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Bornbusch SL, Bamford A, Thacher P, Crosier A, Marinari P, Bortner R, Garelle D, Livieri T, Santymire R, Comizzoli P, Maslanka M, Maldonado JE, Koepfli KP, Muletz-Wolz CR, DeCandia AL. Markers of fertility in reproductive microbiomes of male and female endangered black-footed ferrets (Mustela nigripes). Commun Biol 2024; 7:224. [PMID: 38396133 PMCID: PMC10891159 DOI: 10.1038/s42003-024-05908-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 02/09/2024] [Indexed: 02/25/2024] Open
Abstract
Reproductive microbiomes contribute to reproductive health and success in humans. Yet data on reproductive microbiomes, and links to fertility, are absent for most animal species. Characterizing these links is pertinent to endangered species, such as black-footed ferrets (Mustela nigripes), whose populations show reproductive dysfunction and rely on ex-situ conservation husbandry. To understand microbial contributions to animal reproductive success, we used 16S rRNA amplicon sequencing to characterize male (prepuce) and female (vaginal) microbiomes of 59 black-footed ferrets at two ex-situ facilities and in the wild. We analyzed variation in microbiome structure according to markers of fertility such as numbers of viable and non-viable offspring (females) and sperm concentration (males). Ferret vaginal microbiomes showed lower inter-individual variation compared to prepuce microbiomes. In both sexes, wild ferrets harbored potential soil bacteria, perhaps reflecting their fossorial behavior and exposure to natural soil microbiomes. Vaginal microbiomes of ex-situ females that produced non-viable litters had greater phylogenetic diversity and distinct composition compared to other females. In males, sperm concentration correlated with varying abundances of bacterial taxa (e.g., Lactobacillus), mirroring results in humans and highlighting intriguing dynamics. Characterizing reproductive microbiomes across host species is foundational for understanding microbial biomarkers of reproductive success and for augmenting conservation husbandry.
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Affiliation(s)
- Sally L Bornbusch
- Center for Conservation Genomics, Smithsonian's National Zoo & Conservation Biology Institute, Washington, DC, USA.
- Department of Nutrition Science, Smithsonian's National Zoo & Conservation Biology Institute, Washington, DC, USA.
| | | | - Piper Thacher
- Center for Conservation Genomics, Smithsonian's National Zoo & Conservation Biology Institute, Washington, DC, USA
- Smithsonian-Mason School of Conservation, George Mason University, Front Royal, VA, USA
| | - Adrienne Crosier
- Center for Animal Care Services, Smithsonian's National Zoo & Conservation Biology Institute, Front Royal, VA, USA
| | - Paul Marinari
- Center for Animal Care Services, Smithsonian's National Zoo & Conservation Biology Institute, Front Royal, VA, USA
| | - Robyn Bortner
- National Black-Footed Ferret Conservation Center, US Fish and Wildlife Service, Carr, CO, USA
| | - Della Garelle
- National Black-Footed Ferret Conservation Center, US Fish and Wildlife Service, Carr, CO, USA
| | | | | | - Pierre Comizzoli
- Center for Species Survival, Smithsonian's National Zoo & Conservation Biology Institute, Front Royal, VA, USA
| | - Michael Maslanka
- Department of Nutrition Science, Smithsonian's National Zoo & Conservation Biology Institute, Washington, DC, USA
| | - Jesús E Maldonado
- Center for Conservation Genomics, Smithsonian's National Zoo & Conservation Biology Institute, Washington, DC, USA
| | - Klaus-Peter Koepfli
- Smithsonian-Mason School of Conservation, George Mason University, Front Royal, VA, USA
- Center for Species Survival, Smithsonian's National Zoo & Conservation Biology Institute, Front Royal, VA, USA
| | - Carly R Muletz-Wolz
- Center for Conservation Genomics, Smithsonian's National Zoo & Conservation Biology Institute, Washington, DC, USA
| | - Alexandra L DeCandia
- Center for Conservation Genomics, Smithsonian's National Zoo & Conservation Biology Institute, Washington, DC, USA
- Department of Biology, Georgetown University, Washington, DC, USA
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2
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The Connection between Immunocompetence and Reproduction in Wildlife. Life (Basel) 2023; 13:life13030785. [PMID: 36983939 PMCID: PMC10051471 DOI: 10.3390/life13030785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/07/2023] [Accepted: 03/14/2023] [Indexed: 03/17/2023] Open
Abstract
Reproduction rate is important for the survival of animal populations. During gravidity, a trade-off occurs between the individual well-being of gravid females and investment in offspring. Due to the high synthesis and energy requirements for the growing fetus, other physiological activities are downregulated in pregnant females. This causes changes in the composition of the reproductive microbiome and a decreased immune response to presented antigens and pathogens. As a result, the immunocompetence of gravid wild animals declines. In general, therefore, increased infection rates during pregnancy can be observed in all wildlife species studied. In the course of evolution, however, this has apparently evolved as a suitable strategy to ensure the survival of the population as a whole.
