Age. Front Cell Infect Microbiol 2021; 10:557515. [PMID: 33552996 PMCID: PMC7859112 DOI: 10.3389/fcimb.2020.557515] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Accepted: 12/03/2020] [Indexed: 12/12/2022] Open
Abstract
Background Chronic constipation is one of the most prevalent functional gastrointestinal disorders, yet its etiology is multifactorial, and the pathophysiological mechanism is still unclear. Previous studies have shown that the gut microbiota of constipated patients differs from healthy controls; however, many discrepancies exist in the findings, and no clear link has been confirmed between chronic constipation and changes in the gut microbiota. Growing evidence indicates that age, gender, and hormone levels can affect the composition of gut microbiota. The aim of this study is to examine the overall changes in gut microbiota within a specific sub-population of patients, namely, constipated women of reproductive age. Methods We carried out a cross-sectional study comparing the fecal microbial composition of 30 healthy women and 29 constipated women using 16S rRNA gene sequencing. Only women of reproductive age were recruited to reduce the effects of age, gender, and hormone levels on the microbiome, and to prevent conflating the impact of these factors with the effects of constipation. Results There were obvious differences in the gut microbiota in constipated women of reproductive age compared with the healthy controls, manifesting mainly as a significant increase in the abundance of Bacteroides (p < 0.05) and a significant decrease in the abundance of Proteobacteria (p < 0.01). The overall composition of the gut microbiota in each group was different, which was reflected in the ratios of Firmicutes to Bacteroidetes (F/B), which was 1.52 in the constipated group vs. 2.21 in the healthy group. Additionally, there was a significant decrease in butyrate-producing bacteria, like Roseburia and Fusicatenibacter (p < 0.01). Conclusion The overall composition of the gut microbiota changed in constipated women of reproductive age, characterized by a loss in Proteobacteria and an increase in Bacteroidetes. Furthermore, the abundance of some butyrate-producing bacteria also reduced. These changes may reflect the unique interactions between host and some bacteria, or some bacterial metabolic products, which may be important targets for future studies to explore the pathogenesis of constipation.
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Affiliation(s)
- Hongxia Li
- Department of General Surgery, Bethune Hospital Affiliated to Shanxi Medical University, Taiyuan, China
| | - Jianwei Chen
- Department of General Surgery, Bethune Hospital Affiliated to Shanxi Medical University, Taiyuan, China
| | - Xiaojing Ren
- Key Laboratory of Chemical Biology and Molecular Engineering of National Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan, China
| | - Chuanli Yang
- Key Laboratory of Chemical Biology and Molecular Engineering of National Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan, China
| | - Shuai Liu
- Department of General Surgery, Bethune Hospital Affiliated to Shanxi Medical University, Taiyuan, China
| | - Xinshu Bai
- Department of General Surgery, Bethune Hospital Affiliated to Shanxi Medical University, Taiyuan, China
| | - Shuhua Shan
- Key Laboratory of Chemical Biology and Molecular Engineering of National Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan, China
| | - Xiushan Dong
- Department of General Surgery, Bethune Hospital Affiliated to Shanxi Medical University, Taiyuan, China
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38
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Disentangling the Relative Roles of Vertical Transmission, Subsequent Colonizations, and Diet on Cockroach Microbiome Assembly. mSphere 2021; 6:6/1/e01023-20. [PMID: 33408228 PMCID: PMC7845597 DOI: 10.1128/msphere.01023-20] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
