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Stapleton TE, Lindsey LM, Sundar H, Dearing MD. Rodents consuming the same toxic diet harbor a unique functional core microbiome. Anim Microbiome 2024; 6:43. [PMID: 39080711 DOI: 10.1186/s42523-024-00330-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 07/16/2024] [Indexed: 08/02/2024] Open
Abstract
Gut microbiota are intrinsic to an herbivorous lifestyle, but very little is known about how plant secondary compounds (PSCs), which are often toxic, influence these symbiotic partners. Here we interrogated the possibility of unique functional core microbiomes in populations of two species of woodrat (Neotoma lepida and bryanti) that have independently converged to feed on the same toxic diet (creosote bush; Larrea tridentata) and compared them to populations that do not feed on creosote bush. Leveraging this natural experiment, we collected samples across a large geographic region in the U.S. desert southwest from 20 populations (~ 150 individuals) with differential ingestion of creosote bush and analyzed three gut regions (foregut, cecum, hindgut) using16S sequencing and shotgun metagenomics. In each gut region sampled, we found a distinctive set of microbes in individuals feeding on creosote bush that were more abundant than other ASVs, enriched in creosote feeding woodrats, and occurred more frequently than would be predicted by chance. Creosote core members were from microbial families e.g., Eggerthellaceae, known to metabolize plant secondary compounds and three of the identified core KEGG orthologs (4-hydroxybenzoate decarboxylase, benzoyl-CoA reductase subunit B, and 2-pyrone-4, 6-dicarboxylate lactonase) coded for enzymes that play important roles in metabolism of plant secondary compounds. The results support the hypothesis that the ingestion of creosote bush sculpts the microbiome across all major gut regions to select for functional characteristics associated with the degradation of the PSCs in this unique diet.
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Affiliation(s)
- Tess E Stapleton
- School of Biological Sciences, University of Utah, 257 South 1400 East, Salt Lake City, UT, 84112, USA.
| | - LeAnn M Lindsey
- School of Computing, University of Utah, 50 Central Campus Dr, Salt Lake City, UT, 84112, USA
| | - Hari Sundar
- School of Computing, University of Utah, 50 Central Campus Dr, Salt Lake City, UT, 84112, USA
| | - M Denise Dearing
- School of Biological Sciences, University of Utah, 257 South 1400 East, Salt Lake City, UT, 84112, USA
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2
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Li K, Li WJ, Liang K, Li FF, Qin GQ, Liu JH, Zhang YL, Li XJ. Gut microorganisms of Locusta migratoria in various life stages and its possible influence on cellulose digestibility. mSystems 2024; 9:e0060024. [PMID: 38888356 PMCID: PMC11264664 DOI: 10.1128/msystems.00600-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Accepted: 05/13/2024] [Indexed: 06/20/2024] Open
Abstract
Locusta migratoria is an important phytophagous pest, and its gut microbial communities play an important role in cellulose degradation. In this study, the gut microbial and cellulose digestibility dynamics of Locusta migratoria were jointly analyzed using high-throughput sequencing and anthrone colorimetry. The results showed that the gut microbial diversity and cellulose digestibility across life stages were dynamically changing. The species richness of gut bacteria was significantly higher in eggs than in larvae and imago, the species richness and cellulose digestibility of gut bacteria were significantly higher in early larvae (first and second instars) than in late larvae (third to fifth instars), and the diversity of gut bacteria and cellulose digestibility were significantly higher in imago than in late larvae. There is a correlation between the dynamics of gut bacterial communities and cellulose digestibility. Enterobacter, Lactococcus, and Pseudomonas are the most abundant genera throughout all life stages. Six strains of highly efficient cellulolytic bacteria were screened, which were dominant gut bacteria. Carboxymethyl cellulase activity (CMCA) and filter paper activity (FPA) experiments revealed that Pseudomonas had the highest cellulase enzyme activity. This study provides a new way for the screening of cellulolytic bacteria and lays the foundation for developing insects with significant biomass into cellulose-degrading bioreactors. IMPORTANCE Cellulose is the most abundant and cheapest renewable resource in nature, but its degradation is difficult, so finding efficient cellulose degradation methods is an urgent challenge. Locusta migratoria is a large group of agricultural pests, and the large number of microorganisms that inhabit their intestinal tracts play an important role in cellulose degradation. We analyzed the dynamics of Locusta migratoria gut microbial communities and cellulose digestibility using a combination of high-throughput sequencing technology and anthrone colorimetry. The results revealed that the gut microbial diversity and cellulose digestibility were dynamically changed at different life stages. In addition, we explored the intestinal bacterial community of Locusta migratoria across life stages and its correlation with cellulose digestibility. The dominant bacterial genera at different life stages of Locusta migratoria were uncovered and their carboxymethyl cellulase activity (CMCA) and filter paper activity (FPA) were determined. This study provides a new avenue for screening cellulolytic bacteria and lays the foundation for developing insects with significant biomass into cellulose-degrading bioreactors.
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Affiliation(s)
- Kai Li
- The Key Laboratory of Zoological Systematics and Application, School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, China
| | - Wen-Jing Li
- The Key Laboratory of Zoological Systematics and Application, School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, China
| | - Ke Liang
- The Key Laboratory of Zoological Systematics and Application, School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, China
| | - Fei-Fei Li
- The Key Laboratory of Zoological Systematics and Application, School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, China
| | - Guo-Qing Qin
- The Key Laboratory of Zoological Systematics and Application, School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, China
| | - Jia-Hao Liu
- The Key Laboratory of Zoological Systematics and Application, School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, China
| | - Yu-Long Zhang
- The Key Laboratory of Zoological Systematics and Application, School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, China
| | - Xin-Jiang Li
- The Key Laboratory of Zoological Systematics and Application, School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, China
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3
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DeCandia AL, Adeduro L, Thacher P, Crosier A, Marinari P, Bortner R, Garelle D, Livieri T, Santymire R, Comizzoli P, Maslanka M, Maldonado JE, Koepfli KP, Muletz-Wolz C, Bornbusch SL. Gut bacterial composition shows sex-specific shifts during breeding season in ex situ managed black-footed ferrets. J Hered 2024; 115:385-398. [PMID: 37886904 DOI: 10.1093/jhered/esad065] [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: 07/11/2023] [Revised: 10/16/2023] [Accepted: 10/26/2023] [Indexed: 10/28/2023] Open
Abstract
The gut microbiome of mammals engages in a dynamic relationship with the body and contributes to numerous physiological processes integral to overall health. Understanding the factors shaping animal-associated bacterial communities is therefore paramount to the maintenance and management in ex situ wildlife populations. Here, we characterized the gut microbiome of 48 endangered black-footed ferrets (Mustela nigripes) housed at Smithsonian's National Zoo and Conservation Biology Institute (Front Royal, Virginia, USA). We collected longitudinal fecal samples from males and females across two distinct reproductive seasons to consider the role of host sex and reproductive physiology in shaping bacterial communities, as measured using 16S rRNA amplicon sequencing. Within each sex, gut microbial composition differed between breeding and non-breeding seasons, with five bacterial taxa emerging as differentially abundant. Between sexes, female and male microbiomes were similar during non-breeding season but significantly different during breeding season, which may result from sex-specific physiological changes associated with breeding. Finally, we found low overall diversity consistent with other mammalian carnivores alongside high relative abundances of potentially pathogenic microbes such as Clostridium, Escherichia, Paeniclostridium, and (to a lesser degree) Enterococcus-all of which have been associated with gastrointestinal or reproductive distress in mammalian hosts, including black-footed ferrets. We recommend further study of these microbes and possible therapeutic interventions to promote more balanced microbial communities. These results have important implications for ex situ management practices that can improve the gut microbial health and long-term viability of black-footed ferrets.
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Affiliation(s)
- Alexandra L DeCandia
- Biology Department, Georgetown University, Washington, DC, United States
- Center for Conservation Genomics, Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC, United States
| | - Laura Adeduro
- Biology Department, Georgetown University, Washington, DC, United States
| | - Piper Thacher
- Center for Conservation Genomics, Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC, United States
- Smithsonian-Mason School of Conservation, George Mason University, Front Royal, VA, United States
| | - Adrienne Crosier
- Center for Animal Care Sciences, Smithsonian's National Zoo and Conservation Biology Institute, Front Royal, VA, United States
| | - Paul Marinari
- Center for Animal Care Sciences, Smithsonian's National Zoo and Conservation Biology Institute, Front Royal, VA, United States
| | - Robyn Bortner
- National Black-Footed Ferret Conservation Center, Carr, CO, United States
| | - Della Garelle
- National Black-Footed Ferret Conservation Center, Carr, CO, United States
| | - Travis Livieri
- Prairie Wildlife Research, Stevens Point, WI, United States
| | - Rachel Santymire
- Biology Department, Georgia State University, Atlanta, GA, United States
| | - Pierre Comizzoli
- Center for Species Survival, Smithsonian's National Zoo and Conservation Biology Institute, Front Royal, VA, United States
| | - Michael Maslanka
- Department of Nutrition Science, Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC, United States
| | - Jesús E Maldonado
- Center for Conservation Genomics, Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC, United States
| | - Klaus-Peter Koepfli
- Smithsonian-Mason School of Conservation, George Mason University, Front Royal, VA, United States
- Center for Species Survival, Smithsonian's National Zoo and Conservation Biology Institute, Front Royal, VA, United States
| | - Carly Muletz-Wolz
- Center for Conservation Genomics, Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC, United States
| | - Sally L Bornbusch
- Center for Conservation Genomics, Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC, United States
- Department of Nutrition Science, Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC, United States
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4
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Sardar P, Almeida A, Pedicord VA. Integrating functional metagenomics to decipher microbiome-immune interactions. Immunol Cell Biol 2024. [PMID: 38952337 DOI: 10.1111/imcb.12798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 06/04/2024] [Accepted: 06/13/2024] [Indexed: 07/03/2024]
Abstract
Microbial metabolites can be viewed as the cytokines of the microbiome, transmitting information about the microbial and metabolic environment of the gut to orchestrate and modulate local and systemic immune responses. Still, many immunology studies focus solely on the taxonomy and community structure of the gut microbiota rather than its functions. Early sequencing-based microbiota profiling approaches relied on PCR amplification of small regions of bacterial and fungal genomes to facilitate identification of the microbes present. However, recent microbiome analysis methods, particularly shotgun metagenomic sequencing, now enable culture-independent profiling of microbiome functions and metabolites in addition to taxonomic characterization. In this review, we showcase recent advances in functional metagenomics methods and applications and discuss the current limitations and potential avenues for future development. Importantly, we highlight a few examples of key areas of opportunity in immunology research where integrating functional metagenomic analyses of the microbiome can substantially enhance a mechanistic understanding of microbiome-immune interactions and their contributions to health and disease states.