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Contreras MJ, Núñez-Montero K, Bruna P, Zárate A, Pezo F, García M, Leal K, Barrientos L. Mammals' sperm microbiome: current knowledge, challenges, and perspectives on metagenomics of seminal samples. Front Microbiol 2023; 14:1167763. [PMID: 37138598 PMCID: PMC10149849 DOI: 10.3389/fmicb.2023.1167763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 03/31/2023] [Indexed: 05/05/2023] Open
Abstract
Bacterial growth is highly detrimental to sperm quality and functionality. However, during the last few years, using sequencing techniques with a metagenomic approach, it has been possible to deepen the study of bacteria-sperm relationships and describe non-culturable species and synergistic and antagonistic relationships between the different species in mammalian animals. We compile the recent metagenomics studies performed on mammalian semen samples and provide updated evidence to understand the importance of the microbial communities in the results of sperm quality and sperm functionality of males, looking for future perspectives on how these technologies can collaborate in the development of andrological knowledge.
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Affiliation(s)
- María José Contreras
- Extreme Environments Biotechnology Lab, Center of Excellence in Translational Medicine, Universidad de La Frontera, Temuco, Chile
| | - Kattia Núñez-Montero
- Facultad de Ciencias de la Salud, Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Temuco, Chile
| | - Pablo Bruna
- Extreme Environments Biotechnology Lab, Center of Excellence in Translational Medicine, Universidad de La Frontera, Temuco, Chile
| | - Ana Zárate
- Extreme Environments Biotechnology Lab, Center of Excellence in Translational Medicine, Universidad de La Frontera, Temuco, Chile
| | - Felipe Pezo
- Escuela de Medicina Veterinaria, Facultad de Recursos Naturales y Medicina Veterinaria, Universidad Santo Tomás, Santiago, Chile
| | - Matías García
- Extreme Environments Biotechnology Lab, Center of Excellence in Translational Medicine, Universidad de La Frontera, Temuco, Chile
| | - Karla Leal
- Extreme Environments Biotechnology Lab, Center of Excellence in Translational Medicine, Universidad de La Frontera, Temuco, Chile
| | - Leticia Barrientos
- Extreme Environments Biotechnology Lab, Center of Excellence in Translational Medicine, Universidad de La Frontera, Temuco, Chile
- Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Temuco, Chile
- *Correspondence: Leticia Barrientos,
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4
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Female reproduction and the microbiota in mammals: Where are we? Theriogenology 2022; 194:144-153. [DOI: 10.1016/j.theriogenology.2022.10.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 09/20/2022] [Accepted: 10/04/2022] [Indexed: 11/07/2022]
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Leclaire S, Pineaux M, Blanchard P, White J, Hatch SA. Microbiota composition and diversity of multiple body sites vary according to reproductive performance in a seabird. Mol Ecol 2022; 32:2115-2133. [PMID: 35152516 DOI: 10.1111/mec.16398] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 01/03/2022] [Accepted: 02/07/2022] [Indexed: 11/30/2022]
Abstract
The microbiota is suggested to be a fundamental contributor to host reproduction and survival, but associations between microbiota and fitness are rare, especially for wild animals. Here, we tested the association between microbiota and two proxies of breeding performance in multiple body sites of the black-legged kittiwake, a seabird species. First we found that, in females, nonbreeders (i.e., birds that did not lay eggs) hosted different microbiota composition to that of breeders in neck and flank feathers, in the choanae, in the outer-bill and in the cloacae, but not in preen feathers and tracheae. These differences in microbiota might reflect variations in age or individual quality between breeders and nonbreeders. Second, we found that better