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Harten L, Chen X, de Marcas L, Rachum A, Handel M, Goldshtein A, Levi MF, Rosencwaig S, Yovel Y. Time-mapping and future-oriented behavior in free-ranging wild fruit bats. Curr Biol 2024; 34:3005-3010.e4. [PMID: 38906144 DOI: 10.1016/j.cub.2024.05.046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 04/15/2024] [Accepted: 05/23/2024] [Indexed: 06/23/2024]
Abstract
Episodic memory and mental time travel have been viewed as uniquely human traits.1,2,3 This view began to shift with the development of behavioral criteria to assess what is referred to as "episodic-like memory" in animals.4,5 Key findings have ranged from evidence of what-where-when memory in scrub-jays, rats, and bees; through decision-making that impacts future foraging in frugivorous primates; to evidence of planning based on future needs in scrub-jays and tool use planning in great apes.4,6,7,8,9,10,11,12,13 Field studies of these issues have been rare, though there is field-based evidence for future-oriented behaviors in primates.8,10,14,15 We report evidence that free-ranging wild fruit bats rely on mental temporal maps and exhibit future-oriented behaviors when foraging. We tracked young bats as they navigated and foraged, documenting every tree they visited over many months. We prevented the bats from foraging outside for different time periods and monitored their foraging decisions, revealing that the bats map the spatiotemporal patterns of resources in their environment. Following a long period in captivity, the bats did not visit those trees that were no longer providing fruit. We show that this time-mapping ability requires experience and is lacking in inexperienced bats. Careful analysis of the bats' movement and foraging choices indicated that they plan which tree to visit while still in the colony, thus exhibiting future-oriented behavior and delayed gratification on a nightly basis. Our findings demonstrate how the need for spatiotemporal mental mapping can drive the evolution of high cognitive abilities that were previously considered exclusive to humans.
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Affiliation(s)
- Lee Harten
- School of Zoology, Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel; Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Xing Chen
- School of Zoology, Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Lior de Marcas
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Adi Rachum
- School of Zoology, Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Michal Handel
- School of Zoology, Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Aya Goldshtein
- School of Zoology, Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | | | - Shira Rosencwaig
- National Public Health Laboratory, Ministry of Health, Tel Aviv 6810416, Israel
| | - Yossi Yovel
- School of Zoology, Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel; Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel.
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Grieneisen L, Hays A, Cook E, Blekhman R, Tecot S. Temporal patterns of gut microbiota in lemurs (Eulemur rubriventer) living in intact and disturbed habitats in a novel sample type. Am J Primatol 2024:e23656. [PMID: 38873762 DOI: 10.1002/ajp.23656] [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: 06/01/2023] [Revised: 05/20/2024] [Accepted: 06/06/2024] [Indexed: 06/15/2024]
Abstract
The gut microbiome is a plastic phenotype; gut microbial composition is highly variable across an individual host's lifetime and between host social groups, and this variation has consequences for host health. However, we do not yet fully understand how longitudinal microbial dynamics and their social drivers may be influenced by ecological stressors, such as habitat degradation. Answering these questions is difficult in most wild animal systems, as it requires long-term collections of matched host, microbiome, and environmental trait data. To test if temporal and social influences on microbiome composition differ by the history of human disturbance, we leveraged banked, desiccated fecal samples collected over 5 months in 2004 from two ecologically distinct populations of wild, red-bellied lemurs (Eulemur rubriventer) that are part of a long-term study system. We found that social group explained more variation in microbiome composition than host population membership did, and that temporal variation in common microbial taxa was similar between populations, despite differences in history of human disturbance. Furthermore, we found that social group membership and collection month were both more important than individual lemur identity. Taken together, our results suggest that synchronized environments use can lead to synchronized microbial dynamics over time, even between habitats of varying quality, and that desiccated samples could become a viable approach for studying primate gut microbiota. Our work opens the door for other projects to utilize historic biological sample data sets to answer novel temporal microbiome questions in an ecological context.
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Affiliation(s)
- Laura Grieneisen
- Department of Biology, University of British Columbia-Okanagan Campus, Kelowna, BC, Canada
| | - Allison Hays
- Laboratory for the Evolutionary Endocrinology of Primates, University of Arizona, Tucson, AZ, USA
- School of Anthropology, University of Arizona, Tucson, AZ, USA
| | - Erica Cook
- Laboratory for the Evolutionary Endocrinology of Primates, University of Arizona, Tucson, AZ, USA
| | - Ran Blekhman
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Stacey Tecot
- Laboratory for the Evolutionary Endocrinology of Primates, University of Arizona, Tucson, AZ, USA
- School of Anthropology, University of Arizona, Tucson, AZ, USA
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Daybog I, Kolodny O. A computational framework for resolving the microbiome diversity conundrum. Nat Commun 2023; 14:7977. [PMID: 38042865 PMCID: PMC10693575 DOI: 10.1038/s41467-023-42768-4] [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: 11/24/2022] [Accepted: 10/20/2023] [Indexed: 12/04/2023] Open
Abstract
Recent empirical studies offer conflicting findings regarding the relation between host fitness and the composition of its microbiome, a conflict which we term 'the microbial β- diversity conundrum'. The microbiome is crucial for host wellbeing and survival. Surprisingly, different healthy individuals' microbiome compositions, even in the same population, often differ dramatically, contrary to the notion that a vital trait should be highly conserved. Moreover, gnotobiotic individuals exhibit highly deleterious phenotypes, supporting the view that the microbiome is paramount to host fitness. However, the introduction of almost arbitrarily selected microbiota into the system often achieves a significant rescue effect of the deleterious phenotypes. This is true even for microbiota from soil or phylogenetically distant host species, highlighting an apparent paradox. We suggest several solutions to the paradox using a computational framework, simulating the population dynamics of hosts and their microbiomes over multiple generations. The answers invoke factors such as host population size, the specific mode of microbial contribution to host fitness, and typical microbiome richness, offering solutions to the conundrum by highlighting scenarios where even when a host's fitness is determined in full by its microbiome composition, this composition has little effect on the natural selection dynamics of the population.
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Affiliation(s)
- Itay Daybog
- Department of Ecology, Evolution and Behavior, The A. Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel.
| | - Oren Kolodny
- Department of Ecology, Evolution and Behavior, The A. Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel.
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4
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Kearns PJ, Winter AS, Woodhams DC, Northup DE. The Mycobiome of Bats in the American Southwest Is Structured by Geography, Bat Species, and Behavior. MICROBIAL ECOLOGY 2023; 86:1565-1574. [PMID: 37126126 DOI: 10.1007/s00248-023-02230-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 04/23/2023] [Indexed: 06/19/2023]
Abstract
Bats are widespread mammals that play key roles in ecosystems as pollinators and insectivores. However, there is a paucity of information about bat-associated microbes, in particular their fungal communities, despite the important role microbes play in host health and overall host function. The emerging fungal disease, white-nose syndrome, presents a potential challenge to the bat microbiome and understanding healthy bat-associated taxa will provide valuable information about potential microbiome-pathogen interactions. To address this knowledge gap, we collected 174 bat fur/skin swabs from 14 species of bats captured in five locations in New Mexico and Arizona and used high-throughput sequencing of the fungal internal transcribed (ITS) region to characterize bat-associated fungal communities. Our results revealed a highly heterogeneous bat mycobiome that was structured by geography and bat species. Furthermore, our data suggest that bat-associated fungal communities are affected by bat foraging, indicating the bat skin microbiota is dynamic on short time scales. Finally, despite the strong effects of site and species, we found widespread and abundant taxa from several taxonomic groups including the genera Alternaria and Metschnikowia that have the potential to be inhibitory towards fungal and bacterial pathogens.
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Affiliation(s)
- Patrick J Kearns
- Department of Biology, University of Massachusetts Boston, Boston, MA, 02125, USA.
| | - Ara S Winter
- Department of Biology, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Douglas C Woodhams
- Department of Biology, University of Massachusetts Boston, Boston, MA, 02125, USA
| | - Diana E Northup
- Department of Biology, University of New Mexico, Albuquerque, NM, 87131, USA
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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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Manus MB, Sardaro MLS, Dada O, Davis MI, Romoff MR, Torello SG, Ubadigbo E, Wu RC, Miller ES, Amato KR. Interactions with alloparents are associated with the diversity of infant skin and fecal bacterial communities in Chicago, United States. Am J Hum Biol 2023:e23972. [PMID: 37632331 DOI: 10.1002/ajhb.23972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 07/20/2023] [Accepted: 07/21/2023] [Indexed: 08/28/2023] Open
Abstract
INTRODUCTION Social interactions shape the infant microbiome by providing opportunities for caregivers to spread bacteria through physical contact. With most research focused on the impact of maternal-infant contact on the infant gut microbiome, it is unclear how alloparents (i.e., caregivers other than the parents) influence the bacterial communities of infant body sites that are frequently contacted during bouts of caregiving, including the skin. METHODS To begin to understand how allocare may influence the diversity of the infant microbiome, detailed questionnaire data on infant-alloparent relationships and specific allocare behaviors were coupled with skin and fecal microbiome samples (four body sites) from 48 infants living in Chicago, United States. RESULTS Data from 16S rRNA gene amplicon sequencing indicated that infant skin and fecal bacterial diversity showed strong associations (positive and negative) to having female adult alloparents. Alloparental feeding and co-sleeping displayed stronger associations to infant bacterial diversity compared to playing or holding. The associations with allocare behaviors differed in magnitude and direction across infant body sites. Bacterial relative abundances varied by infant-alloparent relationship and breastfeeding status. CONCLUSION This study provides some of the first evidence of an association between allocare and infant skin and fecal bacterial diversity. The results suggest that infants' exposure to bacteria from the social environment may vary based on infant-alloparent relationships and allocare behaviors. Since the microbiome influences immune system development, variation in allocare that impacts the diversity of infant bacterial communities may be an underexplored dimension of the social determinants of health in early life.