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Affiliation(s)
- Puspendu Sardar
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge, UK
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Alexandre Almeida
- Department of Veterinary Medicine, University of Cambridge School of Biological Sciences, Cambridge, UK
| | - Virginia A Pedicord
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge, UK
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, UK
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Williams CE, Fontaine SS. Commentary: The microbial dependence continuum: Towards a comparative physiology approach to understand host reliance on microbes. Comp Biochem Physiol A Mol Integr Physiol 2024; 296:111690. [PMID: 38964709 DOI: 10.1016/j.cbpa.2024.111690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 06/28/2024] [Accepted: 06/30/2024] [Indexed: 07/06/2024]
Abstract
Comparative physiologists often compare physiological traits across organisms to understand the selective pressures influencing their evolution in different environments. Traditionally focused on the organisms themselves, comparative physiology has more recently incorporated studies of the microbiome-the communities of microbes living in and on animals that influence host physiology. In this commentary, we describe the utility of applying a comparative framework to study the microbiome, particularly in understanding how hosts vary in their dependence on microbial communities for physiological function, a concept we term the "microbial dependence continuum". This hypothesis suggests that hosts exist on a spectrum ranging from high to low reliance on their microbiota. Certain physiological traits may be highly dependent on microbes for proper function in some species but microbially independent in others. Comparative physiology can elucidate the selective pressures driving species along this continuum. Here, we discuss the microbial dependence continuum in detail and how comparative physiology can be useful to study it. Then, we discuss two example traits, herbivory and flight, where comparative physiology has helped reveal the selective pressures influencing host dependence on microbial communities. Lastly, we discuss useful experimental approaches for studying the microbial dependence continuum in a comparative physiology context.
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Affiliation(s)
- Claire E Williams
- University of Nevada, Department of Biology, 1664 N Virginia St, Reno, NV 89557, USA.
| | - Samantha S Fontaine
- Kent State University, Department of Biological Sciences, 800 E Summit St, Kent, OH, USA. https://twitter.com/sammiefontaine
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Storm MB, Arfaoui EMR, Simelane P, Denlinger J, Dias CA, da Conceição AG, Monadjem A, Bohmann K, Poulsen M, Bodawatta KH. Diet components associated with specific bacterial taxa shape overall gut community compositions in omnivorous African viverrids. Ecol Evol 2024; 14:e11486. [PMID: 39005885 PMCID: PMC11239323 DOI: 10.1002/ece3.11486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 05/14/2024] [Accepted: 05/15/2024] [Indexed: 07/16/2024] Open
Abstract
Gut bacterial communities provide flexibility to hosts during dietary changes. Despite the increasing number of studies exploring the associations between broader dietary guilds of mammalian hosts and their gut bacteria, it is generally unclear how diversity and variability in consumed diets link to gut bacterial taxa in wild non-primate mammals, particularly in omnivores. Here, we contribute to filling this gap by exploring consumed diets and gut bacterial community compositions with metabarcoding of faecal samples for two African mammals, Civettictis civetta and Genetta spp., from the family Viverridae. For each individual sample, we characterised bacterial communities and identified dietary taxa by sequencing vertebrate, invertebrate and plant markers. This led us to establish diet compositions that diverged from what has previously been found from visual identification methods. Specifically, while the two genera have been categorised into the same dietary guild, we detected more animal dietary items than plant items in C. civetta, while in Genetta spp., we observed the opposite. We further found that individuals with similar diets have similar gut bacterial communities within both genera. This association tended to be driven by specific links between dietary items and gut bacterial genera, rather than communities as a whole, implying diet-driven selection for specific gut microbes in individual wild hosts. Our findings underline the importance of molecular tools for improving characterisations of omnivorous mammalian diets and highlight the opportunities for simultaneously disentangling links between diets and gut symbionts. Such insights can inform robustness and flexibility in host-microbe symbioses to dietary change associated with seasonal and habitat changes.
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Affiliation(s)
- Malou B. Storm
- Section for Ecology and Evolution, Department of BiologyUniversity of CopenhagenCopenhagenDenmark
- Section for Molecular Ecology and EvolutionGlobe Institute, University of CopenhagenCopenhagenDenmark
| | - Emilia M. R. Arfaoui
- Section for Ecology and Evolution, Department of BiologyUniversity of CopenhagenCopenhagenDenmark
- Section for Molecular Ecology and EvolutionGlobe Institute, University of CopenhagenCopenhagenDenmark
| | - Phumlile Simelane
- Department of Biological SciencesUniversity of EswatiniKwaluseniEswatini
| | | | | | | | - Ara Monadjem
- Department of Biological SciencesUniversity of EswatiniKwaluseniEswatini
- Mammal Research Institute, Department of Zoology and EntomologyUniversity of PretoriaHatfield, PretoriaSouth Africa
| | - Kristine Bohmann
- Section for Molecular Ecology and EvolutionGlobe Institute, University of CopenhagenCopenhagenDenmark
| | - Michael Poulsen
- Section for Ecology and Evolution, Department of BiologyUniversity of CopenhagenCopenhagenDenmark
| | - Kasun H. Bodawatta
- Section for Molecular Ecology and EvolutionGlobe Institute, University of CopenhagenCopenhagenDenmark
- Natural History Museum of DenmarkUniversity of CopenhagenCopenhagenDenmark
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7
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Zhu W, Chang L, Zhang M, Chen Q, Sui L, Shen C, Jiang J. Microbial diversity in mountain-dwelling amphibians: The combined effects of host and climatic factors. iScience 2024; 27:109907. [PMID: 38812552 PMCID: PMC11135016 DOI: 10.1016/j.isci.2024.109907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 11/30/2023] [Accepted: 05/02/2024] [Indexed: 05/31/2024] Open
Abstract
Comprehending the determinants of host-associated microbiota is pivotal in microbial ecology. Yet, the links between climatic factors and variations in host-associated microbiota necessitate further clarification. Mountain-dwelling amphibians, with limited dispersal abilities, serve as valuable models for addressing these questions. Our study, using 126 amphibian-associated microbial samples (64 gut and 62 skin) and 101 environmental microbial samples (51 soil and 50 water) from the eastern Tibetan Plateau, revealed host factors as primary drivers of the variations in host-associated microbiota. However, climatic factors contributed to additional variations in gut microbial beta-diversity and skin microbial function. Water microbiota were identified as a significant contributor to the amphibian-associated microbiomes, with their climate-driven variations mediating an indirect association between the variations in climatic factors and host-associated microbiota. These findings extend our understanding of the assembly of host-associated microbiota in amphibians, emphasizing the significance of microbiota in evaluating the impact of climate change on animals.
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Affiliation(s)
- Wei Zhu
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Liming Chang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Meihua Zhang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Qiheng Chen
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lulu Sui
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Cheng Shen
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Jianping Jiang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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8
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Yin J, Yuan D, Xu Z, Wu Y, Chen Z, Xiang X. Significant Differences in Intestinal Bacterial Communities of Sympatric Bean Goose, Hooded Crane, and Domestic Goose. Animals (Basel) 2024; 14:1688. [PMID: 38891737 PMCID: PMC11170997 DOI: 10.3390/ani14111688] [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: 05/07/2024] [Revised: 05/25/2024] [Accepted: 06/01/2024] [Indexed: 06/21/2024] Open
Abstract
The host's physiological well-being is intricately associated with the gut microbiota. However, previous studies regarding the intestinal microbiota have focused on domesticated or captive birds. This study used high-throughput sequencing technology to identify the gut bacterial communities of sympatric bean geese, hooded cranes, and domestic geese. The results indicated that the gut bacterial diversity in domestic geese and hooded cranes showed considerably higher diversity than bean geese. The gut bacterial community compositions varied significantly among the three hosts (p < 0.05). Compared to the hooded crane, the bean goose and domestic goose were more similar in their genotype and evolutionary history, with less difference in the bacterial community composition and assembly processes between the two species. Thus, the results might support the crucial role of host genotypes on their gut microbiota. The gut bacteria of wild hooded cranes and bean geese had a greater capacity for energy metabolism compared to domestic geese, suggesting that wild birds may rely more on their gut microbiota to survive in cold conditions. Moreover, the intestines of the three hosts were identified as harboring potential pathogens. The relative abundance of pathogens was higher in the hooded crane compared to the other two species. The hooded crane gut bacterial community assemblage revealed the least deterministic process with the lowest filtering/selection on the gut microbiota, which might have been a reason for the highest number of pathogens result. Compared to the hooded crane, the sympatric bean goose showed the least diversity and relative abundance of pathogens. The intestinal bacterial co-occurrence network showed the highest stability in the bean goose, potentially enhancing host resistance to adverse environments and reducing the susceptibility to pathogen invasion. In this study, the pathogens were also discovered to overlap among the three hosts, reminding us to monitor the potential for pathogen transmission between poultry and wild birds. Overall, the current findings have the potential to enhance the understanding of gut bacterial and pathogenic community structures in poultry and wild birds.
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Affiliation(s)
- Jing Yin
- School of Resources and Environmental Engineering, Anhui University, Hefei 230601, China; (J.Y.); (D.Y.); (Z.X.); (Y.W.)
- Anhui Shengjin Lake Wetland Ecology National Long-Term Scientific Research Base, Chizhou 247230, China
| | - Dandan Yuan
- School of Resources and Environmental Engineering, Anhui University, Hefei 230601, China; (J.Y.); (D.Y.); (Z.X.); (Y.W.)
- Anhui Shengjin Lake Wetland Ecology National Long-Term Scientific Research Base, Chizhou 247230, China
| | - Ziqiu Xu
- School of Resources and Environmental Engineering, Anhui University, Hefei 230601, China; (J.Y.); (D.Y.); (Z.X.); (Y.W.)
| | - Yuannuo Wu
- School of Resources and Environmental Engineering, Anhui University, Hefei 230601, China; (J.Y.); (D.Y.); (Z.X.); (Y.W.)
- Anhui Shengjin Lake Wetland Ecology National Long-Term Scientific Research Base, Chizhou 247230, China
| | - Zhong Chen
- School of Resources and Environmental Engineering, Anhui University, Hefei 230601, China; (J.Y.); (D.Y.); (Z.X.); (Y.W.)
- Anhui Shengjin Lake Wetland Ecology National Long-Term Scientific Research Base, Chizhou 247230, China
- International Collaborative Research Center for Huangshan Biodiversity and Tibetan Macaque Behavioral Ecology, Hefei 230601, China
| | - Xingjia Xiang
- School of Resources and Environmental Engineering, Anhui University, Hefei 230601, China; (J.Y.); (D.Y.); (Z.X.); (Y.W.)