A multitude of factors affect the assemblies of complex microbial communities associated with animal hosts, with implications for community flexibility, resilience, and long-term stability; however, their relative effects have rarely been deduced. Here, we use a tractable lab model to quantify the relative and combined effects of parental transmission (egg case microbiome present/reduced), gut inocula (cockroach versus termite gut provisioned), and varying diets (matched or unmatched with gut inoculum source) on gut microbiota structure of hatchlings of the omnivorous cockroach Shelfordella lateralis using 16S rRNA gene (rDNA) amplicon sequencing. We show that the presence of a preexisting bacterial community via vertical transmission of microbes on egg cases reduces subsequent microbial invasion, suggesting priority effects that allow initial colonizers to take a strong hold and which stabilize the microbiome. However, subsequent inoculation sources more strongly affect ultimate community composition and their ecological networks, with distinct host-taxon-of-origin effects on which bacteria establish. While this is so, communities respond flexibly to specific diets in ways that consequently impact predicted community functions. In conclusion, our findings suggest that inoculations drive communities toward different stable states depending on colonization and extinction events, through ecological host-microbe relations and interactions with other gut bacteria, while diet in parallel shapes the functional capabilities of these microbiomes. These effects may lead to consistent microbial communities that maximize the extended phenotype that the microbiota provides the host, particularly if microbes spend most of their lives in host-associated environments.IMPORTANCE When host fitness is dependent on gut microbiota, microbial community flexibility and reproducibility enhance host fitness by allowing fine-tuned environmental tracking and sufficient stability for host traits to evolve. Our findings lend support to the importance of vertically transmitted early-life microbiota as stabilizers, through interactions with potential colonizers, which may contribute to ensuring that the microbiota aligns within host fitness-enhancing parameters. Subsequent colonizations are driven by microbial composition of the sources available, and we confirm that host-taxon-of-origin affects stable subsequent communities, while communities at the same time retain sufficient flexibility to shift in response to available diets. Microbiome structure is thus the result of the relative impact and combined effects of inocula and fluctuations driven by environment-specific microbial sources and digestive needs. These affect short-term community structure on an ecological time scale but could ultimately shape host species specificities in microbiomes across evolutionary time, if environmental conditions prevail.
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39
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Narat V, Amato KR, Ranger N, Salmona M, Mercier-Delarue S, Rupp S, Ambata P, Njouom R, Simon F, Giles-Vernick T, LeGoff J. A multi-disciplinary comparison of great ape gut microbiota in a central African forest and European zoo. Sci Rep 2020; 10:19107. [PMID: 33154444 PMCID: PMC7645722 DOI: 10.1038/s41598-020-75847-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 10/15/2020] [Indexed: 01/01/2023] Open
Abstract
Comparisons of mammalian gut microbiota across different environmental conditions shed light on the diversity and composition of gut bacteriome and suggest consequences for human and animal health. Gut bacteriome comparisons across different environments diverge in their results, showing no generalizable patterns linking habitat and dietary degradation with bacterial diversity. The challenge in drawing general conclusions from such studies lies in the broad terms describing diverse habitats ("wild", "captive", "pristine"). We conducted 16S ribosomal RNA gene sequencing to characterize intestinal microbiota of free-ranging sympatric chimpanzees and gorillas in southeastern Cameroon and sympatric chimpanzees and gorillas in a European zoo. We conducted participant-observation and semi-structured interviews among people living near these great apes to understand better their feeding habits and habitats. Unexpectedly, bacterial diversity (ASV, Faith PD and Shannon) was higher among zoo gorillas than among those in the Cameroonian forest, but zoo and Cameroonian chimpanzees showed no difference. Phylogeny was a strong driver of species-specific microbial composition. Surprisingly, zoo gorilla microbiota more closely resembled that of zoo chimpanzees than of Cameroonian gorillas. Zoo living conditions and dietary similarities may explain these results. We encourage multidisciplinary approach integrating environmental sampling and anthropological evaluation to characterize better diverse environmental conditions of such investigations.