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Affiliation(s)
- Melissa B Manus
- Department of Anthropology, Northwestern University, Evanston, Illinois, USA
| | - Maria Luisa Savo Sardaro
- Department of Anthropology, Northwestern University, Evanston, Illinois, USA
- Department of Human Science and Promotion of the Quality of Life, University of San Raffaele, Rome, Italy
| | - Omolola Dada
- Department of Anthropology, Northwestern University, Evanston, Illinois, USA
| | - Maya I Davis
- Department of Anthropology, Northwestern University, Evanston, Illinois, USA
| | - Melissa R Romoff
- Department of Anthropology, Northwestern University, Evanston, Illinois, USA
| | - Stephanie G Torello
- Department of Anthropology, Northwestern University, Evanston, Illinois, USA
| | - Esther Ubadigbo
- Department of Anthropology, Northwestern University, Evanston, Illinois, USA
| | - Rebecca C Wu
- Department of Anthropology, Northwestern University, Evanston, Illinois, USA
| | - Emily S Miller
- Department of Obstetrics and Gynecology, Division of Maternal Fetal Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Katherine R Amato
- Department of Anthropology, Northwestern University, Evanston, Illinois, USA
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7
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Roche KE, Bjork JR, Dasari MR, Grieneisen L, Jansen D, Gould TJ, Gesquiere LR, Barreiro LB, Alberts SC, Blekhman R, Gilbert JA, Tung J, Mukherjee S, Archie EA. Universal gut microbial relationships in the gut microbiome of wild baboons. eLife 2023; 12:e83152. [PMID: 37158607 PMCID: PMC10292843 DOI: 10.7554/elife.83152] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 05/08/2023] [Indexed: 05/10/2023] Open
Abstract
Ecological relationships between bacteria mediate the services that gut microbiomes provide to their hosts. Knowing the overall direction and strength of these relationships is essential to learn how ecology scales up to affect microbiome assembly, dynamics, and host health. However, whether bacterial relationships are generalizable across hosts or personalized to individual hosts is debated. Here, we apply a robust, multinomial logistic-normal modeling framework to extensive time series data (5534 samples from 56 baboon hosts over 13 years) to infer thousands of correlations in bacterial abundance in individual baboons and test the degree to which bacterial abundance correlations are 'universal'. We also compare these patterns to two human data sets. We find that, most bacterial correlations are weak, negative, and universal across hosts, such that shared correlation patterns dominate over host-specific correlations by almost twofold. Further, taxon pairs that had inconsistent correlation signs (either positive or negative) in different hosts always had weak correlations within hosts. From the host perspective, host pairs with the most similar bacterial correlation patterns also had similar microbiome taxonomic compositions and tended to be genetic relatives. Compared to humans, universality in baboons was similar to that in human infants, and stronger than one data set from human adults. Bacterial families that showed universal correlations in human infants were often universal in baboons. Together, our work contributes new tools for analyzing the universality of bacterial associations across hosts, with implications for microbiome personalization, community assembly, and stability, and for designing microbiome interventions to improve host health.
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Affiliation(s)
- Kimberly E Roche
- Program in Computational Biology and Bioinformatics, Duke UniversityDurhamUnited States
| | - Johannes R Bjork
- University of Groningen and University Medical Center Groningen, Department of Gastroenterology and HepatologyGroningenNetherlands
- University of Groningen and University Medical Center Groningen, Department of GeneticsGroningenNetherlands
- Department of Biological Sciences, University of Notre DameNotre DameUnited States
| | - Mauna R Dasari
- Department of Biological Sciences, University of Notre DameNotre DameUnited States
| | - Laura Grieneisen
- Department of Biology, University of British Columbia-Okanagan CampusKelownaCanada
| | - David Jansen
- Department of Biological Sciences, University of Notre DameNotre DameUnited States
| | - Trevor J Gould
- Department of Ecology, Evolution, and Behavior, University of MinnesotaMinneapolisUnited States
| | | | - Luis B Barreiro
- Committee on Genetics, Genomics, and Systems Biology, University of ChicagoChicagoUnited States
- Section of Genetic Medicine, Department of Medicine, University of ChicagoChicagoUnited States
- Committee on Immunology, University of ChicagoChicagoUnited States
| | - Susan C Alberts
- Department of Biology, Duke UniversityDurhamUnited States
- Department of Evolutionary Anthropology, Duke UniversityDurhamUnited States
- Duke University Population Research Institute, Duke UniversityDurhamUnited States
| | - Ran Blekhman
- Section of Genetic Medicine, Department of Medicine, University of ChicagoChicagoUnited States
| | - Jack A Gilbert
- Department of Pediatrics and the Scripps Institution of Oceanography, University of California, San DiegoSan DiegoUnited States
| | - Jenny Tung
- Department of Biology, Duke UniversityDurhamUnited States
- Department of Evolutionary Anthropology, Duke UniversityDurhamUnited States
- Duke University Population Research Institute, Duke UniversityDurhamUnited States
- Department of Primate Behavior and Evolution, Max Planck Institute for Evolutionary AnthropologyLeipzigGermany
| | - Sayan Mukherjee
- Program in Computational Biology and Bioinformatics, Duke UniversityDurhamUnited States
- Departments of Statistical Science, Mathematics, Computer Science, and Bioinformatics & Biostatistics, Duke UniversityDurhamUnited States
- Center for Scalable Data Analytics and Artificial Intelligence, University of LeipzigLeipzigGermany
- Max Plank Institute for Mathematics in the Natural SciencesLeipzigGermany
| | - Elizabeth A Archie
- Department of Biological Sciences, University of Notre DameNotre DameUnited States
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8
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Berman TS, Weinberg M, Moreno KR, Czirják GÁ, Yovel Y. In sickness and in health: the dynamics of the fruit bat gut microbiota under a bacterial antigen challenge and its association with the immune response. Front Immunol 2023; 14:1152107. [PMID: 37114064 PMCID: PMC10126333 DOI: 10.3389/fimmu.2023.1152107] [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: 01/27/2023] [Accepted: 03/27/2023] [Indexed: 04/29/2023] Open
Abstract
Introduction Interactions between the gut microbiome (GM) and the immune system influence host health and fitness. However, few studies have investigated this link and GM dynamics during disease in wild species. Bats (Mammalia: Chiroptera) have an exceptional ability to cope with intracellular pathogens and a unique GM adapted to powered flight. Yet, the contribution of the GM to bat health, especially immunity, or how it is affected by disease, remains unknown. Methods Here, we examined the dynamics of the Egyptian fruit bats' (Rousettus aegyptiacus) GM during health and disease. We provoked an inflammatory response in bats using lipopolysaccharides (LPS), an endotoxin of Gram-negative bacteria. We then measured the inflammatory marker haptoglobin, a major acute phase protein in bats, and analyzed the GM (anal swabs) of control and challenged bats using high-throughput 16S rRNA sequencing, before the challenge, 24h and 48h post challenge. Results We revealed that the antigen challenge causes a shift in the composition of the bat GM (e.g., Weissella, Escherichia, Streptococcus). This shift was significantly correlated with haptoglobin concentration, but more strongly with sampling time. Eleven bacterial sequences were correlated with haptoglobin concentration and nine were found to be potential predictors of the strength of the immune response, and implicit of infection severity, notably Weissella and Escherichia. The bat GM showed high resilience, regaining the colony's group GM composition rapidly, as bats resumed foraging and social activities. Conclusion Our results demonstrate a tight link between bat immune response and changes in their GM, and emphasize the importance of integrating microbial ecology in ecoimmunological studies of wild species. The resilience of the GM may provide this species with an adaptive advantage to cope with infections and maintain colony health.
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Affiliation(s)
- Tali S. Berman
- Department of Zoology, Tel Aviv University, Tel Aviv – Yafo, Israel
- *Correspondence: Tali S. Berman, ; Maya Weinberg,
| | - Maya Weinberg
- Department of Zoology, Tel Aviv University, Tel Aviv – Yafo, Israel
- *Correspondence: Tali S. Berman, ; Maya Weinberg,
| | - Kelsey R. Moreno
- Department of Zoology, Tel Aviv University, Tel Aviv – Yafo, Israel
| | - Gábor Á. Czirják
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Yossi Yovel
- Department of Zoology, Tel Aviv University, Tel Aviv – Yafo, Israel
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv – Yafo, Israel
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9
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Federici L, Masulli M, De Laurenzi V, Allocati N. An overview of bats microbiota and its implication in transmissible diseases. Front Microbiol 2022; 13:1012189. [PMID: 36338090 PMCID: PMC9631491 DOI: 10.3389/fmicb.2022.1012189] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 10/03/2022] [Indexed: 11/17/2022] Open
Abstract
Recent pandemic events have raised the attention of the public on the interactions between human and environment, with particular regard to the more and more feasible transmission to humans of micro-organisms hosted by wild-type species, due to the increasing interspecies contacts originating from human’s activities. Bats, due to their being flying mammals and their increasing promiscuity with humans, have been recognized as hosts frequently capable of transmitting disease-causing microorganisms. Therefore, it is of considerable interest and importance to have a picture as clear as possible of the microorganisms that are hosted by bats. Here we focus on our current knowledge on bats microbiota. We review the most recent literature on this subject, also in view of the bat’s body compartments, their dietary preferences and their habitat. Several pathogenic bacteria, including many carrying multidrug resistance, are indeed common guests of these small mammals, underlining the importance of preserving their habitat, not only to protect them from anthropogenic activities, but also to minimize the spreading of infectious diseases.