- Anhui Shengjin Lake Wetland Ecology National Long-Term Scientific Research Base, Chizhou 247230, China
- International Collaborative Research Center for Huangshan Biodiversity and Tibetan Macaque Behavioral Ecology, Hefei 230601, China
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Horváthová T, Lafuente E, Bartels J, Wallisch J, Vorburger C. Tolerance to environmental pollution in the freshwater crustacean Asellus aquaticus: A role for the microbiome. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13252. [PMID: 38783543 PMCID: PMC11116767 DOI: 10.1111/1758-2229.13252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 03/13/2024] [Indexed: 05/25/2024]
Abstract
Freshwater habitats are frequently contaminated by diverse chemicals of anthropogenic origin, collectively referred to as micropollutants, that can have detrimental effects on aquatic life. The animals' tolerance to micropollutants may be mediated by their microbiome. If polluted aquatic environments select for contaminant-degrading microbes, the acquisition of such microbes by the host may increase its tolerance to pollution. Here we tested for the potential effects of the host microbiome on the growth and survival of juvenile Asellus aquaticus, a widespread freshwater crustacean. Using faecal microbiome transplants, we provided newly hatched juveniles with the microbiome isolated from donor adults reared in either clean or micropollutant-contaminated water and, after transplantation, recipient juveniles were reared in water with and without micropollutants. The experiment revealed a significant negative effect of the micropollutants on the survival of juvenile isopods regardless of the received faecal microbiome. The micropollutants had altered the composition of the bacterial component of the donors' microbiome, which in turn influenced the microbiome of juvenile recipients. Hence, we show that relatively high environmental concentrations of micropollutants reduce survival and alter the microbiome composition of juvenile A. aquaticus, but we have no evidence that tolerance to micropollutants is modulated by their microbiome.
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Affiliation(s)
- Terézia Horváthová
- Department of Aquatic EcologyEawagDübendorfSwitzerland
- Institute of Soil Biology and BiochemistryBiology Centre CASČeské BudějoviceCzechia
| | - Elvira Lafuente
- Department of Aquatic EcologyEawagDübendorfSwitzerland
- Instituto Gulbenkian de CiênciaOeirasPortugal
| | | | | | - Christoph Vorburger
- Department of Aquatic EcologyEawagDübendorfSwitzerland
- D‐USYS, Department of Environmental Systems ScienceETH ZürichZürichSwitzerland
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10
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Hu B, Wang JM, Zhang QX, Xu J, Xing YN, Wang B, Han SY, He HX. Enterococcus faecalis provides protection during scavenging in carrion crow ( Corvus corone). Zool Res 2024; 45:451-463. [PMID: 38583936 PMCID: PMC11188602 DOI: 10.24272/j.issn.2095-8137.2023.320] [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: 11/23/2023] [Accepted: 12/29/2023] [Indexed: 04/09/2024] Open
Abstract
The gut microbiota significantly influences host physiology and provides essential ecosystem services. While diet can affect the composition of the gut microbiota, the gut microbiota can also help the host adapt to specific dietary habits. The carrion crow ( Corvus corone), an urban facultative scavenger bird, hosts an abundance of pathogens due to its scavenging behavior. Despite this, carrion crows infrequently exhibit illness, a phenomenon related to their unique physiological adaptability. At present, however, the role of the gut microbiota remains incompletely understood. In this study, we performed a comparative analysis using 16S rRNA amplicon sequencing technology to assess colonic content in carrion crows and 16 other bird species with different diets in Beijing, China. Our findings revealed that the dominant gut microbiota in carrion crows was primarily composed of Proteobacteria (75.51%) and Firmicutes (22.37%). Significant differences were observed in the relative abundance of Enterococcus faecalis among groups, highlighting its potential as a biomarker of facultative scavenging behavior in carrion crows. Subsequently, E. faecalis isolated from carrion crows was transplanted into model mice to explore the protective effects of this bacterial community against Salmonella enterica infection. Results showed that E. faecalis down-regulated the expression of pro-inflammatory cytokines tumor necrosis factor alpha (TNF-α), interferon gamma (IFN-γ), and interleukin 6 (IL-6), prevented S. enterica colonization, and regulated the composition of gut microbiota in mice, thereby modulating the host's immune regulatory capacity. Therefore, E. faecalis exerts immunoregulatory and anti-pathogenic functions in carrion crows engaged in scavenging behavior, offering a representative case of how the gut microbiota contributes to the protection of hosts with specialized diets.
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Affiliation(s)
- Bin Hu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jia-Min Wang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qing-Xun Zhang
- Beijing Milu Ecological Research Center, Beijing 102600, China
| | - Jing Xu
- Beijing Capital International Airport Co., Ltd., Beijing 101300, China
| | - Ya-Nan Xing
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bo Wang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shu-Yi Han
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hong-Xuan He
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China. E-mail:
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11
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Ma ZS, Shi P. Critical complex network structures in animal gastrointestinal tract microbiomes. Anim Microbiome 2024; 6:23. [PMID: 38702785 PMCID: PMC11067214 DOI: 10.1186/s42523-024-00291-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Accepted: 01/21/2024] [Indexed: 05/06/2024] Open
Abstract
BACKGROUND Living things from microbes to their hosts (plants, animals and humans) interact with each other, and their relationships may be described with complex network models. The present study focuses on the critical network structures, specifically the core/periphery nodes and backbones (paths of high-salience skeletons) in animal gastrointestinal microbiomes (AGMs) networks. The core/periphery network (CPN) mirrors nearly ubiquitous nestedness in ecological communities, particularly dividing the network as densely interconnected core-species and periphery-species that only sparsely linked to the core. Complementarily, the high-salience skeleton network (HSN) mirrors the pervasive asymmetrical species interactions (strictly microbial species correlations), particularly forming heterogenous pathways in AGM networks with both "backbones" and "rural roads" (regular or weak links). While the cores and backbones can act as critical functional structures, the periphery nodes and weak links may stabilize network functionalities through redundancy. RESULTS Here, we build and analyze 36 pairs of CPN/HSN for the AGMs based on 4903 gastrointestinal-microbiome samples containing 473,359 microbial species collected from 318 animal species covering all vertebrate and four major invertebrate classes. The network analyses were performed at host species, order, class, phylum, kingdom scales and diet types with selected and comparative taxon pairs. Besides diet types, the influence of host phylogeny, measured with phylogenetic (evolutionary) timeline or "age", were integrated into the analyses. For example, it was found that the evolutionary trends of three primary microbial phyla (Bacteroidetes/Firmicutes/Proteobacteria) and their pairwise abundance-ratios in animals do not mirror the patterns in modern humans phylogenetically, although they are consistent in terms of diet types. CONCLUSIONS Overall, the critical network structures of AGMs are qualitatively and structurally similar to those of the human gut microbiomes. Nevertheless, it appears that the critical composition (the three phyla of Bacteroidetes, Firmicutes, and Proteobacteria) in human gut microbiomes has broken the evolutionary trend from animals to humans, possibly attributable to the Anthropocene epoch and reflecting the far-reaching influences of agriculture and industrial revolution on the human gut microbiomes. The influences may have led to the deviations between modern humans and our hunter-gather ancestors and animals.
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Affiliation(s)
- Zhanshan Sam Ma
- Computational Biology and Medical Ecology Lab, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China.
- Faculty of Arts and Science, Harvard Forest, Harvard University, Cambridge, MA, 02138, USA.
| | - Peng Shi
- Evolutionary and Functional Genomics Lab, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China.
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12
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Amin A, Mekadim C, Modrackova N, Bolechova P, Mrazek J, Neuzil-Bunesova V. Microbiome composition and presence of cultivable commensal groups of Southern Tamanduas (Tamandua tetradactyla) varies with captive conditions. Anim Microbiome 2024; 6:21. [PMID: 38698458 PMCID: PMC11064412 DOI: 10.1186/s42523-024-00311-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 04/18/2024] [Indexed: 05/05/2024] Open
Abstract
Southern Tamanduas (Tamandua tetradactyla) belong to the specialized placental myrmecophages. There is not much information about their intestinal microbiome. Moreover, due to their food specialization, it is difficult to create an adequate diet under breeding conditions. Therefore, we used 16S rDNA amplicon sequencing to analyze the fecal microbiome of captive Southern Tamanduas from four locations in the Czech Republic and evaluated the impact of the incoming diet and facility conditions on microbiome composition. Together with the microbiome analysis, we also quantified and identified cultivable commensals. The anteater fecal microbiome was dominated by the phyla Bacillota and Bacteroidota, while Pseudomonadota, Spirochaetota, and Actinobacteriota were less abundant. At the taxonomic family level, Lachnospiraceae, Prevotellaceae, Bacteroidaceae, Oscillospiraceae, Erysipelotrichaceae, Spirochaetaceae, Ruminococcaceae, Leuconostocaceae, and Streptococcaceae were mainly represented in the fecal microbiome of animals from all locations. Interestingly, Lactobacillaceae dominated in the location with a zoo-made diet. These animals also had significantly lower diversity of gut microbiome in comparison with animals from other locations fed mainly with a complete commercial diet. Moreover, captive conditions of analyzed anteater included other factors such as the enrichment of the diet with insect-based products, probiotic interventions, the presence of other animals in the exposure, which can potentially affect the composition of the microbiome and cultivable microbes. In total, 63 bacterial species from beneficial commensal to opportunistic pathogen were isolated and identified using MALDI-TOF MS in the set of more than one thousand selected isolates. Half of the detected species were present in the fecal microbiota of most animals, the rest varied across animals and locations.
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Affiliation(s)
- Ahmad Amin
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 165 00, Prague 6, Czech Republic
| | - Chahrazed Mekadim
- Institute of Animal Physiology and Genetics, The Czech Academy of Sciences, v. v. i., Videnska 1083, 142 20, Prague, Czech Republic
| | - Nikol Modrackova
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 165 00, Prague 6, Czech Republic
| | - Petra Bolechova
- Department of Ethology and Companion Animal Science, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, Kamycka 129, 165 00, Prague 6, Czech Republic
| | - Jakub Mrazek
- Institute of Animal Physiology and Genetics, The Czech Academy of Sciences, v. v. i., Videnska 1083, 142 20, Prague, Czech Republic
| | - Vera Neuzil-Bunesova
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 165 00, Prague 6, Czech Republic.