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Affiliation(s)
- Victor Narat
- Eco-anthropologie, UMR7206 CNRS/MNHN/Université de Paris, Site du Musée de L'Homme, Paris, France
- Institut Pasteur, Anthropology and Ecology of Disease Emergence Unit, Paris, France
| | - Katherine R Amato
- Department of Anthropology, Northwestern University, Evanston, USA
- Humans and the Microbiome, CIFAR, Toronto, Canada
| | - Noémie Ranger
- Université de Paris, Equipe INSIGHT, Inserm U976, 75010, Paris, France
| | - Maud Salmona
- Université de Paris, Equipe INSIGHT, Inserm U976, 75010, Paris, France
- Département des Agents Infectieux, Virologie et Greffes, AP-HP, Hôpital Saint-Louis, 75010, Paris, France
| | | | - Stephanie Rupp
- Department of Anthropology, City University of New York - Lehman College, New York, NY, USA
| | - Philippe Ambata
- Ministry of Agriculture and Rural Development, Yaounde, Cameroon
| | | | - François Simon
- Université de Paris, Equipe INSIGHT, Inserm U976, 75010, Paris, France
| | - Tamara Giles-Vernick
- Institut Pasteur, Anthropology and Ecology of Disease Emergence Unit, Paris, France.
- Humans and the Microbiome, CIFAR, Toronto, Canada.
| | - Jérôme LeGoff
- Université de Paris, Equipe INSIGHT, Inserm U976, 75010, Paris, France.
- Département des Agents Infectieux, Virologie et Greffes, AP-HP, Hôpital Saint-Louis, 75010, Paris, France.
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40
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Li Y, Chen T, Liang J, Li Y, Huang Z. Seasonal variation in the gut microbiota of rhesus macaques inhabiting limestone forests of southwest Guangxi, China. Arch Microbiol 2020; 203:787-798. [PMID: 33057745 DOI: 10.1007/s00203-020-02069-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 09/29/2020] [Accepted: 10/01/2020] [Indexed: 11/27/2022]
Abstract
Data on the gut microbiota of animals can provide new insights into dietary ecology of hosts, consequently assisting in understanding their adaptation strategy and evolutionary potential. We studied the gut microbiota composition and function of the wild rhesus macaques (Macaca mulatta) using 16S rRNA sequencing method. Our results revealed that the gut microbiota of the wild rhesus macaques was dominated by Firmicutes, Bacteroidetes, and Spirochaetes. Diversity and richness of gut microbiota were higher during the dry season than the rainy season. Specifically, higher proportions of Firmicutes, Tenericutes, Cyanobacteria, and unclassified bacteria at the phylum level and more Coprococcus at the genus level were detected in the dry season. Predictive functional analysis showed that pathways associated with carbohydrate metabolism and drug resistance (antimicrobial and antineoplastic) were richer in the dry season. These seasonal differences in microbiota could be due to their heavier dependence on leaf-based diet in the dry season. Additionally, macaques in limestone forests had a higher percentage of Spirochaetes, probably suggesting that the proportion of fruits in dietary composition also play an important role in the gut microbiota. We concluded that diet was strongly linked to the diversity, composition, and function of the gut microbiota in the wild groups of rhesus macaques living in the limestone forest, highlighting the importance of diet in the gut microbiota of macaques and the need to conduct further study on the adaptation strategy in response of environmental changes in the ground of gut microbiota.
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Affiliation(s)
- Yuhui Li
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, China
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, No. 15 Yu Cai Road, Guilin, China
| | - Ting Chen
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, China
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, No. 15 Yu Cai Road, Guilin, China
| | - Jipeng Liang
- Administration Centre of Guangxi Chongzuo White-headed Langur National Nature Reserve, Chongzuo, China
| | - Youbang Li
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, China.
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, No. 15 Yu Cai Road, Guilin, China.
| | - Zhonghao Huang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, China.
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, No. 15 Yu Cai Road, Guilin, China.