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Affiliation(s)
- Luca Federici
- Department of Innovative Technologies in Medicine and Dentistry, University “G. d' Annunzio”, Chieti, Italy
- Center for Advanced Studies and Technology (CAST), University “G. d' Annunzio”, Chieti, Italy
| | - Michele Masulli
- Department of Innovative Technologies in Medicine and Dentistry, University “G. d' Annunzio”, Chieti, Italy
| | - Vincenzo De Laurenzi
- Department of Innovative Technologies in Medicine and Dentistry, University “G. d' Annunzio”, Chieti, Italy
- Center for Advanced Studies and Technology (CAST), University “G. d' Annunzio”, Chieti, Italy
| | - Nerino Allocati
- Department of Innovative Technologies in Medicine and Dentistry, University “G. d' Annunzio”, Chieti, Italy
- *Correspondence: Nerino Allocati,
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10
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Kitrinos C, Bell RB, Bradley BJ, Kamilar JM. Hair Microbiome Diversity within and across Primate Species. mSystems 2022; 7:e0047822. [PMID: 35876529 PMCID: PMC9426569 DOI: 10.1128/msystems.00478-22] [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: 05/26/2022] [Accepted: 07/05/2022] [Indexed: 12/24/2022] Open
Abstract
Primate hair and skin are substrates upon which social interactions occur and are host-pathogen interfaces. While human hair and skin microbiomes display body site specificity and immunological significance, little is known about the nonhuman primate (NHP) hair microbiome. Here, we collected hair samples (n = 158) from 8 body sites across 12 NHP species housed at three zoological institutions in the United States to examine the following: (1) the diversity and composition of the primate hair microbiome and (2) the factors predicting primate hair microbiome diversity and composition. If both environmental and evolutionary factors shape the microbiome, then we expect significant differences in microbiome diversity across host body sites, sexes, institutions, and species. We found our samples contained high abundances of gut-, respiratory-, and environment-associated microbiota. In addition, multiple factors predicted microbiome diversity and composition, although host species identity outweighed sex, body site, and institution as the strongest predictor. Our results suggest that hair microbial communities are affected by both evolutionary and environmental factors and are relatively similar across nonhuman primate body sites, which differs from the human condition. These findings have important implications for understanding the biology and conservation of wild and captive primates and the uniqueness of the human microbiome. IMPORTANCE We created the most comprehensive primate hair and skin data set to date, including data from 12 nonhuman primate species sampled from 8 body regions each. We find that the nonhuman primate hair microbiome is distinct from the human hair and skin microbiomes in that it is relatively uniform-as opposed to distinct-across body regions and is most abundant in gut-, environment-, and respiratory-associated microbiota rather than human skin-associated microbiota. Furthermore, we found that the nonhuman primate hair microbiome varies with host species identity, host sex, host environment, and host body site, with host species identity being the strongest predictor. This result demonstrates that nonhuman primate hair microbiome diversity varies with both evolutionary and environmental factors and within and across primate species. These findings have important implications for understanding the biology and conservation of wild and captive primates and the uniqueness of the human microbiome.
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Affiliation(s)
- Catherine Kitrinos
- Department of Anthropology, University of Massachusetts, Amherst, Massachusetts, USA
| | - Rachel B. Bell
- Graduate Program in Organismic and Evolution Biology, University of Massachusetts, Amherst, Massachusetts, USA
| | - Brenda J. Bradley
- Center for the Advanced Study of Human Paleobiology, The George Washington University, Washington, DC, USA
- Department of Anthropology, The George Washington University, Washington, DC, USA
| | - Jason M. Kamilar
- Department of Anthropology, University of Massachusetts, Amherst, Massachusetts, USA
- Graduate Program in Organismic and Evolution Biology, University of Massachusetts, Amherst, Massachusetts, USA
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11
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Björk JR, Dasari MR, Roche K, Grieneisen L, Gould TJ, Grenier JC, Yotova V, Gottel N, Jansen D, Gesquiere LR, Gordon JB, Learn NH, Wango TL, Mututua RS, Kinyua Warutere J, Siodi L, Mukherjee S, Barreiro LB, Alberts SC, Gilbert JA, Tung J, Blekhman R, Archie EA. Synchrony and idiosyncrasy in the gut microbiome of wild baboons. Nat Ecol Evol 2022; 6:955-964. [PMID: 35654895 PMCID: PMC9271586 DOI: 10.1038/s41559-022-01773-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 04/20/2022] [Indexed: 01/04/2023]
Abstract
Human gut microbial dynamics are highly individualized, making it challenging to link microbiota to health and to design universal microbiome therapies. This individuality is typically attributed to variation in host genetics, diets, environments and medications but it could also emerge from fundamental ecological forces that shape microbiota more generally. Here, we leverage extensive gut microbial time series from wild baboons-hosts who experience little interindividual dietary and environmental heterogeneity-to test whether gut microbial dynamics are synchronized across hosts or largely idiosyncratic. Despite their shared lifestyles, baboon microbiota were only weakly synchronized. The strongest synchrony occurred among baboons living in the same social group, probably because group members range over the same habitat and simultaneously encounter the same sources of food and water. However, this synchrony was modest compared to each host's personalized dynamics. In support, host-specific factors, especially host identity, explained, on average, more than three times the deviance in longitudinal dynamics compared to factors shared with social group members and ten times the deviance of factors shared across the host population. These results contribute to mounting evidence that highly idiosyncratic gut microbiomes are not an artefact of modern human environments and that synchronizing forces in the gut microbiome (for example, shared environments, diets and microbial dispersal) are not strong enough to overwhelm key drivers of microbiome personalization, such as host genetics, priority effects, horizontal gene transfer and functional redundancy.
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Affiliation(s)
- Johannes R Björk
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA.
| | - Mauna R Dasari
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Kim Roche
- Program in Computational Biology and Bioinformatics, Duke University, Durham, NC, USA
| | - Laura Grieneisen
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, USA
| | - Trevor J Gould
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, USA
| | - Jean-Christophe Grenier
- Department of Genetics, CHU Sainte Justine Research Center, Montréal, Quebec, Canada
- Research Center, Montreal Heart Institute, Montréal, Quebec, Canada
| | - Vania Yotova
- Department of Genetics, CHU Sainte Justine Research Center, Montréal, Quebec, Canada
| | - Neil Gottel
- Department of Pediatrics and the Scripps Institution of Oceanography, University of California, San Diego, San Diego, CA, USA
| | - David Jansen
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | | | | | - Niki H Learn
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Tim L Wango
- Amboseli Baboon Research Project, Amboseli National Park, Amboseli, Kenya
- The Department of Veterinary Anatomy and Animal Physiology, University of Nairobi, Nairobi, Kenya
| | - Raphael S Mututua
- Amboseli Baboon Research Project, Amboseli National Park, Amboseli, Kenya
| | - J Kinyua Warutere
- Amboseli Baboon Research Project, Amboseli National Park, Amboseli, Kenya
| | - Long'ida Siodi
- Amboseli Baboon Research Project, Amboseli National Park, Amboseli, Kenya
| | - Sayan Mukherjee
- Program in Computational Biology and Bioinformatics, Duke University, Durham, NC, USA
| | - Luis B Barreiro
- Department of Medicine, Section of Genetic Medicine, University of Chicago, Chicago, IL, USA
| | - Susan C Alberts
- Department of Biology, Duke University, Durham, NC, USA
- Department of Evolutionary Anthropology, Duke University, Durham, NC, USA
- Duke University Population Research Institute, Duke University, Durham, NC, USA
| | - Jack A Gilbert
- Department of Pediatrics and the Scripps Institution of Oceanography, University of California, San Diego, San Diego, CA, USA
| | - Jenny Tung
- Department of Biology, Duke University, Durham, NC, USA
- Department of Evolutionary Anthropology, Duke University, Durham, NC, USA
- Duke University Population Research Institute, Duke University, Durham, NC, USA
- Canadian Institute for Advanced Research, Toronto, Ontario, Canada
| | - Ran Blekhman
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, USA
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Minneapolis, MN, USA
| | - Elizabeth A Archie
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA.
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12
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Forsythe A, Fontaine N, Bissonnette J, Hayashi B, Insuk C, Ghosh S, Kam G, Wong A, Lausen C, Xu J, Cheeptham N. Microbial isolates with Anti-Pseudogymnoascus destructans activities from Western Canadian bat wings. Sci Rep 2022; 12:9895. [PMID: 35701553 PMCID: PMC9198084 DOI: 10.1038/s41598-022-14223-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 06/02/2022] [Indexed: 11/29/2022] Open
Abstract
Pseudogymnoascus destructans (Pd) is the causative agent of white-nose syndrome, which has resulted in the death of millions of bats in North America (NA) since 2006. Based on mortalities in eastern NA, the westward spread of infections likely poses a significant threat to western NA bats. To help prevent/reduce Pd infections in bats in western NA, we isolated bacteria from the wings of wild bats and screened for inhibitory activity against Pd. In total, we obtained 1,362 bacterial isolates from 265 wild bats of 13 species in western Canada. Among the 1,362 isolates, 96 showed inhibitory activity against Pd based on a coculture assay. The inhibitory activities varied widely among these isolates, ranging from slowing fungal growth to complete inhibition. Interestingly, host bats containing isolates with anti-Pd activities were widely distributed, with no apparent geographic or species-specific pattern. However, characteristics of roosting sites and host demography showed significant associations with the isolation of anti-Pd bacteria. Specifically, anthropogenic roosts and swabs from young males had higher frequencies of anti-Pd bacteria than those from natural roosts and those from other sex and age-groups, respectively. These anti-Pd bacteria could be potentially used to help mitigate the impact of WNS. Field trials using these as well as additional microbes from future screenings are needed in order to determine their effectiveness for the prevention and treatment against WNS.
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Affiliation(s)
- Adrian Forsythe
- Department of Biology, Faculty of Science, McMaster University, Hamilton, ON, L8S 4K1, Canada
| | - Nick Fontaine
- Department of Biological Sciences, Faculty of Science, Thompson Rivers University, Kamloops, BC, V2C 08C, Canada
| | - Julianna Bissonnette
- Department of Biological Sciences, Faculty of Science, Thompson Rivers University, Kamloops, BC, V2C 08C, Canada
| | - Brandon Hayashi
- Department of Biological Sciences, Faculty of Science, Thompson Rivers University, Kamloops, BC, V2C 08C, Canada
| | - Chadabhorn Insuk
- Department of Biology, Faculty of Science, McMaster University, Hamilton, ON, L8S 4K1, Canada.,Department of Biological Sciences, Faculty of Science, Thompson Rivers University, Kamloops, BC, V2C 08C, Canada
| | - Soumya Ghosh
- Department of Biological Sciences, Faculty of Science, Thompson Rivers University, Kamloops, BC, V2C 08C, Canada.,Department of Genetics, Natural and Agricultural Sciences, University of the Free State, Bloemfontein, South Africa
| | - Gabrielle Kam
- Department of Biological Sciences, Faculty of Science, Thompson Rivers University, Kamloops, BC, V2C 08C, Canada
| | - Aaron Wong
- Department of Biological Sciences, Faculty of Science, Thompson Rivers University, Kamloops, BC, V2C 08C, Canada
| | - Cori Lausen
- Wildlife Conservation Society Canada, P.O. Box 606, Kaslo, BC, V0G 1M0, Canada.
| | - Jianping Xu
- Department of Biology, Faculty of Science, McMaster University, Hamilton, ON, L8S 4K1, Canada.
| | - Naowarat Cheeptham
- Department of Biological Sciences, Faculty of Science, Thompson Rivers University, Kamloops, BC, V2C 08C, Canada.