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13
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Jenkins L, McKnight DT, Parks M, Byer NW, Oliaro FJ, Thompson D, Scott R. Variable effects of captivity on microbiomes in populations of IUCN-endangered Blanding's turtles (Emydoidea blandingii). J Appl Microbiol 2024; 135:lxae121. [PMID: 38755020 DOI: 10.1093/jambio/lxae121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 04/26/2024] [Accepted: 05/15/2024] [Indexed: 05/18/2024]
Abstract
AIMS Microbiome composition is increasingly considered in species reintroduction efforts and may influence survival and reproductive success. Many turtle species are threatened by anthropogenic pressures and are frequently raised in captivity for reintroduction efforts, yet little is known about turtle microbiome composition in either wild or captive settings. Here, we investigated trends in microbiome composition of captive and wild IUCN-endangered Blanding's turtles (Emydoidea blandingii). METHODS AND RESULTS We amplified and sequenced the V4 region of the 16S rDNA locus from plastron, cloaca, and water samples of wild E. blandingii adults and two populations of captive E. blandingii juveniles being raised for headstarting. Plastron, cloaca, and water-associated microbiomes differed strongly from each other and were highly variable among captive sites and between captive and wild sites. Across plastron, cloaca, and water-associated microbial communities, microbial diversity changed over time, but not in a predictable direction between captive sites. Plastron beta diversity correlated with growth rate in captive samples, indicating that external microbiomes may correlate with individual fitness. CONCLUSIONS Our results indicate that external and internal microbiomes vary between captive and wild turtles and may reflect differences in fitness of captive-raised individuals.
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Affiliation(s)
- Lauren Jenkins
- Nicholas School of the Environment, Duke University, Durham, NC 27708, United States
- Department of Biology, Wheaton College, Wheaton, IL 60187, United States
| | | | - Matthew Parks
- Department of Biology, University of Central Oklahoma, Edmond, OK 73034, United States
| | - Nathan W Byer
- Division of Natural Resources, Cleveland Metroparks, Cleveland, OH 44144, United States
| | - Francis J Oliaro
- Conservation Research Department, John G. Shedd Aquarium, Chicago, IL 60605, United States
| | - Dan Thompson
- Forest Preserve District of DuPage County, Wheaton, IL 60189, United States
| | - Rodney Scott
- Department of Biology, Wheaton College, Wheaton, IL 60187, United States
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14
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Deehan EC, Mocanu V, Madsen KL. Effects of dietary fibre on metabolic health and obesity. Nat Rev Gastroenterol Hepatol 2024; 21:301-318. [PMID: 38326443 DOI: 10.1038/s41575-023-00891-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/18/2023] [Indexed: 02/09/2024]
Abstract
Obesity and metabolic syndrome represent a growing epidemic worldwide. Body weight is regulated through complex interactions between hormonal, neural and metabolic pathways and is influenced by numerous environmental factors. Imbalances between energy intake and expenditure can occur due to several factors, including alterations in eating behaviours, abnormal satiation and satiety, and low energy expenditure. The gut microbiota profoundly affects all aspects of energy homeostasis through diverse mechanisms involving effects on mucosal and systemic immune, hormonal and neural systems. The benefits of dietary fibre on metabolism and obesity have been demonstrated through mechanistic studies and clinical trials, but many questions remain as to how different fibres are best utilized in managing obesity. In this Review, we discuss the physiochemical properties of different fibres, current findings on how fibre and the gut microbiota interact to regulate body weight homeostasis, and knowledge gaps related to using dietary fibres as a complementary strategy. Precision medicine approaches that utilize baseline microbiota and clinical characteristics to predict individual responses to fibre supplementation represent a new paradigm with great potential to enhance weight management efficacy, but many challenges remain before these approaches can be fully implemented.
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Affiliation(s)
- Edward C Deehan
- Department of Food Science and Technology, University of Nebraska, Lincoln, NE, USA
- Nebraska Food for Health Center, Lincoln, NE, USA
| | - Valentin Mocanu
- Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
| | - Karen L Madsen
- Department of Medicine, University of Alberta, Edmonton, Alberta, Canada.
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15
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Su C, Xie T, Jiang L, Wang Y, Wang Y, Nie R, Zhao Y, He B, Ma J, Yang Q, Hao J. Host genetics and larval host plant modulate microbiome structure and evolution underlying the intimate insect-microbe-plant interactions in Parnassius species on the Qinghai-Tibet Plateau. Ecol Evol 2024; 14:e11218. [PMID: 38606343 PMCID: PMC11007261 DOI: 10.1002/ece3.11218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 02/09/2024] [Accepted: 03/20/2024] [Indexed: 04/13/2024] Open
Abstract
Insects harbor a remarkable diversity of gut microbiomes critical for host survival, health, and fitness, but the mechanism of this structured symbiotic community remains poorly known, especially for the insect group consisting of many closely related species that inhabit the Qinghai-Tibet Plateau. Here, we firstly analyzed population-level 16S rRNA microbial dataset, comprising 11 Parnassius species covering 5 subgenera, from 14 populations mostly sampled in mountainous regions across northwestern-to-southeastern China, and meanwhile clarified the relative importance of multiple factors on gut microbial community structure and evolution. Our findings indicated that both host genetics and larval host plant modulated gut microbial diversity and community structure. Moreover, the effect analysis of host genetics and larval diet on gut microbiomes showed that host genetics played a critical role in governing the gut microbial beta diversity and the symbiotic community structure, while larval host plant remarkably influenced the functional evolution of gut microbiomes. These findings of the intimate insect-microbe-plant interactions jointly provide some new insights into the correlation among the host genetic background, larval host plant, the structure and evolution of gut microbiome, as well as the mechanisms of high-altitude adaptation in closely related species of this alpine butterfly group.
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Affiliation(s)
- Chengyong Su
- College of Life SciencesAnhui Normal UniversityWuhuChina
| | - Tingting Xie
- College of Life SciencesAnhui Normal UniversityWuhuChina
| | - Lijun Jiang
- College of Life SciencesAnhui Normal UniversityWuhuChina
| | - Yunliang Wang
- College of Life SciencesAnhui Normal UniversityWuhuChina
- College of Physical EducationAnhui Normal UniversityWuhuChina
| | - Ying Wang
- College of Life SciencesAnhui Normal UniversityWuhuChina
- College of Physical EducationAnhui Normal UniversityWuhuChina
| | - Ruie Nie
- College of Life SciencesAnhui Normal UniversityWuhuChina
| | - Youjie Zhao
- College of Life SciencesAnhui Normal UniversityWuhuChina
| | - Bo He
- College of Life SciencesAnhui Normal UniversityWuhuChina
| | - Junye Ma
- Key Laboratory of Palaeobiology and Petroleum Stratigraphy, Center for Excellence in Life and Palaeoenvironment, Nanjing Institute of Geology and PaleontologyChinese Academy of SciencesNanjingChina
| | - Qun Yang
- Key Laboratory of Palaeobiology and Petroleum Stratigraphy, Center for Excellence in Life and Palaeoenvironment, Nanjing Institute of Geology and PaleontologyChinese Academy of SciencesNanjingChina
- Nanjing CollegeUniversity of Chinese Academy of SciencesNanjingChina
| | - Jiasheng Hao
- College of Life SciencesAnhui Normal UniversityWuhuChina
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16
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Zhang M, Zhou Y, Cui X, Zhu L. The Potential of Co-Evolution and Interactions of Gut Bacteria-Phages in Bamboo-Eating Pandas: Insights from Dietary Preference-Based Metagenomic Analysis. Microorganisms 2024; 12:713. [PMID: 38674657 PMCID: PMC11051890 DOI: 10.3390/microorganisms12040713] [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: 01/16/2024] [Revised: 03/26/2024] [Accepted: 03/28/2024] [Indexed: 04/28/2024] Open
Abstract
Bacteria and phages are two of the most abundant biological entities in the gut microbiome, and diet and host phylogeny are two of the most critical factors influencing the gut microbiome. A stable gut bacterial community plays a pivotal role in the host's physiological development and immune health. A phage is a virus that directly infects bacteria, and phages' close associations and interactions with bacteria are essential for maintaining the stability of the gut bacterial community and the entire microbial ecosystem. Here, we utilized 99 published metagenomic datasets from 38 mammalian species to investigate the relationship (diversity and composition) and potential interactions between gut bacterial and phage communities and the impact of diet and phylogeny on these communities. Our results highlight the co-evolutionary potential of bacterial-phage interactions within the mammalian gut. We observed a higher alpha diversity in gut bacteria than in phages and identified positive correlations between bacterial and phage compositions. Furthermore, our study revealed the significant influence of diet and phylogeny on mammalian gut bacterial and phage communities. We discovered that the impact of dietary factors on these communities was more pronounced than that of phylogenetic factors at the order level. In contrast, phylogenetic characteristics had a more substantial influence at the family level. The similar omnivorous dietary preference and closer phylogenetic relationship (family Ursidae) may contribute to the similarity of gut bacterial and phage communities between captive giant panda populations (GPCD and GPYA) and omnivorous animals (OC; including Sun bear, brown bear, and Asian black bear). This study employed co-occurrence microbial network analysis to reveal the potential interaction patterns between bacteria and phages. Compared to other mammalian groups (carnivores, herbivores, and omnivores), the gut bacterial and phage communities of bamboo-eating species (giant pandas and red pandas) exhibited a higher level of interaction. Additionally, keystone species and modular analysis showed the potential role of phages in driving and maintaining the interaction patterns between bacteria and phages in captive giant pandas. In sum, gaining a comprehensive understanding of the interaction between the gut microbiota and phages in mammals is of great significance, which is of great value in promoting healthy and sustainable mammals and may provide valuable insights into the conservation of wildlife populations, especially endangered animal species.
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Affiliation(s)
| | | | | | - Lifeng Zhu
- College of Life Sciences, Nanjing Normal University, Nanjing 210098, China; (M.Z.); (Y.Z.); (X.C.)
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17
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Tannock GW. Understanding the gut microbiota by considering human evolution: a story of fire, cereals, cooking, molecular ingenuity, and functional cooperation. Microbiol Mol Biol Rev 2024; 88:e0012722. [PMID: 38126754 PMCID: PMC10966955 DOI: 10.1128/mmbr.00127-22] [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] [Indexed: 12/23/2023] Open
Abstract
SUMMARYThe microbial community inhabiting the human colon, referred to as the gut microbiota, is mostly composed of bacterial species that, through extensive metabolic networking, degrade and ferment components of food and human secretions. The taxonomic composition of the microbiota has been extensively investigated in metagenomic studies that have also revealed details of molecular processes by which common components of the human diet are metabolized by specific members of the microbiota. Most studies of the gut microbiota aim to detect deviations in microbiota composition in patients relative to controls in the hope of showing that some diseases and conditions are due to or exacerbated by alterations to the gut microbiota. The aim of this review is to consider the gut microbiota in relation to the evolution of Homo sapiens which was heavily influenced by the consumption of a nutrient-dense non-arboreal diet, limited gut storage capacity, and acquisition of skills relating to mastering fire, cooking, and cultivation of cereal crops. The review delves into the past to gain an appreciation of what is important in the present. A holistic view of "healthy" microbiota function is proposed based on the evolutionary pathway shared by humans and gut microbes.