female breeders (i.e., with higher body condition, earlier laying date, heavier eggs, larger clutch, and higher hatching success) had lower abundance of several Corynebacteriaceae in cloaca than poorer female breeders, suggesting that these bacteria might be pathogenic. Third, in females, better breeders had different microbiota composition and lower microbiota diversity in feathers, especially in preen feathers. They had also reduced dispersion in microbiota composition across body sites. These results might suggest that good breeding females are able to control their feather microbiota-potentially through preen secretions-more tightly than poor breeding females. We did not find strong evidence for an association between reproductive outcome and microbiota in males. Our results are consistent with the hypothesis that natural variation in the microbiota is associated with differences in host fitness in wild animals, but the causal relationships remain to be investigated.
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Affiliation(s)
- Sarah Leclaire
- Laboratoire Evolution et Diversité Biologique (EDB) UMR5174 Université Toulouse 3 Paul Sabatier CNRS, IRD Toulouse France
| | - Maxime Pineaux
- Laboratoire Evolution et Diversité Biologique (EDB) UMR5174 Université Toulouse 3 Paul Sabatier CNRS, IRD Toulouse France
| | - Pierrick Blanchard
- Laboratoire Evolution et Diversité Biologique (EDB) UMR5174 Université Toulouse 3 Paul Sabatier CNRS, IRD Toulouse France
| | - Joël White
- Laboratoire Evolution et Diversité Biologique (EDB) UMR5174 Université Toulouse 3 Paul Sabatier CNRS, IRD Toulouse France
- ENSFEA Castanet‐Tolosan France
| | - Scott A Hatch
- Institute for Seabird Research and Conservation Anchorage AK 99516 USA
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6
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Comizzoli P, Power ML, Bornbusch SL, Muletz-Wolz CR. Interactions between reproductive biology and microbiomes in wild animal species. Anim Microbiome 2021; 3:87. [PMID: 34949226 PMCID: PMC8697499 DOI: 10.1186/s42523-021-00156-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 12/18/2021] [Indexed: 12/24/2022] Open
Abstract
Many parts of the animal body harbor microbial communities, known as animal-associated microbiomes, that affect the regulation of physiological functions. Studies in human and animal models have demonstrated that the reproductive biology and such microbiomes also interact. However, this concept is poorly studied in wild animal species and little is known about the implications to fertility, parental/offspring health, and survival in natural habitats. The objective of this review is to (1) specify the interactions between animals' reproductive biology, including reproductive signaling, pregnancy, and offspring development, and their microbiomes, with an emphasis on wild species and (2) identify important research gaps as well as areas for further studies. While microbiomes present in the reproductive tract play the most direct role, other bodily microbiomes may also contribute to facilitating reproduction. In fish, amphibians, reptiles, birds, and mammals, endogenous processes related to the host physiology and behavior (visual and olfactory reproductive signals, copulation) can both influence and be influenced by the structure and function of microbial communities. In addition, exposures to maternal microbiomes in mammals (through vagina, skin, and milk) shape the offspring microbiomes, which, in turn, affects health later in life. Importantly, for all wild animal species, host-associated microbiomes are also influenced by environmental variations. There is still limited literature on wild animals compared to the large body of research on model species and humans. However, the few studies in wild species clearly highlight the necessity of increased research in rare and endangered animals to optimize conservation efforts in situ and ex situ. Thus, the link between microbiomes and reproduction is an emerging and critical component in wild animal conservation.