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41
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Grieneisen L, Muehlbauer AL, Blekhman R. Microbial control of host gene regulation and the evolution of host-microbiome interactions in primates. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190598. [PMID: 32772669 PMCID: PMC7435160 DOI: 10.1098/rstb.2019.0598] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/19/2020] [Indexed: 12/23/2022] Open
Abstract
Recent comparative studies have found evidence consistent with the action of natural selection on gene regulation across primate species. Other recent work has shown that the microbiome can regulate host gene expression in a wide range of relevant tissues, leading to downstream effects on immunity, metabolism and other biological systems in the host. In primates, even closely related host species can have large differences in microbiome composition. One potential consequence of these differences is that host species-specific microbial traits could lead to differences in gene expression that influence primate physiology and adaptation to local environments. Here, we will discuss and integrate recent findings from primate comparative genomics and microbiome research, and explore the notion that the microbiome can influence host evolutionary dynamics by affecting gene regulation across primate host species. This article is part of the theme issue 'The role of the microbiome in host evolution'.
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Affiliation(s)
- Laura Grieneisen
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Amanda L. Muehlbauer
- Department of Ecology, Evolution and Behavior, University of Minnesota, Minneapolis, MN 55455, USA
| | - Ran Blekhman
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA
- Department of Ecology, Evolution and Behavior, University of Minnesota, Minneapolis, MN 55455, USA
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42
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Jiménez RR, Alvarado G, Sandoval J, Sommer S. Habitat disturbance influences the skin microbiome of a rediscovered neotropical-montane frog. BMC Microbiol 2020; 20:292. [PMID: 32962670 PMCID: PMC7509932 DOI: 10.1186/s12866-020-01979-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 09/15/2020] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND The skin microbiome serves as a first line defense against pathogens in vertebrates. In amphibians, it has the potential to protect against the chytrid fungus Batrachochytrium dendrobatis (Bd), a likely agent of amphibian declines. Alteration of the microbiome associated with unfavorable environmental changes produced by anthropogenic activities may make the host more susceptible to pathogens. Some amphibian species that were thought to be "extinct" have been rediscovered years after population declines in the late 1980s probably due to evolved Bd-resistance and are now threatened by anthropogenic land-use changes. Understanding the effects of habitat disturbance on the host skin microbiome is relevant for understanding the health of these species, along with its susceptibility to pathogens such as Bd. Here, we investigate the influence of habitat alteration on the skin bacterial communities as well as specifically the putative Bd-inhibitory bacterial communities of the montane frog Lithobates vibicarius. This species, after years of not being observed, was rediscovered in small populations inhabiting undisturbed and disturbed landscapes, and with continuous presence of Bd. RESULTS We found that cutaneous bacterial communities of tadpoles and adults differed between undisturbed and disturbed habitats. The adults from disturbed habitats exhibited greater community dispersion than those from undisturbed habitats. We observed a higher richness of putative Bd-inhibitory bacterial strains in adults from disturbed habitats than in those from undisturbed habitats, as well as a greater number of these potential protective bacteria with a high relative abundance. CONCLUSIONS Our findings support the microbial "Anna Karenina principle", in which disturbance is hypothesized to cause greater microbial dispersion in communities, a so-called dysbiosis, which is a response of animal microbiomes to stress factors that decrease the ability of the host or its microbiome to regulate community composition. On the positive side, the high richness and relative abundance of putative Bd-inhibitory bacteria may indicate the development of a defense mechanism that enhances Bd-protection, attributed to a co-occurrence of more than 30-years of host and pathogen in these disturbed habitats. Our results provide important insight into the influence of human-modified landscapes on the skin microbiome and health implications of Bd-survivor species.