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Affiliation(s)
- Gerald W. Tannock
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
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18
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Vargas-Gastélum L, Romer AS, Ghotbi M, Dallas JW, Alexander NR, Moe KC, McPhail KL, Neuhaus GF, Shadmani L, Spatafora JW, Stajich JE, Tabima JF, Walker DM. Herptile gut microbiomes: a natural system to study multi-kingdom interactions between filamentous fungi and bacteria. mSphere 2024; 9:e0047523. [PMID: 38349154 PMCID: PMC10964425 DOI: 10.1128/msphere.00475-23] [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: 08/22/2023] [Accepted: 01/10/2024] [Indexed: 03/27/2024] Open
Abstract
Reptiles and amphibians (herptiles) are some of the most endangered and threatened species on the planet and numerous conservation strategies are being implemented with the goal of ensuring species recovery. Little is known, however, about the gut microbiome of wild herptiles and how it relates to the health of these populations. Here, we report results from the gut microbiome characterization of both a broad survey of herptiles, and the correlation between the fungus Basidiobolus, and the bacterial community supported by a deeper, more intensive sampling of Plethodon glutinosus, known as slimy salamanders. We demonstrate that bacterial communities sampled from frogs, lizards, and salamanders are structured by the host taxonomy and that Basidiobolus is a common and natural component of these wild gut microbiomes. Intensive sampling of multiple hosts across the ecoregions of Tennessee revealed that geography and host:geography interactions are strong predictors of distinct Basidiobolus operational taxonomic units present within a given host. Co-occurrence analyses of Basidiobolus and bacterial community diversity support a correlation and interaction between Basidiobolus and bacteria, suggesting that Basidiobolus may play a role in structuring the bacterial community. We further the hypothesis that this interaction is advanced by unique specialized metabolism originating from horizontal gene transfer from bacteria to Basidiobolus and demonstrate that Basidiobolus is capable of producing a diversity of specialized metabolites including small cyclic peptides.IMPORTANCEThis work significantly advances our understanding of biodiversity and microbial interactions in herptile microbiomes, the role that fungi play as a structural and functional members of herptile gut microbiomes, and the chemical functions that structure microbiome phenotypes. We also provide an important observational system of how the gut microbiome represents a unique environment that selects for novel metabolic functions through horizontal gene transfer between fungi and bacteria. Such studies are needed to better understand the complexity of gut microbiomes in nature and will inform conservation strategies for threatened species of herpetofauna.
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Affiliation(s)
- Lluvia Vargas-Gastélum
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - Alexander S. Romer
- Department of Biology, Middle Tennessee State University, Murfreesboro, Tennessee, USA
| | - Marjan Ghotbi
- Research Division 3, Marine Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Jason W. Dallas
- Department of Biology, Middle Tennessee State University, Murfreesboro, Tennessee, USA
| | - N. Reed Alexander
- Department of Biology, Middle Tennessee State University, Murfreesboro, Tennessee, USA
| | - Kylie C. Moe
- Department of Biology, Middle Tennessee State University, Murfreesboro, Tennessee, USA
| | - Kerry L. McPhail
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon, USA
| | - George F. Neuhaus
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon, USA
| | - Leila Shadmani
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, California, USA
| | - Joseph W. Spatafora
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - Jason E. Stajich
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, California, USA
- Institute for Integrative Genome Biology, University of California, Riverside, California, USA
| | - Javier F. Tabima
- Department of Biology, Clark University, Worcester, Massachusetts, USA
| | - Donald M. Walker
- Department of Biology, Middle Tennessee State University, Murfreesboro, Tennessee, USA
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19
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Bertoldo G, Broccanello C, Tondello A, Cappellozza S, Saviane A, Kovitvadhi A, Concheri G, Cullere M, Stevanato P, Zotte AD, Squartini A. Determining the hierarchical order by which intestinal tract, administered diet, and individual relay can shape the gut microbiome of fattening quails. PLoS One 2024; 19:e0298321. [PMID: 38512802 PMCID: PMC10956773 DOI: 10.1371/journal.pone.0298321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Accepted: 01/18/2024] [Indexed: 03/23/2024] Open
Abstract
A bacterial metabarcoding approach was used to compare the microbiome composition of caecal and faecal samples from fattening Japanese quails (Coturnix coturnix japonica) fed three different diet regimes. The tested feedstuffs included (1) a commercial diet for fattening quails, (2) a commercial diet containing 12% full-fat silkworm (Bombyx mori) pupae meal, and (3) a commercial diet containing 12% defatted silkworm pupae meal. The aim of the experiment was to verify the relative effect of three variables (diet type, gut tract comparing caecum to rectum, and individual animal) in determining the level of bacterial community dissimilarity to rank the relevance of each of the three factors in affecting and shaping community composition. To infer such ranking, the communities resulting from the high-throughput sequencing from each sample were used to calculate the Bray-Curtis distances in all the pairwise combinations, whereby identical communities would score 0 and totally different ones would yield the maximum distance, equal to 1. The results indicated that the main driver of divergence was the gut tract, as distances between caecal and faecal samples were higher on average, irrespective of diet composition, which scored second in rank, and of whether they had been sampled from the same individual, which was the least effective factor. Simpson's species diversity indexes was not significantly different when comparing tracts or diets, while community evenness was reduced in full-fat silkworm diet-fed animals. The identities of the differentially displayed taxa that were statistically significant as a function of gut tract and diet regimen are discussed in light of their known physiological and functional traits.
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Affiliation(s)
- Giovanni Bertoldo
- Department of Agronomy, Food, Natural Resources, Animals and Environment, DAFNAE, University of Padova, Padova, Italy
| | - Chiara Broccanello
- Department of Agronomy, Food, Natural Resources, Animals and Environment, DAFNAE, University of Padova, Padova, Italy
| | - Alessandra Tondello
- Department of Agronomy, Food, Natural Resources, Animals and Environment, DAFNAE, University of Padova, Padova, Italy
| | - Silvia Cappellozza
- Council for Agricultural Research and Economics, Research Centre for Agriculture and Environment, Sericulture Laboratory of Padua, Padova, Italy
| | - Alessio Saviane
- Council for Agricultural Research and Economics, Research Centre for Agriculture and Environment, Sericulture Laboratory of Padua, Padova, Italy
| | - Attawit Kovitvadhi
- Department of Physiology, Faculty of Veterinary Medicine, Kasetsart University, Bangkok, Thailand
| | - Giuseppe Concheri
- Department of Agronomy, Food, Natural Resources, Animals and Environment, DAFNAE, University of Padova, Padova, Italy
| | - Marco Cullere
- Department of Animal Medicine, Production and Health, MAPS, University of Padova, Padova, Italy
| | - Piergiorgio Stevanato
- Department of Agronomy, Food, Natural Resources, Animals and Environment, DAFNAE, University of Padova, Padova, Italy
| | - Antonella Dalle Zotte
- Department of Animal Medicine, Production and Health, MAPS, University of Padova, Padova, Italy
| | - Andrea Squartini
- Department of Agronomy, Food, Natural Resources, Animals and Environment, DAFNAE, University of Padova, Padova, Italy
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20
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González A, Fullaondo A, Odriozola A. Impact of evolution on lifestyle in microbiome. ADVANCES IN GENETICS 2024; 111:149-198. [PMID: 38908899 DOI: 10.1016/bs.adgen.2024.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/24/2024]
Abstract
This chapter analyses the interaction between microbiota and humans from an evolutionary point of view. Long-term interactions between gut microbiota and host have been generated as a result of dietary choices through coevolutionary processes, where mutuality of advantage is essential. Likewise, the characteristics of the intestinal environment have made it possible to describe different intrahost evolutionary mechanisms affecting microbiota. For its part, the intestinal microbiota has been of great importance in the evolution of mammals, allowing the diversification of dietary niches, phenotypic plasticity and the selection of host phenotypes. Although the origin of the human intestinal microbial community is still not known with certainty, mother-offspring transmission plays a key role, and it seems that transmissibility between individuals in adulthood also has important implications. Finally, it should be noted that certain aspects inherent to modern lifestyle, including refined diets, antibiotic intake, exposure to air pollutants, microplastics, and stress, could negatively affect the diversity and composition of our gut microbiota. This chapter aims to combine current knowledge to provide a comprehensive view of the interaction between microbiota and humans throughout evolution.
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Affiliation(s)
- Adriana González
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Spain.
| | - Asier Fullaondo
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Adrián Odriozola
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Spain
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21
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von Hoyningen-Huene AJE, Bang C, Rausch P, Rühlemann M, Fokt H, He J, Jensen N, Knop M, Petersen C, Schmittmann L, Zimmer T, Baines JF, Bosch TCG, Hentschel U, Reusch TBH, Roeder T, Franke A, Schulenburg H, Stukenbrock E, Schmitz RA. The archaeome in metaorganism research, with a focus on marine models and their bacteria-archaea interactions. Front Microbiol 2024; 15:1347422. [PMID: 38476944 PMCID: PMC10927989 DOI: 10.3389/fmicb.2024.1347422] [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: 11/30/2023] [Accepted: 02/01/2024] [Indexed: 03/14/2024] Open
Abstract
Metaorganism research contributes substantially to our understanding of the interaction between microbes and their hosts, as well as their co-evolution. Most research is currently focused on the bacterial community, while archaea often remain at the sidelines of metaorganism-related research. Here, we describe the archaeome of a total of eleven classical and emerging multicellular model organisms across the phylogenetic tree of life. To determine the microbial community composition of each host, we utilized a combination of archaea and bacteria-specific 16S rRNA gene amplicons. Members of the two prokaryotic domains were described regarding their community composition, diversity, and richness in each multicellular host. Moreover, association with specific hosts and possible interaction partners between the bacterial and archaeal communities were determined for the marine models. Our data show that the archaeome in marine hosts predominantly consists of Nitrosopumilaceae and Nanoarchaeota, which represent keystone taxa among the porifera. The presence of an archaeome in the terrestrial hosts varies substantially. With respect to abundant archaeal taxa, they harbor a higher proportion of methanoarchaea over the aquatic environment. We find that the archaeal community is much less diverse than its bacterial counterpart. Archaeal amplicon sequence variants are usually host-specific, suggesting adaptation through co-evolution with the host. While bacterial richness was higher in the aquatic than the terrestrial hosts, a significant difference in diversity and richness between these groups could not be observed in the archaeal dataset. Our data show a large proportion of unclassifiable archaeal taxa, highlighting the need for improved cultivation efforts and expanded databases.