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13
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Jorge F, Dheilly NM, Froissard C, Wainwright E, Poulin R. Consistency of Bacterial Communities in a Parasitic Worm: Variation Throughout the Life Cycle and Across Geographic Space. MICROBIAL ECOLOGY 2022; 83:724-738. [PMID: 34136952 DOI: 10.1007/s00248-021-01774-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 05/12/2021] [Indexed: 06/12/2023]
Abstract
Microbial communities within metazoans are increasingly linked with development, health and behaviour, possibly functioning as integrated evolutionary units with the animal in which they live. This would require microbial communities to show some consistency both ontogenetically (across life stages) and geographically (among populations). We characterise the bacteriome of the parasitic trematode Philophthalmus attenuatus, which undergoes major life cycle transitions, and test whether its bacteriome remains consistent on developmental and spatial scales. Based on sequencing the prokaryotic 16S SSU rRNA gene, we compared the parasite bacteriome (i) across three life stages (rediae in snails, cercariae exiting snails, adults in birds) in one locality and (ii) among three geographic localities for rediae only. We found that each life stage harbours a bacteriome different from that of its host (except the adult stage) and the external environment. Very few bacterial taxa were shared among life stages, suggesting substantial ontogenetic turnover in bacteriome composition. Rediae from the three different localities also had different bacteriomes, with dissimilarities increasing with geographical distance. However, rediae from different localities nevertheless shared more bacterial taxa than did different life stages from the same locality. Changes in the bacteriome along the parasite's developmental history but some degree of geographical stability within a given life stage point toward non-random, stage-specific acquisition, selection and/or propagation of bacteria.
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Affiliation(s)
- Fátima Jorge
- Department of Zoology, University of Otago, P.O. Box 56, Dunedin, 9054, New Zealand
| | - Nolwenn M Dheilly
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, USA
- ANSES, Agence Nationale de Sécurité Sanitaire de L'Alimentation, de l'Environnement et du Travail - Laboratoire de Ploufragan-Plouzané, Unité Génétique Virale de Biosécurité, Ploufragan, France
| | - Céline Froissard
- Department of Zoology, University of Otago, P.O. Box 56, Dunedin, 9054, New Zealand
| | - Eleanor Wainwright
- Department of Zoology, University of Otago, P.O. Box 56, Dunedin, 9054, New Zealand
| | - Robert Poulin
- Department of Zoology, University of Otago, P.O. Box 56, Dunedin, 9054, New Zealand.
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14
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Do gastrointestinal microbiomes play a role in bats' unique viral hosting capacity? Trends Microbiol 2022; 30:632-642. [PMID: 35034797 DOI: 10.1016/j.tim.2021.12.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 12/14/2021] [Accepted: 12/17/2021] [Indexed: 11/20/2022]
Abstract
Bats are reservoirs for zoonotic viruses, which they tolerate without experiencing disease. Research focused on deciphering mechanisms of virus tolerance in bats has rarely considered the influence of their gastrointestinal tract (GIT) microbiome. In mammals, GIT microbiomes influence infections through their effect on host physiology, immunity, nutrition, and behavior. Bat GIT microbiomes more closely resemble the Proteobacteria-dominated GIT microbiomes of birds than those of other mammals. As an adaptation to flight, bats have rapid GIT transit times which may reduce the stability of their microbiome, constrain nutrient uptake, and affect pathogen exposure and evolution of tolerance mechanisms. Experimental and longitudinal studies are needed to understand the function of bats' GIT microbiomes and their role in modulating viral infection dynamics.
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15
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Natural selection for imprecise vertical transmission in host-microbiota systems. Nat Ecol Evol 2022; 6:77-87. [PMID: 34949814 PMCID: PMC9901532 DOI: 10.1038/s41559-021-01593-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 10/19/2021] [Indexed: 02/08/2023]
Abstract
How and when the microbiome modulates host adaptation remains an evolutionary puzzle, despite evidence that the extended genetic repertoire of the microbiome can shape host phenotypes and fitness. One complicating factor is that the microbiome is often transmitted imperfectly across host generations, leading to questions about the degree to which the microbiome contributes to host adaptation. Here, using an evolutionary model, we demonstrate that decreasing vertical transmission fidelity can increase microbiome variation, and thus phenotypic variation, across hosts. When the most beneficial microbial genotypes change unpredictably from one generation to the next (for example, in variable environments), hosts can maximize fitness by increasing the microbiome variation among offspring, as this improves the chance of there being an offspring with the right microbial combination for the next generation. Imperfect vertical transmission can therefore be adaptive in varying environments. We characterize how selection on vertical transmission is shaped by environmental conditions, microbiome changes during host development and the contribution of other factors to trait variation. We illustrate how environmentally dependent microbial effects can favour intermediate transmission and set our results in the context of examples from natural systems. We also suggest research avenues to empirically test our predictions. Our model provides a basis to understand the evolutionary pathways that potentially led to the wide diversity of microbe transmission patterns found in nature.
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16
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Yarlagadda K, Razik I, Malhi RS, Carter GG. Social convergence of gut microbiomes in vampire bats. Biol Lett 2021; 17:20210389. [PMID: 34727703 PMCID: PMC8563296 DOI: 10.1098/rsbl.2021.0389] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 10/11/2021] [Indexed: 12/12/2022] Open
Abstract
The 'social microbiome' can fundamentally shape the costs and benefits of group-living, but understanding social transmission of microbes in free-living animals is challenging due to confounding effects of kinship and shared environments (e.g. highly associated individuals often share the same spaces, food and water). Here, we report evidence for convergence towards a social microbiome among introduced common vampire bats, Desmodus rotundus, a highly social species in which adults feed only on blood, and engage in both mouth-to-body allogrooming and mouth-to-mouth regurgitated food sharing. Shotgun sequencing of samples from six zoos in the USA, 15 wild-caught bats from a colony in Belize and 31 bats from three colonies in Panama showed that faecal microbiomes were more similar within colonies than between colonies. To assess microbial transmission, we created an experimentally merged group of the Panama bats from the three distant sites by housing these bats together for four months. In this merged colony, we found evidence that dyadic gut microbiome similarity increased with both clustering and oral contact, leading to microbiome convergence among introduced bats. Our findings demonstrate that social interactions shape microbiome similarity even when controlling for past social history, kinship, environment and diet.
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Affiliation(s)
- Karthik Yarlagadda
- Department of Anthropology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Imran Razik
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA
- Smithsonian Tropical Research Institute, Balboa, Ancón, Panama
| | - Ripan S. Malhi
- Department of Anthropology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Program in Ecology, Evolution and Conservation Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Gerald G. Carter
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA
- Smithsonian Tropical Research Institute, Balboa, Ancón, Panama
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17
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Perofsky AC, Ancel Meyers L, Abondano LA, Di Fiore A, Lewis RJ. Social groups constrain the spatiotemporal dynamics of wild sifaka gut microbiomes. Mol Ecol 2021; 30:6759-6775. [PMID: 34558751 DOI: 10.1111/mec.16193] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 08/25/2021] [Accepted: 09/17/2021] [Indexed: 12/29/2022]
Abstract
Primates acquire gut microbiota from conspecifics through direct social contact and shared environmental exposures. Host behaviour is a prominent force in structuring gut microbial communities, yet the extent to which group or individual-level forces shape the long-term dynamics of gut microbiota is poorly understood. We investigated the effects of three aspects of host sociality (social groupings, dyadic interactions, and individual dispersal between groups) on gut microbiome composition and plasticity in 58 wild Verreaux's sifaka (Propithecus verreauxi) from six social groups. Over the course of three dry seasons in a 5-year period, the six social groups maintained distinct gut microbial signatures, with the taxonomic composition of individual communities changing in tandem among coresiding group members. Samples collected from group members during each season were more similar than samples collected from single individuals across different years. In addition, new immigrants and individuals with less stable social ties exhibited elevated rates of microbiome turnover across seasons. Our results suggest that permanent social groupings shape the changing composition of commensal and mutualistic gut microbial communities and thus may be important drivers of health and resilience in wild primate populations.