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Affiliation(s)
- Randall R Jiménez
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Albert-Einstein Allee 11, 89069, Ulm, Germany.
| | - Gilbert Alvarado
- Laboratory of Comparative Wildlife Pathology, School of Veterinary Medicine and Animal Sciences, University of São Paulo, Av. Orlando Marques de Paiva 87, São Paulo, Brazil
- Laboratory of Experimental and Comparative Pathology (LAPECOM), Biology School, University of Costa Rica, San José, Costa Rica
| | - José Sandoval
- Laboratory of Experimental and Comparative Pathology (LAPECOM), Biology School, University of Costa Rica, San José, Costa Rica
| | - Simone Sommer
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Albert-Einstein Allee 11, 89069, Ulm, Germany
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43
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Microbial transmission in animal social networks and the social microbiome. Nat Ecol Evol 2020; 4:1020-1035. [DOI: 10.1038/s41559-020-1220-8] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 05/11/2020] [Indexed: 12/15/2022]
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44
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Chen T, Li Y, Liang J, Li Y, Huang Z. Variations in the gut microbiota of sympatric François’ langurs and rhesus macaques living in limestone forests in southwest Guangxi, China. Glob Ecol Conserv 2020. [DOI: 10.1016/j.gecco.2020.e00929] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
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45
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Haworth SE, White KS, Côté SD, Shafer ABA. Space, time and captivity: quantifying the factors influencing the fecal microbiome of an alpine ungulate. FEMS Microbiol Ecol 2020; 95:5519850. [PMID: 31210274 DOI: 10.1093/femsec/fiz095] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 06/15/2019] [Indexed: 12/21/2022] Open
Abstract
The community of microorganisms in the gut is affected by host species, diet and environment and is linked to normal functioning of the host organism. Although the microbiome fluctuates in response to host demands and environmental changes, there are core groups of microorganisms that remain relatively constant throughout the hosts lifetime. Ruminants are mammals that rely on highly specialized digestive and metabolic modifications, including microbiome adaptations, to persist in extreme environments. Here, we assayed the fecal microbiome of four mountain goat (Oreamnos americanus) populations in western North America. We quantified fecal microbiome diversity and composition among groups in the wild and captivity, across populations and in a single group over time. There were no differences in community evenness or diversity across groups, although we observed a decreasing diversity trend across summer months. Pairwise sample estimates grouped the captive population distinctly from the wild populations, and moderately grouped the southern wild group distinctly from the two northern wild populations. We identified 33 genera modified by captivity, with major differences in key groups associated with cellulose degradation that likely reflect differences in diet. Our findings are consistent with other ruminant studies and provide baseline microbiome data in this enigmatic species, offering valuable insights into the health of wild alpine ungulates.
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Affiliation(s)
- Sarah E Haworth
- Forensics Program, Trent University, K9J 7B8 Peterborough, Canada.,Environmental and Life Sciences Graduate Program, Trent University, 7K9J 7B8 Peterborough, Canada
| | - Kevin S White
- Division of Wildlife Conservation, Alaska Department of Fish and Game, Juneau, AK 99802, USA
| | - Steeve D Côté
- Département de Biologie and Centre for Northern Studies, Université Laval, Québec G1V 0A6, Canada
| | - Aaron B A Shafer
- Forensics Program, Trent University, K9J 7B8 Peterborough, Canada.,Environmental and Life Sciences Graduate Program, Trent University, 7K9J 7B8 Peterborough, Canada
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46
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The Gut Microbiota Communities of Wild Arboreal and Ground-Feeding Tropical Primates Are Affected Differently by Habitat Disturbance. mSystems 2020; 5:5/3/e00061-20. [PMID: 32457237 PMCID: PMC7253362 DOI: 10.1128/msystems.00061-20] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Gut microbiota diversity has become the subject of extensive research in human and nonhuman animals, linking diversity and composition to gut function and host health. Because wild primates are good indicators of tropical ecosystem health, we developed the idea that they are a suitable model to observe the consequences of advancing global change (e.g., habitat degradation) on gut microbiota. So far, most of the studies focus mainly on gut bacteria; however, they