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Affiliation(s)
| | - Corinna Bang
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Philipp Rausch
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Malte Rühlemann
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
- Hannover Medical School, Institute for Medical Microbiology and Hospital Epidemiology, Hannover, Germany
| | - Hanna Fokt
- Section of Evolutionary Medicine, Institute for Experimental Medicine, Kiel University, Kiel, Germany
- Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Jinru He
- Cell and Developmental Biology, Zoological Institute, Kiel University, Kiel, Germany
| | - Nadin Jensen
- Institute for General Microbiology, Kiel University, Kiel, Germany
| | - Mirjam Knop
- Department of Molecular Physiology, Zoology, Kiel University, Kiel, Germany
| | - Carola Petersen
- Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Germany
| | - Lara Schmittmann
- Research Unit Ocean Dynamics, GEOMAR Helmholtz Institute for Ocean Research Kiel, Kiel, Germany
| | - Thorsten Zimmer
- Institute for General Microbiology, Kiel University, Kiel, Germany
- Research Unit Marine Symbioses, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - John F. Baines
- Section of Evolutionary Medicine, Institute for Experimental Medicine, Kiel University, Kiel, Germany
- Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Thomas C. G. Bosch
- Cell and Developmental Biology, Zoological Institute, Kiel University, Kiel, Germany
| | - Ute Hentschel
- Marine Evolutionary Ecology, GEOMAR Helmholtz Center for Ocean Research, Kiel, Germany
- Christian-Albrechts-Universität Kiel, Kiel, Germany
| | - Thorsten B. H. Reusch
- Research Unit Marine Symbioses, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
- Christian-Albrechts-Universität Kiel, Kiel, Germany
| | - Thomas Roeder
- Department of Molecular Physiology, Zoology, Kiel University, Kiel, Germany
- German Center for Lung Research (DZL), Airway Research Center North (ARCN), Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Hinrich Schulenburg
- Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Germany
- Antibiotic Resistance Group, Max-Planck Institute for Evolutionary Biology, Plön, Germany
| | - Eva Stukenbrock
- Max Planck Institute for Evolutionary Biology, Plön, Germany
- Environmental Genomics, Christian-Albrechts University of Kiel, Kiel, Germany
| | - Ruth A. Schmitz
- Institute for General Microbiology, Kiel University, Kiel, Germany
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22
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Bunker ME, Weiss SL. The reproductive microbiome and maternal transmission of microbiota via eggs in Sceloporus virgatus. FEMS Microbiol Ecol 2024; 100:fiae011. [PMID: 38308517 PMCID: PMC10873522 DOI: 10.1093/femsec/fiae011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 01/18/2024] [Accepted: 01/30/2024] [Indexed: 02/04/2024] Open
Abstract
Maternal transmission of microbes occurs across the animal kingdom and is vital for offspring development and long-term health. The mechanisms of this transfer are most well-studied in humans and other mammals but are less well-understood in egg-laying animals, especially those with no parental care. Here, we investigate the transfer of maternal microbes in the oviparous phrynosomatid lizard, Sceloporus virgatus. We compared the microbiota of three maternal tissues-oviduct, cloaca, and intestine-to three offspring sample types: egg contents and eggshells on the day of oviposition, and hatchling intestinal tissue on the day of hatching. We found that maternal identity is an important factor in hatchling microbiome composition, indicating that maternal transmission is occurring. The maternal cloacal and oviductal communities contribute to offspring microbiota in all three sample types, with minimal microbes sourced from maternal intestines. This indicates that the maternal reproductive microbiome is more important for microbial inheritance than the gut microbiome, and the tissue-level variation of the adult S. virgatus microbiota must develop as the hatchling matures. Despite differences between adult and hatchling communities, offspring microbiota were primarily members of the Enterobacteriaceae and Yersiniaceae families (Phylum Proteobacteria), consistent with this and past studies of adult S. virgatus microbiomes.
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Affiliation(s)
- Marie E Bunker
- Department of Biology, University of Puget Sound, 1500 N. Warner Street, Tacoma, WA 98416, United States
| | - Stacey L Weiss
- Department of Biology, University of Puget Sound, 1500 N. Warner Street, Tacoma, WA 98416, United States
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23
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Gao SM, Fei HL, Li Q, Lan LY, Huang LN, Fan PF. Eco-evolutionary dynamics of gut phageome in wild gibbons (Hoolock tianxing) with seasonal diet variations. Nat Commun 2024; 15:1254. [PMID: 38341424 PMCID: PMC10858875 DOI: 10.1038/s41467-024-45663-8] [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: 06/25/2023] [Accepted: 01/30/2024] [Indexed: 02/12/2024] Open
Abstract
It has been extensively studied that the gut microbiome provides animals flexibility to adapt to food variability. Yet, how gut phageome responds to diet variation of wild animals remains unexplored. Here, we analyze the eco-evolutionary dynamics of gut phageome in six wild gibbons (Hoolock tianxing) by collecting individually-resolved fresh fecal samples and parallel feeding behavior data for 15 consecutive months. Application of complementary viral and microbial metagenomics recovers 39,198 virulent and temperate phage genomes from the feces. Hierarchical cluster analyses show remarkable seasonal diet variations in gibbons. From high-fruit to high-leaf feeding period, the abundances of phage populations are seasonally fluctuated, especially driven by the increased abundance of virulent phages that kill the Lachnospiraceae hosts, and a decreased abundance of temperate phages that piggyback the Bacteroidaceae hosts. Functional profiling reveals an enrichment through horizontal gene transfers of toxin-antitoxin genes on temperate phage genomes in high-leaf season, potentially conferring benefits to their prokaryotic hosts. The phage-host ecological dynamics are driven by the coevolutionary processes which select for tail fiber and DNA primase genes on virulent and temperate phage genomes, respectively. Our results highlight complex phageome-microbiome interactions as a key feature of the gibbon gut microbial ecosystem responding to the seasonal diet.
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Affiliation(s)
- Shao-Ming Gao
- School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, PR China
| | - Han-Lan Fei
- School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, PR China
- College of Life Science, China West Normal University, Nanchong, 637002, PR China
| | - Qi Li
- School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, PR China
| | - Li-Ying Lan
- School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, PR China
| | - Li-Nan Huang
- School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, PR China.
| | - Peng-Fei Fan
- School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, PR China.
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24
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Liu X, Yu J, Huan Z, Xu M, Song T, Yang R, Zhu W, Jiang J. Comparing the gut microbiota of Sichuan golden monkeys across multiple captive and wild settings: roles of anthropogenic activities and host factors. BMC Genomics 2024; 25:148. [PMID: 38321370 PMCID: PMC10848473 DOI: 10.1186/s12864-024-10041-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 01/22/2024] [Indexed: 02/08/2024] Open
Abstract
BACKGROUND Captivity and artificial food provision are common conservation strategies for the endangered golden snub-nosed monkey (Rhinopithecus roxellana). Anthropogenic activities have been reported to impact the fitness of R. roxellana by altering their gut microbiota, a crucial indicator of animal health. Nevertheless, the degree of divergence in gut microbiota between different anthropogenically-disturbed (AD) R. roxellana and their counterparts in the wild has yet to be elucidated. Here, we conducted a comparative analysis of the gut microbiota across nine populations of R. roxellana spanning China, which included seven captive populations, one wild population, and another wild population subject to artificial food provision. RESULTS Both captivity and food provision significantly altered the gut microbiota. AD populations exhibited common variations, such as increased Bacteroidetes and decreased Firmicutes (e.g., Ruminococcus), Actinobacteria (e.g., Parvibacter), Verrucomicrobia (e.g., Akkermansia), and Tenericutes. Additionally, a reduced Firmicutes/Bacteroidetes ratiosuggested diminished capacity for complex carbohydrate degradation in captive individuals. The results of microbial functional prediction suggested that AD populations displayed heightened microbial genes linked to vitamin and amino acid metabolism, alongside decreased genes associated antibiotics biosynthesis (e.g., penicillin, cephalosporin, macrolides, and clavulanic acid) and secondary metabolite degradation (e.g., naphthalene and atrazine). These microbial alterations implied potential disparities in the health status between AD and wild individuals. AD populations exhibited varying degrees of microbial changes compared to the wild group, implying that the extent of these variations might serve as a metric for assessing the health status of AD populations. Furthermore, utilizing the individual information of captive individuals, we identified associations between variations in the gut microbiota of R. roxellana and host age, as well as pedigree. Older individuals exhibited higher microbial diversity, while a closer genetic relatedness reflected a more similar gut microbiota. CONCLUSIONS Our aim was to assess how anthropogenic activities and host factors influence the gut microbiota of R. roxellana. Anthropogenic activities led to consistent changes in gut microbial diversity and function, while host age and genetic relatedness contributed to interindividual variations in the gut microbiota. These findings may contribute to the establishment of health assessment standards and the optimization of breeding conditions for captive R. roxellana populations.
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Affiliation(s)
- Xuanzhen Liu
- Chengdu Zoo & Chengdu Research Institute of Wildlife, 610081, Chengdu, China
| | - Jianqiu Yu
- Chengdu Zoo & Chengdu Research Institute of Wildlife, 610081, Chengdu, China
| | - Zongjin Huan
- Chengdu Zoo & Chengdu Research Institute of Wildlife, 610081, Chengdu, China
| | - Mei Xu
- Chengdu Zoo & Chengdu Research Institute of Wildlife, 610081, Chengdu, China
| | - Ting Song
- Chengdu Zoo & Chengdu Research Institute of Wildlife, 610081, Chengdu, China
| | - Ruilin Yang
- Chengdu Zoo & Chengdu Research Institute of Wildlife, 610081, Chengdu, China
| | - Wei Zhu
- Chengdu Institute of Biology, Chinese Academy of Sciences, 610041, Chengdu, China.
| | - Jianping Jiang
- Chengdu Institute of Biology, Chinese Academy of Sciences, 610041, Chengdu, China
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25
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Härer A, Rennison DJ. Gut Microbiota Uniqueness Is Associated with Lake Size, a Proxy for Diet Diversity, in Stickleback Fish. Am Nat 2024; 203:284-291. [PMID: 38306277 DOI: 10.1086/727703] [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] [Indexed: 02/04/2024]
Abstract
AbstractOrganismal divergence can be driven by differential resource use and adaptation to different trophic niches. Variation in diet is a major factor shaping the gut microbiota, which is crucial for many aspects of their hosts' biology. However, it remains largely unknown how host diet diversity affects the gut microbiota, and it could be hypothesized that trophic niche width is positively associated with gut microbiota diversity. To test this idea, we sequenced the 16S ribosomal RNA gene from intestinal tissue of 14 threespine stickleback populations from lakes of varying size on Vancouver Island, Canada, that have been shown to differ in trophic niche width. Using lake size as a proxy for trophic ecology, we found evidence for higher gut microbiota uniqueness among individuals from populations with broader trophic niches. While these results suggest that diet diversity might promote gut microbiota diversity, additional work investigating diet and gut microbiota variation of the same host organisms will be necessary. Yet our results motivate the question of how host population diversity (e.g., ecological, morphological, genetic) might interact with the gut microbiota during the adaptation to ecological niches.