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Affiliation(s)
- Amanda C Perofsky
- Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, USA
| | - Lauren Ancel Meyers
- Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, USA.,Santa Fe Institute, Santa Fe, New Mexico, USA
| | - Laura A Abondano
- Department of Anthropology, The University of Texas at Austin, Austin, Texas, USA.,Primate Molecular Ecology and Evolution Laboratory, The University of Texas at Austin, Austin, Texas, USA
| | - Anthony Di Fiore
- Department of Anthropology, The University of Texas at Austin, Austin, Texas, USA.,Primate Molecular Ecology and Evolution Laboratory, The University of Texas at Austin, Austin, Texas, USA
| | - Rebecca J Lewis
- Department of Anthropology, The University of Texas at Austin, Austin, Texas, USA
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18
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Lutz HL, Gilbert JA, Dick CW. Associations between Afrotropical bats, eukaryotic parasites, and microbial symbionts. Mol Ecol 2021; 31:1939-1950. [PMID: 34181795 PMCID: PMC9546020 DOI: 10.1111/mec.16044] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 05/06/2021] [Accepted: 06/16/2021] [Indexed: 01/06/2023]
Abstract
Skin is the largest mammalian organ and the first defensive barrier against the external environment. The skin and fur of mammals can host a wide variety of ectoparasites, many of which are phylogenetically diverse, specialized, and specifically adapted to their hosts. Among hematophagous dipteran parasites, volatile organic compounds (VOCs) are known to serve as important attractants, leading parasites to compatible sources of blood meals. VOCs have been hypothesized to be mediated by host‐associated bacteria, which may thereby indirectly influence parasitism. Host‐associated bacteria may also influence parasitism directly, as has been observed in interactions between animal gut microbiota and malarial parasites. Hypotheses relating bacterial symbionts and eukaryotic parasitism have rarely been tested among humans and domestic animals, and to our knowledge have not been tested in wild vertebrates. In this study, we used Afrotropical bats, hematophagous ectoparasitic bat flies, and haemosporidian (malarial) parasites vectored by bat flies as a model to test the hypothesis that the vertebrate host microbiome is linked to parasitism in a wild system. We identified significant correlations between bacterial community composition of the skin and dipteran ectoparasite prevalence across four major bat lineages, as well as striking differences in skin microbial network characteristics between ectoparasitized and nonectoparasitized bats. We also identified links between the oral microbiome and presence of malarial parasites among miniopterid bats. Our results support the hypothesis that microbial symbionts may serve as indirect mediators of parasitism among eukaryotic hosts and parasites. see also the Perspective by Kelly A. Speer
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Affiliation(s)
- Holly L Lutz
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.,Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.,Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, IL, USA
| | - Jack A Gilbert
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.,Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Carl W Dick
- Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, IL, USA.,Department of Biology, Western Kentucky University, Bowling Green, KY, USA
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19
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Abstract
In the Anthropocene, humans, domesticated animals, wildlife, and their environments are interconnected, especially as humans advance further into wildlife habitats. Wildlife gut microbiomes play a vital role in host health. Changes to wildlife gut microbiomes due to anthropogenic disturbances, such as habitat fragmentation, can disrupt natural gut microbiota homeostasis and make animals vulnerable to infections that may become zoonotic. However, it remains unclear whether the disruption to wildlife gut microbiomes is caused by habitat fragmentation per se or the combination of habitat fragmentation with additional anthropogenic disturbances, such as contact with humans, domesticated animals, invasive species, and their pathogens. Here, we show that habitat fragmentation per se does not impact the gut microbiome of a generalist rodent species native to Central America, Tome's spiny rat Proechimys semispinosus, but additional anthropogenic disturbances do. Indeed, compared to protected continuous and fragmented forest landscapes that are largely untouched by other human activities, the gut microbiomes of spiny rats inhabiting human-disturbed fragmented landscapes revealed a reduced alpha diversity and a shifted and more dispersed beta diversity. Their microbiomes contained more taxa associated with domesticated animals and their potential pathogens, suggesting a shift in potential metagenome functions. On the one hand, the compositional shift could indicate a degree of gut microbial adaption known as metagenomic plasticity. On the other hand, the greater variation in community structure and reduced alpha diversity may signal a decline in beneficial microbial functions and illustrate that gut adaption may not catch up with anthropogenic disturbances, even in a generalist species with large phenotypic plasticity, with potentially harmful consequences to both wildlife and human health.
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20
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Egert-Berg K, Handel M, Goldshtein A, Eitan O, Borissov I, Yovel Y. Fruit bats adjust their foraging strategies to urban environments to diversify their diet. BMC Biol 2021; 19:123. [PMID: 34134697 PMCID: PMC8210355 DOI: 10.1186/s12915-021-01060-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 05/30/2021] [Indexed: 11/18/2022] Open
Abstract
Background Urbanization is one of the most influential processes on our globe, putting a great number of species under threat. Some species learn to cope with urbanization, and a few even benefit from it, but we are only starting to understand how they do so. In this study, we GPS tracked Egyptian fruit bats from urban and rural populations to compare their movement and foraging in urban and rural environments. Because fruit trees are distributed differently in these two environments, with a higher diversity in urban environments, we hypothesized that foraging strategies will differ too. Results When foraging in urban environments, bats were much more exploratory than when foraging in rural environments, visiting more sites per hour and switching foraging sites more often on consecutive nights. By doing so, bats foraging in settlements diversified their diet in comparison to rural bats, as was also evident from their choice to often switch fruit species. Interestingly, the location of the roost did not dictate the foraging grounds, and we found that many bats choose to roost in the countryside but nightly commute to and forage in urban environments. Conclusions Bats are unique among small mammals in their ability to move far rapidly. Our study is an excellent example of how animals adjust to environmental changes, and it shows how such mobile mammals might exploit the new urban fragmented environment that is taking over our landscape. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01060-x.
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Affiliation(s)
- Katya Egert-Berg
- Sagol School of Neuroscience, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Michal Handel
- School of Zoology, Faculty of Life Sciences, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Aya Goldshtein
- School of Zoology, Faculty of Life Sciences, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Ofri Eitan
- School of Zoology, Faculty of Life Sciences, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Ivailo Borissov
- School of Zoology, Faculty of Life Sciences, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Yossi Yovel
- Sagol School of Neuroscience, Tel Aviv University, 6997801, Tel Aviv, Israel. .,School of Zoology, Faculty of Life Sciences, Tel Aviv University, 6997801, Tel Aviv, Israel. .,Wissenschaftskolleg zu Berlin, Berlin, Germany.
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21
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The presence of Pseudogymnoascus destructans, a fungal pathogen of bats, correlates with changes in microbial metacommunity structure. Sci Rep 2021; 11:11685. [PMID: 34083632 PMCID: PMC8175404 DOI: 10.1038/s41598-021-91118-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 05/18/2021] [Indexed: 02/04/2023] Open
Abstract
Metacommunity theory provides a framework for how community patterns arise from processes across scales, which is relevant for understanding patterns in host-associated microbial assemblages. Microbial metacommunities may have important roles in host health through interactions with pathogens; however, it is unclear how pathogens affect host microbial metacommunities. Here, we studied relationships between a fungal pathogen and a host-associated microbial metacommunity. We hypothesized that a fungal pathogen of bats, Pseudogymnoascus destructans, correlates with a shift in metacommunity structure and changes in relationships between community composition, and factors shaping these assemblages, such as ecoregion. We sampled bat cutaneous microbial assemblages in the presence/absence of P. destructans and analyzed microbial metacommunity composition and relationships with structuring variables. Absence of P. destructans correlated with a metacommunity characterized by a common core microbial group that was lacking in disease positive bats. Additionally, P. destructans presence correlated with a change in the relationship between community structure and ecoregion. Our results suggest that the fungal pathogen intensifies local processes influencing a microbial metacommunity and highlights the importance of cutaneous microbial assemblages in host-pathogen interactions.
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22
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Moreno KR, Weinberg M, Harten L, Salinas Ramos VB, Herrera M LG, Czirják GÁ, Yovel Y. Sick bats stay home alone: fruit bats practice social distancing when faced with an immunological challenge. Ann N Y Acad Sci 2021; 1505:178-190. [PMID: 33876431 PMCID: PMC9290741 DOI: 10.1111/nyas.14600] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 03/10/2021] [Accepted: 03/18/2021] [Indexed: 12/21/2022]
Abstract
Along with its many advantages, social roosting imposes a major risk of pathogen transmission. How social animals reduce this risk is poorly documented. We used lipopolysaccharide challenge to imitate bacterial infection in both a captive and a free‐living colony of an extremely social, long‐lived mammal—the Egyptian fruit bat. We monitored behavioral and physiological responses using an arsenal of methods, including onboard GPS to track foraging, acceleration sensors to monitor movement, infrared video to record social behavior, and blood samples to measure immune markers. Sick‐like (immune‐challenged) bats exhibited an increased immune response, as well as classic illness symptoms, including fever, weight loss, anorexia, and lethargy. Notably, the bats also exhibited behaviors that would reduce pathogen transfer. They perched alone and appeared to voluntarily isolate themselves from the group by leaving the social cluster, which is extremely atypical for this species. The sick‐like individuals in the open colony ceased foraging outdoors for at least two nights, thus reducing transmission to neighboring colonies. Together, these sickness behaviors demonstrate a strong, integrative immune response that promotes recovery of infected individuals while reducing pathogen transmission inside and outside the roost, including spillover events to other species, such as humans.
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Affiliation(s)
- Kelsey R Moreno
- Department of Zoology, Tel Aviv University, Tel Aviv, Israel
| | - Maya Weinberg
- Department of Zoology, Tel Aviv University, Tel Aviv, Israel
| | - Lee Harten
- Department of Zoology, Tel Aviv University, Tel Aviv, Israel
| | - Valeria B Salinas Ramos
- Department of Agriculture, University of Naples Federico II, Naples, Italy.,Estación de Biología Chamela, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico, Mexico
| | - L Gerardo Herrera M
- Estación de Biología Chamela, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico, Mexico
| | - Gábor Á Czirják
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Yossi Yovel
- Department of Zoology, Tel Aviv University, Tel Aviv, Israel.,Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
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23
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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: 84] [Impact Index Per Article: 28.0] [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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24
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Clarke LJ, Suter L, King R, Bissett A, Bestley S, Deagle BE. Bacterial epibiont communities of panmictic Antarctic krill are spatially structured. Mol Ecol 2021; 30:1042-1052. [PMID: 33300251 DOI: 10.1111/mec.15771] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 10/09/2020] [Accepted: 12/03/2020] [Indexed: 12/28/2022]
Abstract
Antarctic krill (Euphausia superba) are amongst the most abundant animals on Earth, with a circumpolar distribution in the Southern Ocean. Genetic and genomic studies have failed to detect any population structure for the species, suggesting a single panmictic population. However, the hyper-abundance of krill slows the rate of genetic differentiation, masking potential underlying structure. Here we use high-throughput sequencing of bacterial 16S rRNA genes to show that krill bacterial epibiont communities exhibit spatial structuring, driven mainly by distance rather than environmental factors, especially for strongly krill-associated bacteria. Estimating the ecological processes driving bacterial community turnover indicated this was driven by bacterial dispersal limitation increasing with geographic distance. Furthermore, divergent epibiont communities generated from a single krill swarm split between aquarium tanks under near-identical conditions suggests physical isolation in itself can cause krill-associated bacterial communities to diverge. Our findings show that Antarctic krill-associated bacterial communities are geographically structured, in direct contrast with the lack of structure observed for krill genetic and genomic data.