are not the only component of the gut: fungi also serve essential functions in gut homeostasis. Here, for the first time, we explore and measure diversity and composition of both bacterial and fungal microbiota components of two tropical primate species living in highly different habitat types (intact versus degraded forests). Results on their microbiota diversity and composition are discussed in light of conservation issues and potential applications. Human exploitation and destruction of tropical resources are currently threatening innumerable wild animal species, altering natural ecosystems and thus, food resources, with profound effects on gut microbiota. Given their conservation status and the importance to tropical ecosystems, wild nonhuman primates make excellent models to investigate the effect of human disturbance on the diversity of host-associated microbiota. Previous investigations have revealed a loss of fecal bacterial diversity in primates living in degraded compared to intact forests. However, these data are available for a limited number of species, and very limited information is available on the fungal taxa hosted by the gut. Here, we estimated the diversity and composition of gut bacterial and fungal communities in two primates living sympatrically in both human-modified and pristine forests in the Udzungwa Mountains of Tanzania. Noninvasively collected fecal samples of 12 groups of the Udzungwa red colobus (Procolobus gordonorum) (n = 89), a native and endangered primate (arboreal and predominantly leaf-eating), and five groups of the yellow baboon (Papio cynocephalus) (n = 69), a common species of least concern (ground-feeding and omnivorous), were analyzed by the V1-V3 region of the 16S rRNA gene (bacterial) and ITS1-ITS2 (fungal) sequencing. Gut bacterial diversities were associated with habitat in both species, most likely depending on their ecological niches and associated digestive physiology, dietary strategies, and locomotor behavior. In addition, fungal communities also show distinctive traits across hosts and habitat type, highlighting the importance of investigating this relatively unexplored gut component. IMPORTANCE Gut microbiota diversity has become the subject of extensive research in human and nonhuman animals, linking diversity and composition to gut function and host health. Because wild primates are good indicators of tropical ecosystem health, we developed the idea that they are a suitable model to observe the consequences of advancing global change (e.g., habitat degradation) on gut microbiota. So far, most of the studies focus mainly on gut bacteria; however, they are not the only component of the gut: fungi also serve essential functions in gut homeostasis. Here, for the first time, we explore and measure diversity and composition of both bacterial and fungal microbiota components of two tropical primate species living in highly different habitat types (intact versus degraded forests). Results on their microbiota diversity and composition are discussed in light of conservation issues and potential applications.
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47
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Ni Q, He X, Zeng B, Meng X, Xu H, Li Y, Yang M, Li D, Yao Y, Zhang M, Li Y, Fan X, Yang D, Xie M. Variation in Gut Microbiota of Captive Bengal Slow Lorises. Curr Microbiol 2020; 77:2623-2632. [PMID: 32440808 DOI: 10.1007/s00284-020-02035-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 05/14/2020] [Indexed: 12/22/2022]
Abstract
Gastrointestinal microbiome plays an important role in animal metabolism, immune system and pathology associated with health and disease. Many wild slow lorises were confiscated from illegal trade into captivities and experienced a range of changes in living environment and diet. Microbiome analysis contributes to improving captive management by identifying the alteration in their gastrointestinal microbial communities and aiding in determining the factors affecting the health of captive slow lorises. The fecal samples of eighteen Bengal slow lorises (Nycticebus bengalensis) were used to compare gut microbiota from four rescue centers located in Dehong, Gejiu, Nanning and Puer cities of China. The results showed a significant site-dependent difference in microbial community diversity. Similar to other Lorisinae species, the Phyla including Bacteroidetes, Firmicutes and Proteobacteria dominated their gut microbiome composition. The Gejiu group exhibited a higher overall diversity and the unique OTUs, which is resulted from long-term isolated husbandry and heavy human disturbances. The scarcity of gums in the captive diet was likely to cause a lower abundance of Prevotella associated with soluble fiber degradation. The variation of intestinal microbiota in different environments highlights the necessity to improve feed preparation and husbandry management for the captive Bengal slow lorises.