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26
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Pasciullo Boychuck S, Brenner LJ, Gagorik CN, Schamel JT, Baker S, Tran E, vonHoldt BM, Koepfli K, Maldonado JE, DeCandia AL. The gut microbiomes of Channel Island foxes and island spotted skunks exhibit fine-scale differentiation across host species and island populations. Ecol Evol 2024; 14:e11017. [PMID: 38362164 PMCID: PMC10867392 DOI: 10.1002/ece3.11017] [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: 10/25/2023] [Revised: 12/09/2023] [Accepted: 12/11/2023] [Indexed: 02/17/2024] Open
Abstract
California's Channel Islands are home to two endemic mammalian carnivores: island foxes (Urocyon littoralis) and island spotted skunks (Spilogale gracilis amphiala). Although it is rare for two insular terrestrial carnivores to coexist, these known competitors persist on both Santa Cruz Island and Santa Rosa Island. We hypothesized that examination of their gut microbial communities would provide insight into the factors that enable this coexistence, as microbial symbionts often reflect host evolutionary history and contemporary ecology. Using rectal swabs collected from island foxes and island spotted skunks sampled across both islands, we generated 16S rRNA amplicon sequencing data to characterize their gut microbiomes. While island foxes and island spotted skunks both harbored the core mammalian microbiome, host species explained the largest proportion of variation in the dataset. We further identified intraspecific variation between island populations, with greater differentiation observed between more specialist island spotted skunk populations compared to more generalist island fox populations. This pattern may reflect differences in resource utilization following fine-scale niche differentiation. It may further reflect evolutionary differences regarding the timing of intraspecific separation. Considered together, this study contributes to the growing catalog of wildlife microbiome studies, with important implications for understanding how eco-evolutionary processes enable the coexistence of terrestrial carnivores-and their microbiomes-in island environments.
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Affiliation(s)
| | | | | | | | | | - Elton Tran
- Ecology and Evolutionary BiologyPrinceton UniversityPrincetonNew JerseyUSA
| | | | - Klaus‐Peter Koepfli
- Center for Species SurvivalSmithsonian's National Zoo & Conservation Biology InstituteFront RoyalVirginiaUSA
- Smithsonian‐Mason School of ConservationGeorge Mason UniversityFront RoyalVirginiaUSA
| | - Jesús E. Maldonado
- Center for Conservation GenomicsSmithsonian's National Zoo & Conservation Biology InstituteWashingtonDCUSA
| | - Alexandra L. DeCandia
- Biology, Georgetown UniversityWashingtonDCUSA
- Center for Conservation GenomicsSmithsonian's National Zoo & Conservation Biology InstituteWashingtonDCUSA
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27
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Hoffbeck C, Middleton DMRL, Lamar SK, Keall SN, Nelson NJ, Taylor MW. Gut microbiome of the sole surviving member of reptile order Rhynchocephalia reveals biogeographic variation, influence of host body condition and a substantial core microbiota in tuatara across New Zealand. Ecol Evol 2024; 14:e11073. [PMID: 38405409 PMCID: PMC10884523 DOI: 10.1002/ece3.11073] [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: 09/28/2023] [Revised: 01/12/2024] [Accepted: 02/09/2024] [Indexed: 02/27/2024] Open
Abstract
Tuatara are the sole extant species in the reptile order Rhynchocephalia. They are ecologically and evolutionarily unique, having been isolated geographically for ~84 million years and evolutionarily from their closest living relatives for ~250 million years. Here we report the tuatara gut bacterial community for the first time. We sampled the gut microbiota of translocated tuatara at five sanctuaries spanning a latitudinal range of ~1000 km within Aotearoa New Zealand, as well as individuals from the source population on Takapourewa (Stephens Island). This represents a first look at the bacterial community of the order Rhynchocephalia and provides the opportunity to address several key hypotheses, namely that the tuatara gut microbiota: (1) differs from those of other reptile orders; (2) varies among geographic locations but is more similar at sites with more similar temperatures and (3) is shaped by tuatara body condition, parasitism and ambient temperature. We found significant drivers of the microbiota in sampling site, tuatara body condition, parasitism and ambient temperature, suggesting the importance of these factors when considering tuatara conservation. We also derived a 'core' community of shared bacteria across tuatara at many sites, despite their geographic range and isolation. Remarkably, >70% of amplicon sequence variants could not be assigned to known genera, suggesting a largely undescribed gut bacterial community for this ancient host species.
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Affiliation(s)
- Carmen Hoffbeck
- School of Biological SciencesUniversity of AucklandAucklandNew Zealand
| | | | - Sarah K. Lamar
- School of Biological SciencesVictoria University of WellingtonWellingtonNew Zealand
| | - Susan N. Keall
- School of Biological SciencesVictoria University of WellingtonWellingtonNew Zealand
| | - Nicola J. Nelson
- School of Biological SciencesVictoria University of WellingtonWellingtonNew Zealand
| | - Michael W. Taylor
- School of Biological SciencesUniversity of AucklandAucklandNew Zealand
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28
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Ahmad AR, Ridgeway S, Shibl AA, Idaghdour Y, Jha AR. Falcon gut microbiota is shaped by diet and enriched in Salmonella. PLoS One 2024; 19:e0293895. [PMID: 38289900 PMCID: PMC10826950 DOI: 10.1371/journal.pone.0293895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 10/20/2023] [Indexed: 02/01/2024] Open
Abstract
The gut microbiome is increasingly being appreciated as a master regulator of animal health. However, avian gut microbiome studies commonly focus on birds of economic importance and the gut microbiomes of raptors remain underexplored. Here we examine the gut microbiota of 29 captive falcons-raptors of historic importance-in the context of avian evolution by sequencing the V4 region of the 16S rRNA gene. Our results reveal that evolutionary histories and diet are significantly associated with avian gut microbiota in general, whereas diet plays a major role in shaping the falcon gut microbiota. Multiple analyses revealed that gut microbial diversity, composition, and relative abundance of key diet-discriminating bacterial genera in the falcon gut closely resemble those of carnivorous raptors rather than those of their closest phylogenetic relatives. Furthermore, the falcon microbiota is dominated by Firmicutes and contains Salmonella at appreciable levels. Salmonella presence was associated with altered functional capacity of the falcon gut microbiota as its abundance is associated with depletion of multiple predicted metabolic pathways involved in protein mass buildup, muscle maintenance, and enrichment of antimicrobial compound degradation, thus increasing the pathogenic potential of the falcon gut. Our results point to the necessity of screening for Salmonella and other human pathogens in captive birds to safeguard both the health of falcons and individuals who come in contact with these birds.
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Affiliation(s)
- Anique R. Ahmad
- Genetic Heritage Group, Program in Biology, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Samuel Ridgeway
- Program in Biology, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Ahmed A. Shibl
- Genetic Heritage Group, Program in Biology, New York University Abu Dhabi, Abu Dhabi, UAE
| | | | - Aashish R. Jha
- Genetic Heritage Group, Program in Biology, New York University Abu Dhabi, Abu Dhabi, UAE
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29
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Fleischer R, Jones C, Ledezma-Campos P, Czirják GÁ, Sommer S, Gillespie TR, Vicente-Santos A. Gut microbial shifts in vampire bats linked to immunity due to changed diet in human disturbed landscapes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 907:167815. [PMID: 37852483 DOI: 10.1016/j.scitotenv.2023.167815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 09/14/2023] [Accepted: 10/11/2023] [Indexed: 10/20/2023]
Abstract
Anthropogenic land-use change alters wildlife habitats and modifies species composition, diversity, and contacts among wildlife, livestock, and humans. Such human-modified ecosystems have been associated with emerging infectious diseases, threatening human and animal health. However, human disturbance also creates new resources that some species can exploit. Common vampire bats (Desmodus rotundus) in Latin America constitute an important example, as their adaptation to human-modified habitats and livestock blood-feeding has implications for e.g., rabies transmission. Despite the well-known links between habitat degradation and disease emergence, few studies have explored how human-induced disturbance influences wildlife behavioural ecology and health, which can alter disease dynamics. To evaluate links among habitat disturbance, diet shifts, gut microbiota, and immunity, we quantified disturbance around roosting caves of common vampire bats in Costa Rica, measured their long-term diet preferences (livestock or wildlife blood) using stable isotopes of carbon and nitrogen, evaluated innate and adaptive immune markers, and characterized their gut microbiota. We observed that bats from roosting caves with more cattle farming nearby fed more on cattle blood. Moreover, gut microbial richness and the abundance of specific gut microbes differed according to feeding preferences. Interestingly, bats feeding primarily on wildlife blood harboured a higher abundance of the bacteria Edwardsiella sp., which tended to be associated with higher immunoglobulin G levels. Our results highlight how human land-use change may indirectly affect wildlife health and emerging infectious diseases through diet-induced shifts in microbiota, with implications for host immunity and potential consequences for susceptibility to pathogens.
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Affiliation(s)
- Ramona Fleischer
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany.
| | - Christie Jones
- Department of Environmental Sciences, Emory University, Atlanta, GA, USA; Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | | | - Gábor Á Czirják
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Simone Sommer
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany
| | - Thomas R Gillespie
- Department of Environmental Sciences, Emory University, Atlanta, GA, USA; Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA; Program in Population Biology, Ecology, and Evolution, Emory University, Atlanta, GA, USA
| | - Amanda Vicente-Santos
- Program in Population Biology, Ecology, and Evolution, Emory University, Atlanta, GA, USA.