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Affiliation(s)
- Pierre Comizzoli
- Smithsonian Conservation Biology Institute, National Zoological Park, Veterinary Hospital MRC5502, PO Box 37012, Washington, DC 20013 USA
| | - Michael L. Power
- Smithsonian Conservation Biology Institute, National Zoological Park, Veterinary Hospital MRC5502, PO Box 37012, Washington, DC 20013 USA
| | - Sally L. Bornbusch
- Smithsonian Conservation Biology Institute, National Zoological Park, Veterinary Hospital MRC5502, PO Box 37012, Washington, DC 20013 USA
| | - Carly R. Muletz-Wolz
- Smithsonian Conservation Biology Institute, National Zoological Park, Veterinary Hospital MRC5502, PO Box 37012, Washington, DC 20013 USA
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7
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Comizzoli P, Ottinger MA. Understanding Reproductive Aging in Wildlife to Improve Animal Conservation and Human Reproductive Health. Front Cell Dev Biol 2021; 9:680471. [PMID: 34095152 PMCID: PMC8170016 DOI: 10.3389/fcell.2021.680471] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Accepted: 04/27/2021] [Indexed: 11/13/2022] Open
Abstract
Similar to humans and laboratory animals, reproductive aging is observed in wild species-from small invertebrates to large mammals. Aging issues are also prevalent in rare and endangered species under human care as their life expectancy is longer than in the wild. The objectives of this review are to (1) present conserved as well as distinctive traits of reproductive aging in different wild animal species (2) highlight the value of comparative studies to address aging issues in conservation breeding as well as in human reproductive medicine, and (3) suggest next steps forward in that research area. From social insects to mega-vertebrates, reproductive aging studies as well as observations in the wild or in breeding centers often remain at the physiological or organismal scale (senescence) rather than at the germ cell level. Overall, multiple traits are conserved across very different species (depletion of the ovarian reserve or no decline in testicular functions), but unique features also exist (endless reproductive life or unaltered quality of germ cells). There is a broad consensus about the need to fill research gaps because many cellular and molecular processes during reproductive aging remain undescribed. More research in male aging is particularly needed across all species. Furthermore, studies on reproductive aging of target species in their natural habitat (sentinel species) are crucial to define more accurate reproductive indicators relevant to other species, including humans, sharing the same environment. Wild species can significantly contribute to our general knowledge of a crucial phenomenon and provide new approaches to extend the reproductive lifespan.
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Affiliation(s)
- Pierre Comizzoli
- Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, United States
| | - Mary Ann Ottinger
- Department of Biology and Biochemistry, University of Houston, Houston, TX, United States
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8
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Sehnal L, Brammer-Robbins E, Wormington AM, Blaha L, Bisesi J, Larkin I, Martyniuk CJ, Simonin M, Adamovsky O. Microbiome Composition and Function in Aquatic Vertebrates: Small Organisms Making Big Impacts on Aquatic Animal Health. Front Microbiol 2021; 12:567408. [PMID: 33776947 PMCID: PMC7995652 DOI: 10.3389/fmicb.2021.567408] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 02/05/2021] [Indexed: 01/03/2023] Open
Abstract
Aquatic ecosystems are under increasing stress from global anthropogenic and natural changes, including climate change, eutrophication, ocean acidification, and pollution. In this critical review, we synthesize research on the microbiota of aquatic vertebrates and discuss the impact of emerging stressors on aquatic microbial communities using two case studies, that of toxic cyanobacteria and microplastics. Most studies to date are focused on host-associated microbiomes of individual organisms, however, few studies take an integrative approach to examine aquatic vertebrate microbiomes by considering both host-associated and free-living microbiota within an ecosystem. We highlight what is known about microbiota in aquatic ecosystems, with a focus on the interface between water, fish, and marine mammals. Though microbiomes in water vary with geography, temperature, depth, and other factors, core microbial functions such as primary production, nitrogen cycling, and nutrient metabolism are often conserved across aquatic environments. We outline knowledge on the composition and function of tissue-specific microbiomes in fish and marine mammals and discuss the environmental factors influencing their structure. The microbiota of aquatic mammals and fish are highly unique to species and a delicate balance between respiratory, skin, and gastrointestinal microbiota exists within the host. In aquatic vertebrates, water conditions and ecological niche are driving factors behind microbial composition and function. We also generate a comprehensive catalog of marine mammal and fish microbial genera, revealing commonalities in composition and function among aquatic species, and discuss the potential use of microbiomes as indicators of health and ecological status of aquatic ecosystems. We also discuss the importance of a focus on the functional relevance of microbial communities in relation to organism physiology and their ability to overcome stressors related to global change. Understanding the dynamic relationship between aquatic microbiota and the animals they colonize is critical for monitoring water quality and population health.