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Affiliation(s)
- Laurence J Clarke
- Australian Antarctic Division, Kingston, Tas, Australia.,Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tas, Australia.,Antarctic Climate & Ecosystems Cooperative Research Centre, University of Tasmania, Hobart, Tas, Australia
| | - Léonie Suter
- Australian Antarctic Division, Kingston, Tas, Australia
| | - Rob King
- Australian Antarctic Division, Kingston, Tas, Australia
| | - Andrew Bissett
- Commonwealth Scientific and Industrial Research Organisation, Hobart, Tas, Australia
| | - Sophie Bestley
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tas, Australia
| | - Bruce E Deagle
- Australian Antarctic Division, Kingston, Tas, Australia.,Commonwealth Scientific and Industrial Research Organisation, Hobart, Tas, Australia
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25
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Turjeman S, Corl A, Wolfenden A, Tsalyuk M, Lublin A, Choi O, Kamath PL, Getz WM, Bowie RCK, Nathan R. Migration, pathogens and the avian microbiome: A comparative study in sympatric migrants and residents. Mol Ecol 2020; 29:4706-4720. [PMID: 33001530 DOI: 10.1111/mec.15660] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 09/17/2020] [Accepted: 09/18/2020] [Indexed: 12/15/2022]
Abstract
Animals generally benefit from their gastrointestinal microbiome, but the factors that influence the composition and dynamics of their microbiota remain poorly understood. Studies of nonmodel host species can illuminate how microbiota and their hosts interact in natural environments. We investigated the role of migratory behaviour in shaping the gut microbiota of free-ranging barn swallows (Hirundo rustica) by studying co-occurring migrant and resident subspecies sampled during the autumn migration at a migratory bottleneck. We found that within-host microbial richness (α-diversity) was similar between migrant and resident microbial communities. In contrast, we found that microbial communities (β-diversity) were significantly different between groups regarding both microbes present and their relative abundances. Compositional differences were found for 36 bacterial genera, with 27 exhibiting greater abundance in migrants and nine exhibiting greater abundance in residents. There was heightened abundance of Mycoplasma spp. and Corynebacterium spp. in migrants, a pattern shared by other studies of migratory species. Screens for key regional pathogens revealed that neither residents nor migrants carried avian influenza viruses and Newcastle disease virus, suggesting that the status of these diseases did not underlie observed differences in microbiome composition. Furthermore, the prevalence and abundance of Salmonella spp., as determined from microbiome data and cultural assays, were both low and similar across the groups. Overall, our results indicate that microbial composition differs between migratory and resident barn swallows, even when they are conspecific and sympatrically occurring. Differences in host origins (breeding sites) may result in microbial community divergence, and varied behaviours throughout the annual cycle (e.g., migration) could further differentiate compositional structure as it relates to functional needs.
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Affiliation(s)
- Sondra Turjeman
- Movement Ecology Laboratory, Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ammon Corl
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA, USA
| | - Andrew Wolfenden
- Movement Ecology Laboratory, Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Miriam Tsalyuk
- Movement Ecology Laboratory, Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Avishai Lublin
- Division of Avian Diseases, Kimron Veterinary Institute, Bet Dagan, Israel
| | - Olivia Choi
- School of Food and Agriculture, University of Maine, Orono, ME, USA
| | - Pauline L Kamath
- School of Food and Agriculture, University of Maine, Orono, ME, USA
| | - Wayne M Getz
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, USA.,School Mathematical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Rauri C K Bowie
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA, USA.,Department of Integrative Biology, University of California, Berkeley, CA, USA
| | - Ran Nathan
- Movement Ecology Laboratory, Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
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26
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Lemieux-Labonté V, Dorville NASY, Willis CKR, Lapointe FJ. Antifungal Potential of the Skin Microbiota of Hibernating Big Brown Bats ( Eptesicus fuscus) Infected With the Causal Agent of White-Nose Syndrome. Front Microbiol 2020; 11:1776. [PMID: 32793178 PMCID: PMC7390961 DOI: 10.3389/fmicb.2020.01776] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 07/06/2020] [Indexed: 01/01/2023] Open
Abstract
Little is known about skin microbiota in the context of the disease white-nose syndrome (WNS), caused by the fungus Pseudogymnoascus destructans (Pd), that has caused enormous declines of hibernating North American bats over the past decade. Interestingly, some hibernating species, such as the big brown bat (Eptesicus fuscus), appear resistant to the disease and their skin microbiota could play a role. However, a comprehensive analysis of the skin microbiota of E. fuscus in the context of Pd has not been done. In January 2017, we captured hibernating E. fuscus, sampled their skin microbiota, and inoculated them with Pd or sham inoculum. We allowed the bats to hibernate in the lab under controlled conditions for 11 weeks and then sampled their skin microbiota to test the following hypotheses: (1) Pd infection would not disrupt the skin microbiota of Pd-resistant E. fuscus; and (2) microbial taxa with antifungal properties would be abundant both before and after inoculation with Pd. Using high-throughput 16S rRNA gene sequencing, we discovered that beta diversity of Pd-inoculated bats changed more over time than that of sham-inoculated bats. Still, the most abundant taxa in the community were stable throughout the experiment. Among the most abundant taxa, Pseudomonas and Rhodococcus are known for antifungal potential against Pd and other fungi. Thus, in contrast to hypothesis 1, Pd infection destabilized the skin microbiota but consistent with hypothesis 2, bacteria with known antifungal properties remained abundant and stable on the skin. This study is the first to provide a comprehensive survey of skin microbiota of E. fuscus, suggesting potential associations between the bat skin microbiota and resistance to the Pd infection and WNS. These results set the stage for future studies to characterize microbiota gene expression, better understand mechanisms of resistance to WNS, and help develop conservation strategies.
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Affiliation(s)
| | - Nicole A. S.-Y. Dorville
- Department of Biology, Centre for Forest Interdisciplinary Research, The University of Winnipeg, Winnipeg, MB, Canada
| | - Craig K. R. Willis
- Department of Biology, Centre for Forest Interdisciplinary Research, The University of Winnipeg, Winnipeg, MB, Canada
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27
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Harten L, Katz A, Goldshtein A, Handel M, Yovel Y. The ontogeny of a mammalian cognitive map in the real world. Science 2020; 369:194-197. [PMID: 32647001 DOI: 10.1126/science.aay3354] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 05/29/2020] [Indexed: 11/02/2022]
Abstract
How animals navigate over large-scale environments remains a riddle. Specifically, it is debated whether animals have cognitive maps. The hallmark of map-based navigation is the ability to perform shortcuts, i.e., to move in direct but novel routes. When tracking an animal in the wild, it is extremely difficult to determine whether a movement is truly novel because the animal's past movement is unknown. We overcame this difficulty by continuously tracking wild fruit bat pups from their very first flight outdoors and over the first months of their lives. Bats performed truly original shortcuts, supporting the hypothesis that they can perform large-scale map-based navigation. We documented how young pups developed their visual-based map, exemplifying the importance of exploration and demonstrating interindividual differences.
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Affiliation(s)
- Lee Harten
- School of Zoology, Faculty of Life Sciences, Tel Aviv University, 6997801 Tel Aviv, Israel
| | - Amitay Katz
- School of Zoology, Faculty of Life Sciences, Tel Aviv University, 6997801 Tel Aviv, Israel
| | - Aya Goldshtein
- School of Zoology, Faculty of Life Sciences, Tel Aviv University, 6997801 Tel Aviv, Israel
| | - Michal Handel
- School of Zoology, Faculty of Life Sciences, Tel Aviv University, 6997801 Tel Aviv, Israel
| | - Yossi Yovel
- School of Zoology, Faculty of Life Sciences, Tel Aviv University, 6997801 Tel Aviv, Israel. .,Sagol School of Neuroscience, Tel Aviv University, 6997801 Tel Aviv, Israel
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28
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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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29
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Jorge F, Dheilly NM, Poulin R. Persistence of a Core Microbiome Through the Ontogeny of a Multi-Host Parasite. Front Microbiol 2020; 11:954. [PMID: 32508779 PMCID: PMC7248275 DOI: 10.3389/fmicb.2020.00954] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 04/21/2020] [Indexed: 12/25/2022] Open
Abstract
Animal microbiomes influence their development, behavior and interactions with other organisms. Parasitic metazoans also harbor microbial communities; although they are likely to modulate host-parasite interactions, little is known about parasite microbiomes. The persistence of microbial communities throughout the life of a parasite is particularly challenging for helminths with complex life cycles. These parasites undergo major morphological changes during their life, and parasitize host species that are immunologically, physiologically, and phylogenetically very different. Here, using 16S amplicon sequencing, we characterize the microbiome of the trematode Coitocaecum parvum across four of its life stages: sporocysts, metacercariae and adults inhabiting (respectively) snails, crustaceans and fish, as well as free-living cercariae. Our results demonstrate that, at each life stage, the parasite possesses a phylogenetically diverse microbiome, distinct from that of its hosts or the external environment. The parasite's microbiome comprises bacterial taxa specific to each life stage in different hosts, as well as a small core set of taxa that persists across the parasite's whole life. The apparent existence of an ontogenetically and vertically transmitted core microbiome is supported by the findings that the diversity and taxonomic composition of the microbiome does not vary significantly among life stages, and that the main source of microbial taxa at any life stage is the previous life stage. Our results suggest that microbes are an integrated component of the trematode, possibly shaping its phenotype and host-parasite interactions.
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Affiliation(s)
- Fátima Jorge
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Nolwenn M. Dheilly
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, United States
- Unité Génétique Virale de Biosécurité, Laboratoire de Ploufragan-Plouzané, Agence Nationale de Sécurité Sanitaire de l’Alimentation, de l’Environnement et du Travail, Ploufragan, France
| | - Robert Poulin
- Department of Zoology, University of Otago, Dunedin, New Zealand
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30
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Rojas CA, Holekamp KE, Winters AD, Theis KR. Body site-specific microbiota reflect sex and age-class among wild spotted hyenas. FEMS Microbiol Ecol 2020; 96:5700710. [PMID: 31926016 DOI: 10.1093/femsec/fiaa007] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 01/10/2020] [Indexed: 02/06/2023] Open
Abstract
Host-associated microbial communities, henceforth 'microbiota', can affect the physiology and behavior of their hosts. In mammals, host ecological, social and environmental variables are associated with variation in microbial communities. Within individuals in a given mammalian species, the microbiota also partitions by body site. Here, we build on this work and sequence the bacterial 16S rRNA gene to profile the microbiota at six distinct body sites (ear, nasal and oral cavities, prepuce, rectum and anal scent gland) in a population of wild spotted hyenas (Crocuta crocuta), which are highly social, large African carnivores. We inquired whether microbiota at these body sites vary with host sex or social rank among juvenile hyenas, and whether they differ between juvenile females and adult females. We found that the scent gland microbiota differed between juvenile males and juvenile females, whereas the prepuce and rectal microbiota differed between adult females and juvenile females. Social rank, however, was not a significant predictor of microbiota profiles. Additionally, the microbiota varied considerably among the six sampled body sites and exhibited strong specificity among individual hyenas. Thus, our findings suggest that site-specific niche selection is a primary driver of microbiota structure in mammals, but endogenous host factors may also be influential.