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Affiliation(s)
- Qingyong Ni
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, China. .,College of Animal Science and Technology, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, China.
| | - Xin He
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, China.,College of Animal Science and Technology, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, China
| | - Bo Zeng
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, China.,College of Animal Science and Technology, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, China
| | - Xiangyun Meng
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, China.,College of Animal Science and Technology, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, China
| | - Huailiang Xu
- College of Life Science, Sichuan Agricultural University, 46 Xinkang Road, Yaan, 625014, China
| | - Ying Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, China.,College of Animal Science and Technology, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, China
| | - Mingyao Yang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, China.,College of Animal Science and Technology, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, China
| | - Diyan Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, China.,College of Animal Science and Technology, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, China
| | - Yongfang Yao
- College of Life Science, Sichuan Agricultural University, 46 Xinkang Road, Yaan, 625014, China
| | - Mingwang Zhang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, China.,College of Animal Science and Technology, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, China
| | - Yan Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, China.,College of Animal Science and Technology, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, China
| | - Xiaolan Fan
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, China.,College of Animal Science and Technology, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, China
| | - Deying Yang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, China.,College of Animal Science and Technology, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, China
| | - Meng Xie
- College of Life Science, Sichuan Agricultural University, 46 Xinkang Road, Yaan, 625014, China.
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48
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Drea CM. Design, delivery and perception of condition-dependent chemical signals in strepsirrhine primates: implications for human olfactory communication. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190264. [PMID: 32306880 DOI: 10.1098/rstb.2019.0264] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The study of human chemical communication benefits from comparative perspectives that relate humans, conceptually and empirically, to other primates. All major primate groups rely on intraspecific chemosignals, but strepsirrhines present the greatest diversity and specialization, providing a rich framework for examining design, delivery and perception. Strepsirrhines actively scent mark, possess a functional vomeronasal organ, investigate scents via olfactory and gustatory means, and are exquisitely sensitive to chemically encoded messages. Variation in delivery, scent mixing and multimodality alters signal detection, longevity and intended audience. Based on an integrative, 19-species review, the main scent source used (excretory versus glandular) differentiates nocturnal from diurnal or cathemeral species, reflecting differing socioecological demands and evolutionary trajectories. Condition-dependent signals reflect immutable (species, sex, identity, genetic diversity, immunity and kinship) and transient (health, social status, reproductive state and breeding history) traits, consistent with socio-reproductive functions. Sex reversals in glandular elaboration, marking rates or chemical richness in female-dominant species implicate sexual selection of olfactory ornaments in both sexes. Whereas some compounds may be endogenously produced and modified (e.g. via hormones), microbial analyses of different odorants support the fermentation hypothesis of bacterial contribution. The intimate contexts of information transfer and varied functions provide important parallels applicable to olfactory communication in humans. This article is part of the Theo Murphy meeting issue 'Olfactory communication in humans'.
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Affiliation(s)
- Christine M Drea
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708-0383, USA.,Department of Biology, Duke University, Durham, NC 27708-0383, USA
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49
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Host-microbiota interaction helps to explain the bottom-up effects of climate change on a small rodent species. ISME JOURNAL 2020; 14:1795-1808. [PMID: 32313262 PMCID: PMC7305154 DOI: 10.1038/s41396-020-0646-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 03/18/2020] [Accepted: 03/24/2020] [Indexed: 01/02/2023]
Abstract
The population cycles of small rodents have puzzled biologists for centuries. There is a growing recognition of the cascading effects of climate change on the population dynamics of rodents. However, the ultimate cause for the bottom-up effects of precipitation is poorly understood, from a microbial perspective. Here, we conducted a precipitation manipulation experiment in the field, and three feeding trials with controlled diets in the laboratory. We found precipitation supplementation facilitated the recovery of a perennial rhizomatous grass (Leymus chinensis) species, which altered the diet composition and increase the intake of fructose and fructooligosaccharides for Brandt’s vole. Lab results showed that this nutrient shift was accompanied by the modulation of gut microbiota composition and functional pathways (especially for the degradation or biosynthesis of L-histidine). Particularly, the relative abundance of Eubacterium hallii was consistently increased after feeding voles with more L. chinensis, fructose or fructooligosaccharide. These modulations ultimately increased the production of short chain fatty acids (SCFAs) and boosted the growth of vole. This study provides evidence that the precipitation pulses cascades through the plant community to affect rodent gut microbiome. Our results highlight the importance of considering host-microbiota interaction when investigating rodent population responses to climate change.