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Affiliation(s)
- Ludek Sehnal
- RECETOX, Faculty of Science, Masaryk University, Brno, Czechia
| | - Elizabeth Brammer-Robbins
- Department of Large Animal Clinical Sciences, University of Florida, Gainesville, FL, United States.,Department of Physiological Sciences, University of Florida, Gainesville, FL, United States.,Center for Environmental and Human Toxicology, University of Florida, Gainesville, FL, United States
| | - Alexis M Wormington
- Center for Environmental and Human Toxicology, University of Florida, Gainesville, FL, United States.,Department of Environmental and Global Health, University of Florida, Gainesville, FL, United States
| | - Ludek Blaha
- RECETOX, Faculty of Science, Masaryk University, Brno, Czechia
| | - Joe Bisesi
- Center for Environmental and Human Toxicology, University of Florida, Gainesville, FL, United States.,Department of Environmental and Global Health, University of Florida, Gainesville, FL, United States
| | - Iske Larkin
- Department of Large Animal Clinical Sciences, University of Florida, Gainesville, FL, United States
| | - Christopher J Martyniuk
- Department of Physiological Sciences, University of Florida, Gainesville, FL, United States.,Center for Environmental and Human Toxicology, University of Florida, Gainesville, FL, United States
| | - Marie Simonin
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, Angers, France
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9
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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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10
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16S rRNA Gene Amplicon Sequence Data from Feces of Five Species of Wild Animals in Japan. Microbiol Resour Announc 2020; 9:9/22/e00368-20. [PMID: 32467273 PMCID: PMC7256260 DOI: 10.1128/mra.00368-20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We report 16S rRNA amplicon sequence data from feces from 58 wild boars, 60 feral raccoons, 9 wild Japanese badgers, 21 wild masked palm civets, and 8 wild raccoon dogs in Japan. The predominant bacterial taxa in the fecal microbiota were similar in part but varied among the animal species. We report 16S rRNA amplicon sequence data from feces from 58 wild boars, 60 feral raccoons, 9 wild Japanese badgers, 21 wild masked palm civets, and 8 wild raccoon dogs in Japan. The predominant bacterial taxa in the fecal microbiota were similar in part but varied among the animal species.
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11
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16S rRNA Gene Amplicon Sequence Data from Feces of Wild Deer (Cervus nippon) in Japan. Microbiol Resour Announc 2020; 9:9/22/e00346-20. [PMID: 32467271 PMCID: PMC7256258 DOI: 10.1128/mra.00346-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We report 16S rRNA amplicon sequence data from feces of 109 wild deer in Japan. The dominant bacterial taxa in fecal microbiota of wild deer hunted between village and mountainous areas and those living on Miyajima Island and in Nara Park were similar but differed in abundance. We report 16S rRNA amplicon sequence data from feces of 109 wild deer in Japan. The dominant bacterial taxa in fecal microbiota of wild deer hunted between village and mountainous areas and those living on Miyajima Island and in Nara Park were similar but differed in abundance.
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