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Affiliation(s)
- Connie A Rojas
- Department of Integrative Biology, Michigan State University, 288 Farm Lane, East Lansing, MI, 48824, USA.,BEACON Center for the Study of Evolution in Action, Michigan State University, 567 Wilson Rd, East Lansing, MI, 48824, USA.,Ecology, Evolutionary Biology and Behavior, Michigan State University, 293 Farm Lane, East Lansing, MI, 48824, USA
| | - Kay E Holekamp
- Department of Integrative Biology, Michigan State University, 288 Farm Lane, East Lansing, MI, 48824, USA.,BEACON Center for the Study of Evolution in Action, Michigan State University, 567 Wilson Rd, East Lansing, MI, 48824, USA.,Ecology, Evolutionary Biology and Behavior, Michigan State University, 293 Farm Lane, East Lansing, MI, 48824, USA
| | - Andrew D Winters
- Department of Biochemistry, Microbiology and Immunology, Wayne State University School of Medicine, 540 E Canfield St, Detroit, MI, 48201, USA
| | - Kevin R Theis
- BEACON Center for the Study of Evolution in Action, Michigan State University, 567 Wilson Rd, East Lansing, MI, 48824, USA.,Department of Biochemistry, Microbiology and Immunology, Wayne State University School of Medicine, 540 E Canfield St, Detroit, MI, 48201, USA
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31
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Microbiomes in the insectivorous bat species Mops condylurus rapidly converge in captivity. PLoS One 2020; 15:e0223629. [PMID: 32196505 PMCID: PMC7083271 DOI: 10.1371/journal.pone.0223629] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 02/24/2020] [Indexed: 02/06/2023] Open
Abstract
Bats are well known reservoir hosts for RNA and DNA viruses. The use of captive bats in research has intensified over the past decade as researchers aim to examine the virus-reservoir host interface. In this study, we investigated the effects of captivity on the fecal bacterial microbiome of an insectivorous microbat, Mops condylurus, a species that roosts in close proximity to humans and has likely transmitted viral infections to humans. Using amplicon 16S rRNA gene sequencing, we characterized changes in fecal bacterial community composition for individual bats directly at the time of capture and again after six weeks in captivity. We found that microbial community richness by measure of the number of observed operational taxonomic units (OTUs) in bat feces increases in captivity. Importantly, we found the similarity of microbial community structures of fecal microbiomes between different bats to converge during captivity. We propose a six week-acclimatization period prior to carrying out infection studies or other research influenced by the microbiome composition, which may be advantageous to reduce variation in microbiome composition and minimize biological variation inherent to in vivo experimental studies.
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32
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Lewin-Epstein O, Hadany L. Host-microbiome coevolution can promote cooperation in a rock-paper-scissors dynamics. Proc Biol Sci 2020; 287:20192754. [PMID: 32075531 PMCID: PMC7031668 DOI: 10.1098/rspb.2019.2754] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Cooperation is a fundamental behaviour observed in all forms of life. The evolution of cooperation has been widely studied, but almost all theories focused on the cooperating individual and its genes. We suggest a different approach, taking into account the microbes carried by the interacting individuals. Accumulating evidence reveals that microbes can affect their host's well-being and behaviour, yet hosts can evolve mechanisms to resist the manipulations of their microbes. We thus propose that coevolution of microbes with their hosts may favour microbes that induce their host to cooperate. Using computational modelling, we show that microbe-induced cooperation can evolve and be maintained in a wide range of conditions, including when facing hosts' resistance to the microbial effect. We find that host-microbe coevolution leads the population to a rock-paper-scissors dynamics that enables maintenance of cooperation in a polymorphic state. Our results suggest a mechanism for the evolution and maintenance of cooperation that may be relevant to a wide variety of organisms, including cases that are difficult to explain by current theories. This study provides a new perspective on the coevolution of hosts and their microbiome, emphasizing the potential role of microbes in shaping their host's behaviour.
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Affiliation(s)
- Ohad Lewin-Epstein
- Department of Molecular Biology and Ecology of Plants, Tel-Aviv University, Tel-Aviv 6997801, Israel
| | - Lilach Hadany
- Department of Molecular Biology and Ecology of Plants, Tel-Aviv University, Tel-Aviv 6997801, Israel
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33
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Montecino-Latorre D, Goldstein T, Gilardi K, Wolking D, Van Wormer E, Kazwala R, Ssebide B, Nziza J, Sijali Z, Cranfield M, Mazet JAK. Reproduction of East-African bats may guide risk mitigation for coronavirus spillover. ONE HEALTH OUTLOOK 2020; 2:2. [PMID: 33824945 PMCID: PMC7149079 DOI: 10.1186/s42522-019-0008-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 12/13/2019] [Indexed: 05/16/2023]
Abstract
BACKGROUND Bats provide important ecosystem services; however, current evidence supports that they host several zoonotic viruses, including species of the Coronaviridae family. If bats in close interaction with humans host and shed coronaviruses with zoonotic potential, such as the Severe Acute Respiratory Syndrome virus, spillover may occur. Therefore, strategies aiming to mitigate potential spillover and disease emergence, while supporting the conservation of bats and their important ecological roles are needed. Past research suggests that coronavirus shedding in bats varies seasonally following their reproductive cycle; however, shedding dynamics have been assessed in only a few species, which does not allow for generalization of findings across bat taxa and geographic regions. METHODS To assess the generalizability of coronavirus shedding seasonality, we sampled hundreds of bats belonging to several species with different life history traits across East Africa at different times of the year. We assessed, via Bayesian modeling, the hypothesis that chiropterans, across species and spatial domains, experience seasonal trends in coronavirus shedding as a function of the reproductive cycle. RESULTS We found that, beyond spatial, taxonomic, and life history differences, coronavirus shedding is more expected when pups are becoming independent from the dam and that juvenile bats are prone to shed these viruses. CONCLUSIONS These findings could guide policy aimed at the prevention of spillover in limited-resource settings, where longitudinal surveillance is not feasible, by identifying high-risk periods for coronavirus shedding. In these periods, contact with bats should be avoided (for example, by impeding or forbidding people access to caves). Our proposed strategy provides an alternative to culling - an ethically questionable practice that may result in higher pathogen levels - and supports the conservation of bats and the delivery of their key ecosystem services.
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Affiliation(s)
- Diego Montecino-Latorre
- One Health Institute, School of Veterinary Medicine, University of California, Davis, CA USA
| | - Tracey Goldstein
- One Health Institute, School of Veterinary Medicine, University of California, Davis, CA USA
| | - Kirsten Gilardi
- One Health Institute, School of Veterinary Medicine, University of California, Davis, CA USA
- Gorilla Doctors, Mountain Gorilla Veterinary Project Inc, Davis, CA USA
| | - David Wolking
- One Health Institute, School of Veterinary Medicine, University of California, Davis, CA USA
| | - Elizabeth Van Wormer
- One Health Institute, School of Veterinary Medicine, University of California, Davis, CA USA
- Institute of Agriculture and Natural Resources, School of Natural Resources, University of Nebraska, Lincoln, NE USA
| | - Rudovick Kazwala
- College of Veterinary Medicine and Biomedical Sciences, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Benard Ssebide
- Gorilla Doctors, Mountain Gorilla Veterinary Project Inc., Kampala, Uganda
| | - Julius Nziza
- Gorilla Doctors, Mountain Gorilla Veterinary Project Inc., Musanze, Rwanda
| | - Zikankuba Sijali
- College of Veterinary Medicine and Biomedical Sciences, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Michael Cranfield
- One Health Institute, School of Veterinary Medicine, University of California, Davis, CA USA
- Gorilla Doctors, Mountain Gorilla Veterinary Project Inc, Davis, CA USA
| | - PREDICT Consortium
- https://ohi.vetmed.ucdavis.edu/programs-projects/predict-project/authorship
| | - Jonna A. K. Mazet
- One Health Institute, School of Veterinary Medicine, University of California, Davis, CA USA
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34
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Paskey AC, Ng JHJ, Rice GK, Chia WN, Philipson CW, Foo RJH, Cer RZ, Long KA, Lueder MR, Frey KG, Hamilton T, Mendenhall IH, Smith GJ, Wang LF, Bishop-Lilly KA. The temporal RNA virome patterns of a lesser dawn bat ( Eonycteris spelaea) colony revealed by deep sequencing. Virus Evol 2020; 6:veaa017. [PMID: 33747541 PMCID: PMC7079719 DOI: 10.1093/ve/veaa017] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The virosphere is largely unexplored and the majority of viruses are yet to be represented in public sequence databases. Bats are rich reservoirs of viruses, including several zoonoses. In this study, high throughput sequencing (HTS) of viral RNA extracted from swabs of four body sites per bat per timepoint is used to characterize the virome through a longitudinal study of a captive colony of fruit nectar bats, species Eonycteris spelaea in Singapore. Through unbiased shotgun and target enrichment sequencing, we identify both known and previously unknown viruses of zoonotic relevance and define the population persistence and temporal patterns of viruses from families that have the capacity to jump the species barrier. To our knowledge, this is the first study that combines probe-based viral enrichment with HTS to create a viral profile from multiple swab sites on individual bats and their cohort. This work demonstrates temporal patterns of the lesser dawn bat virome, including several novel viruses. Given the known risk for bat-human zoonoses, a more complete understanding of the viral dynamics in South-eastern Asian bats has significant implications for disease prevention and control. The findings of this study will be of interest to U.S. Department of Defense personnel stationed in the Asia-Pacific region and regional public health laboratories engaged in emerging infectious disease surveillance efforts.