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50
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Stoffel MA, Acevedo-Whitehouse K, Morales-Durán N, Grosser S, Chakarov N, Krüger O, Nichols HJ, Elorriaga-Verplancken FR, Hoffman JI. Early sexual dimorphism in the developing gut microbiome of northern elephant seals. Mol Ecol 2020; 29:2109-2122. [PMID: 32060961 DOI: 10.1111/mec.15385] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 02/07/2020] [Accepted: 02/10/2020] [Indexed: 12/13/2022]
Abstract
The gut microbiome is an integral part of a species' ecology, but we know little about how host characteristics impact its development in wild populations. Here, we explored the role of such intrinsic factors in shaping the gut microbiome of northern elephant seals (Mirounga angustirostris) during a critical developmental window of 6 weeks after weaning, when the pups stay ashore without feeding. We found substantial sex differences in the early-life gut microbiome, even though males and females could not yet be distinguished morphologically. Sex and age both explained around 15% of the variation in gut microbial beta diversity, while microbial communities sampled from the same individual showed high levels of similarity across time, explaining another 40% of the variation. Only a small proportion of the variation in beta diversity was explained by health status, assessed by full blood counts, but clinically healthy individuals had a greater microbial alpha diversity than their clinically abnormal peers. Across the post-weaning period, the northern elephant seal gut microbiome was highly dynamic. We found evidence for several colonization and extinction events as well as a decline in Bacteroides and an increase in Prevotella, a pattern that has previously been associated with the transition from nursing to solid food. Lastly, we show that genetic relatedness was correlated with gut microbiome similarity in males but not females, again reflecting early sex differences. Our study represents a naturally diet-controlled and longitudinal investigation of how intrinsic factors shape the early gut microbiome in a species with extreme sex differences in morphology and life history.
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Affiliation(s)
- Martin A Stoffel
- Department of Animal Behaviour, Bielefeld University, Bielefeld, Germany.,School of Natural Sciences and Psychology, Faculty of Science, Liverpool John Moores University, Liverpool, UK.,Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Karina Acevedo-Whitehouse
- Unit for Basic and Applied Microbiology, School of Natural Sciences, Autonomous University of Queretaro, Queretaro, México.,The Marine Mammal Center, Sausalito, CA, USA
| | - Nami Morales-Durán
- Unit for Basic and Applied Microbiology, School of Natural Sciences, Autonomous University of Queretaro, Queretaro, México
| | - Stefanie Grosser
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Planegg-Martinsried, Germany
| | - Nayden Chakarov
- Department of Animal Behaviour, Bielefeld University, Bielefeld, Germany
| | - Oliver Krüger
- Department of Animal Behaviour, Bielefeld University, Bielefeld, Germany
| | - Hazel J Nichols
- Department of Animal Behaviour, Bielefeld University, Bielefeld, Germany.,Department of Biosciences, College of Science, Swansea University, Swansea, UK
| | - Fernando R Elorriaga-Verplancken
- Departamento de Pesquerías y Biología Marina, Centro Interdisciplinario de Ciencias Marinas (CICIMAR-IPN), Instituto Politécnico Nacional, La Paz, Mexico
| | - Joseph I Hoffman
- Department of Animal Behaviour, Bielefeld University, Bielefeld, Germany.,British Antarctic Survey, Cambridge, UK
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