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Affiliation(s)
- Adrian C Paskey
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, 4301 Jones Bridge Rd, Bethesda, MD 20814, USA
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center – Frederick, 8400 Research Plaza, Fort Detrick, MD 21702, USA
- Leidos, 11951 Freedom Dr., Reston, VA 20190, USA
| | - Justin H J Ng
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore 169857
| | - Gregory K Rice
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center – Frederick, 8400 Research Plaza, Fort Detrick, MD 21702, USA
- Leidos, 11951 Freedom Dr., Reston, VA 20190, USA
| | - Wan Ni Chia
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore 169857
| | - Casandra W Philipson
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center – Frederick, 8400 Research Plaza, Fort Detrick, MD 21702, USA
- Defense Threat Reduction Agency, 8725 John J. Kingman Rd., Fort Belvoir, VA 22060, USA
| | - Randy J H Foo
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore 169857
| | - Regina Z Cer
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center – Frederick, 8400 Research Plaza, Fort Detrick, MD 21702, USA
- Leidos, 11951 Freedom Dr., Reston, VA 20190, USA
| | - Kyle A Long
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center – Frederick, 8400 Research Plaza, Fort Detrick, MD 21702, USA
- Leidos, 11951 Freedom Dr., Reston, VA 20190, USA
| | - Matthew R Lueder
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center – Frederick, 8400 Research Plaza, Fort Detrick, MD 21702, USA
- Leidos, 11951 Freedom Dr., Reston, VA 20190, USA
| | - Kenneth G Frey
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center – Frederick, 8400 Research Plaza, Fort Detrick, MD 21702, USA
| | - Theron Hamilton
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center – Frederick, 8400 Research Plaza, Fort Detrick, MD 21702, USA
| | - Ian H Mendenhall
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore 169857
| | - Gavin J Smith
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore 169857
| | - Lin-Fa Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore 169857
| | - Kimberly A Bishop-Lilly
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, 4301 Jones Bridge Rd, Bethesda, MD 20814, USA
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center – Frederick, 8400 Research Plaza, Fort Detrick, MD 21702, USA
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Abstract
This study is the first to provide a comprehensive survey of bacterial symbionts from multiple anatomical sites across a broad taxonomic range of Afrotropical bats, demonstrating significant associations between the bat microbiome and anatomical site, geographic locality, and host identity—but not evolutionary history. This study provides a framework for future systems biology approaches to examine host-symbiont relationships across broad taxonomic scales, emphasizing the need to elucidate the interplay between host ecology and evolutionary history in shaping the microbiome of different anatomical sites. Recent studies of mammalian microbiomes have identified strong phylogenetic effects on bacterial community composition. Bats (Mammalia: Chiroptera) are among the most speciose mammals on the planet and the only mammal capable of true flight. We examined 1,236 16S rRNA amplicon libraries of the gut, oral, and skin microbiota from 497 Afrotropical bats (representing 9 families, 20 genera, and 31 species) to assess the extent to which host ecology and phylogeny predict microbial community similarity in bats. In contrast to recent studies of host-microbe associations in other mammals, we found no correlation between chiropteran phylogeny and bacterial community dissimilarity across the three anatomical sites sampled. For all anatomical sites, we found host species identity and geographic locality to be strong predictors of microbial community composition and observed a positive correlation between elevation and bacterial richness. Last, we identified significantly different bacterial associations within the gut microbiota of insectivorous and frugivorous bats. We conclude that the gut, oral, and skin microbiota of bats are shaped predominantly by ecological factors and do not exhibit the same degree of phylosymbiosis observed in other mammals. IMPORTANCE This study is the first to provide a comprehensive survey of bacterial symbionts from multiple anatomical sites across a broad taxonomic range of Afrotropical bats, demonstrating significant associations between the bat microbiome and anatomical site, geographic locality, and host identity—but not evolutionary history. This study provides a framework for future systems biology approaches to examine host-symbiont relationships across broad taxonomic scales, emphasizing the need to elucidate the interplay between host ecology and evolutionary history in shaping the microbiome of different anatomical sites.
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Björk JR, Dasari M, Grieneisen L, Archie EA. Primate microbiomes over time: Longitudinal answers to standing questions in microbiome research. Am J Primatol 2019; 81:e22970. [PMID: 30941803 PMCID: PMC7193701 DOI: 10.1002/ajp.22970] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 02/05/2019] [Accepted: 03/07/2019] [Indexed: 12/16/2022]
Abstract
To date, most insights into the processes shaping vertebrate gut microbiomes have emerged from studies with cross-sectional designs. While this approach has been valuable, emerging time series analyses on vertebrate gut microbiomes show that gut microbial composition can change rapidly from 1 day to the next, with consequences for host physical functioning, health, and fitness. Hence, the next frontier of microbiome research will require longitudinal perspectives. Here we argue that primatologists, with their traditional focus on tracking the lives of individual animals and familiarity with longitudinal fecal sampling, are well positioned to conduct research at the forefront of gut microbiome dynamics. We begin by reviewing some of the most important ecological processes governing microbiome change over time, and briefly summarizing statistical challenges and approaches to microbiome time series analysis. We then introduce five questions of general interest to microbiome science where we think field-based primate studies are especially well positioned to fill major gaps: (a) Do early life events shape gut microbiome composition in adulthood? (b) Do shifting social landscapes cause gut microbial change? (c) Are gut microbiome phenotypes heritable across variable environments? (d) Does the gut microbiome show signs of host aging? And (e) do gut microbiome composition and dynamics predict host health and fitness? For all of these questions, we highlight areas where primatologists are uniquely positioned to make substantial contributions. We review preliminary evidence, discuss possible study designs, and suggest future directions.
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Affiliation(s)
- Johannes R Björk
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana
| | - Mauna Dasari
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana
| | - Laura Grieneisen
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota
| | - Elizabeth A Archie
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana
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Modesto M, Satti M, Watanabe K, Puglisi E, Morelli L, Huang CH, Liou JS, Miyashita M, Tamura T, Saito S, Mori K, Huang L, Sciavilla P, Sandri C, Spiezio C, Vitali F, Cavalieri D, Perpetuini G, Tofalo R, Bonetti A, Arita M, Mattarelli P. Characterization of Bifidobacterium species in feaces of the Egyptian fruit bat: Description of B. vespertilionis sp. nov. and B. rousetti sp. nov. Syst Appl Microbiol 2019; 42:126017. [PMID: 31585749 DOI: 10.1016/j.syapm.2019.126017] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 08/18/2019] [Accepted: 08/20/2019] [Indexed: 11/16/2022]
Abstract
Fifteen bifidobacterial strains were obtained from faeces of Rousettus aegyptiacus; after grouping them by RAPD PCR only eight were selected and characterized. Analysis of 16S rRNA and of five housekeeping (hsp60, rpoB, clpC, dnaJ, dna G) genes revealed that these eight strains were classified into five clusters: Cluster I (RST 8 and RST 16T), Cluster II (RST 9T and RST 27), Cluster III (RST 7 and RST 11), Cluster IV (RST 19), Cluster V (RST 17) were closest to Bifidobacterium avesanii DSM 100685T (96.3%), Bifidobacterium callitrichos DSM 23973T (99.2% and 99.7%), Bifidobacterium tissieri DSM 100201T (99.7 and 99.2%), Bifidobacterium reuteri DSM 23975 T (98.9%) and Bifidobacterium myosotis DSM 100196T (99.3%), respectively. Strains in Cluster I and strain RST 9 in Cluster II could not be placed within any recognized species while the other ones were identified as known species. The average nucleotide identity values between two novel strains, RST 16T and RST 9T and their closest relatives were lower than 79% and 89%, respectively. In silico DNA-DNA hybridization values for those closest relatives were 32.5 and 42.1%, respectively. Phenotypic and genotypic tests demonstrated that strains in Cluster I and RST 9T in Cluster II represent two novel species for which the names Bifidobacterium vespertilionis sp. nov. (RST 16T=BCRC 81138T=NBRC 113380T=DSM 106025T ; RST 8=BCRC 81135=NBRC 113377) and Bifidobacterium rousetti sp. nov. (RST 9T=BCRC 81136T=NBRC 113378T=DSM 106027T) are proposed.
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Affiliation(s)
- Monica Modesto
- Department of Agricultural Sciences, University of Bologna, Viale Fanin 44, 40127 Bologna, Italy
| | - Maria Satti
- Department of Genetics, SOKENDAI University (National Institute of Genetics), Yata 1111, Mishima, Shizuoka 411-8540, Japan
| | - Koichi Watanabe
- Department of Animal Science and Technology, National Taiwan University, Taipei, Taiwan; Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu, Taiwan
| | - Edoardo Puglisi
- Department for Sustainable Food Processes, Faculty of Agricultural, Food and Environmental Sciences, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza, Italy
| | - Lorenzo Morelli
- Department for Sustainable Food Processes, Faculty of Agricultural, Food and Environmental Sciences, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza, Italy
| | - Chien-Hsun Huang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu, Taiwan
| | - Jong-Shian Liou
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu, Taiwan
| | - Mika Miyashita
- Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), 2-5-8, Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Tomohiko Tamura
- Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), 2-5-8, Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Satomi Saito
- Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), 2-5-8, Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Koji Mori
- Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), 2-5-8, Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Lina Huang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu, Taiwan
| | - Piero Sciavilla
- Department of Agricultural Sciences, University of Bologna, Viale Fanin 44, 40127 Bologna, Italy
| | - Camillo Sandri
- Department of Animal Health Care and Management, Parco Natura Viva - Garda Zoological Park, Bussolengo, Verona, Italy
| | - Caterina Spiezio
- Department of Animal Health Care and Management, Parco Natura Viva - Garda Zoological Park, Bussolengo, Verona, Italy
| | | | | | - Giorgia Perpetuini
- Faculty of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, Teramo, Italy
| | - Rosanna Tofalo
- Faculty of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, Teramo, Italy
| | - Andrea Bonetti
- Department of Agricultural Sciences, University of Bologna, Viale Fanin 44, 40127 Bologna, Italy
| | - Masanori Arita
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan; Bioinformation and DDBJ Center, National Institute of Genetics, Yata 1111, Mishima, Shizuoka 411-8540, Japan
| | - Paola Mattarelli
- Department of Agricultural Sciences, University of Bologna, Viale Fanin 44, 40127 Bologna, Italy.
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