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30
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Osborne OG, Jiménez RR, Byrne AQ, Gratwicke B, Ellison A, Muletz-Wolz CR. Phylosymbiosis shapes skin bacterial communities and pathogen-protective function in Appalachian salamanders. THE ISME JOURNAL 2024; 18:wrae104. [PMID: 38861457 PMCID: PMC11195472 DOI: 10.1093/ismejo/wrae104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 05/09/2024] [Accepted: 06/10/2024] [Indexed: 06/13/2024]
Abstract
Phylosymbiosis is an association between host-associated microbiome composition and host phylogeny. This pattern can arise via the evolution of host traits, habitat preferences, diets, and the co-diversification of hosts and microbes. Understanding the drivers of phylosymbiosis is vital for modelling disease-microbiome interactions and manipulating microbiomes in multi-host systems. This study quantifies phylosymbiosis in Appalachian salamander skin in the context of infection by the fungal pathogen Batrachochytrium dendrobatidis (Bd), while accounting for environmental microbiome exposure. We sampled ten salamander species representing >150M years of divergence, assessed their Bd infection status, and analysed their skin and environmental microbiomes. Our results reveal a significant signal of phylosymbiosis, whereas the local environmental pool of microbes, climate, geography, and Bd infection load had a smaller impact. Host-microbe co-speciation was not evident, indicating that the effect stems from the evolution of host traits influencing microbiome assembly. Bd infection is correlated with host phylogeny and the abundance of Bd-inhibitory bacterial strains, suggesting that the long-term evolutionary dynamics between salamander hosts and their skin microbiomes affect the present-day distribution of the pathogen, along with habitat-linked exposure risk. Five Bd-inhibitory bacterial strains showed unusual generalism: occurring in most host species and habitats. These generalist strains may enhance the likelihood of probiotic manipulations colonising and persisting on hosts. Our results underscore the substantial influence of host-microbiome eco-evolutionary dynamics on environmental health and disease outcomes.
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Affiliation(s)
- Owen G Osborne
- School of Environmental and Natural Sciences, Bangor University, Deiniol Road, Bangor, Gwynedd LL57 2DG, United Kingdom
| | - Randall R Jiménez
- Center for Conservation Genomics, Smithsonian’s National Zoological Park and Conservation Biology Institute, Washington, DC 20008, United States
- International Union for Conservation of Nature, C. 39, Los Yoses, San Jose, 146-2150, Costa Rica
| | - Allison Q Byrne
- Center for Conservation Genomics, Smithsonian’s National Zoological Park and Conservation Biology Institute, Washington, DC 20008, United States
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA 94720-3114, United States
| | - Brian Gratwicke
- Center for Species Survival, Smithsonian’s National Zoological Park and Conservation Biology Institute, Front Royal, VA 22630, United States
| | - Amy Ellison
- School of Environmental and Natural Sciences, Bangor University, Deiniol Road, Bangor, Gwynedd LL57 2DG, United Kingdom
| | - Carly R Muletz-Wolz
- Center for Conservation Genomics, Smithsonian’s National Zoological Park and Conservation Biology Institute, Washington, DC 20008, United States
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31
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Ramos Sarmiento K, Carr A, Diener C, Locey KJ, Gibbons SM. Island biogeography theory provides a plausible explanation for why larger vertebrates and taller humans have more diverse gut microbiomes. THE ISME JOURNAL 2024; 18:wrae114. [PMID: 38904949 PMCID: PMC11253425 DOI: 10.1093/ismejo/wrae114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 05/30/2024] [Accepted: 06/20/2024] [Indexed: 06/22/2024]
Abstract
Prior work has shown a positive scaling relationship between vertebrate body size, human height, and gut microbiome alpha diversity. This observation mirrors commonly observed species area relationships (SARs) in many other ecosystems. Here, we expand these observations to several large datasets, showing that this size-diversity scaling relationship is independent of relevant covariates, like diet, body mass index, age, sex, bowel movement frequency, antibiotic usage, and cardiometabolic health markers. Island biogeography theory (IBT), which predicts that larger islands tend to harbor greater species diversity through neutral demographic processes, provides a simple mechanism for positive SARs. Using a gut-adapted IBT model, we demonstrated that increasing the length of a flow-through ecosystem led to increased species diversity, closely matching our empirical observations. We delve into the possible clinical implications of these SARs in the American Gut cohort. Consistent with prior observations that lower alpha diversity is a risk factor for Clostridioides difficile infection (CDI), we found that individuals who reported a history of CDI were shorter than those who did not and that this relationship was mediated by alpha diversity. We observed that vegetable consumption had a much stronger association with CDI history, which was also partially mediated by alpha diversity. In summary, we find that the positive scaling observed between body size and gut alpha diversity can be plausibly explained by a gut-adapted IBT model, may be related to CDI risk, and vegetable intake appears to independently mitigate this risk, although additional work is needed to validate the potential disease risk implications.
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Affiliation(s)
| | - Alex Carr
- Institute for Systems Biology, Seattle, WA 98109, United States
- Molecular Engineering Graduate Program, University of Washington, Seattle, WA 98195, United States
| | - Christian Diener
- Institute for Systems Biology, Seattle, WA 98109, United States
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, 8010 Graz, Austria
| | - Kenneth J Locey
- Center for Quality, Safety & Value Analytics, Rush University Medical Center, Chicago, IL 60612, United States
| | - Sean M Gibbons
- Institute for Systems Biology, Seattle, WA 98109, United States
- Molecular Engineering Graduate Program, University of Washington, Seattle, WA 98195, United States
- Department of Bioengineering, University of Washington, Seattle, WA 98195, United States
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, United States
- Science Institute, University of Washington, Seattle, WA 98195, United States
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Jarquín-Díaz VH, Ferreira SCM, Balard A, Ďureje Ľ, Macholán M, Piálek J, Bengtsson-Palme J, Kramer-Schadt S, Forslund-Startceva SK, Heitlinger E. Aberrant microbiomes are associated with increased antibiotic resistance gene load in hybrid mice. ISME COMMUNICATIONS 2024; 4:ycae053. [PMID: 38800129 PMCID: PMC11128261 DOI: 10.1093/ismeco/ycae053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 03/11/2024] [Accepted: 04/08/2024] [Indexed: 05/29/2024]
Abstract
Antibiotic resistance is a priority public health problem resulting from eco-evolutionary dynamics within microbial communities and their interaction at a mammalian host interface or geographical scale. The links between mammalian host genetics, bacterial gut community, and antimicrobial resistance gene (ARG) content must be better understood in natural populations inhabiting heterogeneous environments. Hybridization, the interbreeding of genetically divergent populations, influences different components of the gut microbial communities. However, its impact on bacterial traits such as antibiotic resistance is unknown. Here, we present that hybridization might shape bacterial communities and ARG occurrence. We used amplicon sequencing to study the gut microbiome and to predict ARG composition in natural populations of house mice (Mus musculus). We compared gastrointestinal bacterial and ARG diversity, composition, and abundance across a gradient of pure and hybrid genotypes in the European House Mouse Hybrid Zone. We observed an increased overall predicted richness of ARG in hybrid mice. We found bacteria-ARG interactions by their co-abundance and detected phenotypes of extreme abundances in hybrid mice at the level of specific bacterial taxa and ARGs, mainly multidrug resistance genes. Our work suggests that mammalian host genetic variation impacts the gut microbiome and chromosomal ARGs. However, it raises further questions on how the mammalian host genetics impact ARGs via microbiome dynamics or environmental covariates.
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Affiliation(s)
- Víctor Hugo Jarquín-Díaz
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC). Robert-Rössle-Str. 10, 13125 Berlin, Germany
- Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Straße 17, 10315, Berlin, Germany
- Experimental and Clinical Research Center, a cooperation between the Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association and the Charité–Universitätsmedizin, Berlin, Germany
- Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Experimental and Clinical Research Center, Lindenberger Weg 80, 13125, Berlin, Germany
- Department of Molecular Parasitology, Institute for Biology, Humboldt University Berlin (HU). Philippstr. 13, Haus 14, 10115, Berlin, Germany
| | - Susana Carolina Martins Ferreira
- Department of Molecular Parasitology, Institute for Biology, Humboldt University Berlin (HU). Philippstr. 13, Haus 14, 10115, Berlin, Germany
- Division of Computational Systems Biology, Center for Microbiology and Ecological System Science, University of Vienna, Djerassipl. 1, 1030, Vienna, Austria
| | - Alice Balard
- Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Straße 17, 10315, Berlin, Germany
- Department of Molecular Parasitology, Institute for Biology, Humboldt University Berlin (HU). Philippstr. 13, Haus 14, 10115, Berlin, Germany
| | - Ľudovít Ďureje
- Research Facility Studenec, Institute of Vertebrate Biology, Czech Academy of Sciences, Květná 8, 60365, Brno, Czech Republic
| | - Milos Macholán
- Laboratory of Mammalian Evolutionary Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Veveri 97, 60200, Brno, Czech Republic
| | - Jaroslav Piálek
- Research Facility Studenec, Institute of Vertebrate Biology, Czech Academy of Sciences, Květná 8, 60365, Brno, Czech Republic
| | - Johan Bengtsson-Palme
- Division of Systems and Synthetic Biology, Department of Life Sciences, SciLifeLab, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
- Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, SE-413 46, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research (CARe) in Gothenburg, Sweden
| | - Stephanie Kramer-Schadt
- Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Straße 17, 10315, Berlin, Germany
- Institute of Ecology, Technische Universität Berlin, Rothenburgstr. 12, 12165, Berlin, Germany
| | - Sofia Kirke Forslund-Startceva
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC). Robert-Rössle-Str. 10, 13125 Berlin, Germany
- Experimental and Clinical Research Center, a cooperation between the Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association and the Charité–Universitätsmedizin, Berlin, Germany
- Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Experimental and Clinical Research Center, Lindenberger Weg 80, 13125, Berlin, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Berlin, Berlin, Germany
| | - Emanuel Heitlinger
- Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Straße 17, 10315, Berlin, Germany
- Department of Molecular Parasitology, Institute for Biology, Humboldt University Berlin (HU). Philippstr. 13, Haus 14, 10115, Berlin, Germany
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Mazel F, Pitteloud C, Guisan A, Pellissier L. Contrasted host specificity of gut and endosymbiont bacterial communities in alpine grasshoppers and crickets. ISME COMMUNICATIONS 2024; 4:ycad013. [PMID: 38374896 PMCID: PMC10875604 DOI: 10.1093/ismeco/ycad013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 12/18/2023] [Accepted: 12/19/2023] [Indexed: 02/21/2024]
Abstract
Bacteria colonize the body of macroorganisms to form associations ranging from parasitic to mutualistic. Endosymbiont and gut symbiont communities are distinct microbiomes whose compositions are influenced by host ecology and evolution. Although the composition of horizontally acquired symbiont communities can correlate to host species identity (i.e. harbor host specificity) and host phylogeny (i.e. harbor phylosymbiosis), we hypothesize that the microbiota structure of vertically inherited symbionts (e.g. endosymbionts like Wolbachia) is more strongly associated with the host species identity and phylogeny than horizontally acquired symbionts (e.g. most gut symbionts). Here, using 16S metabarcoding on 336 guts from 24 orthopteran species (grasshoppers and crickets) in the Alps, we observed that microbiota correlated to host species identity, i.e. hosts from the same species had more similar microbiota than hosts from different species. This effect was ~5 times stronger for endosymbionts than for putative gut symbionts. Although elevation correlated with microbiome composition, we did not detect phylosymbiosis for endosymbionts and putative gut symbionts: closely related host species did not harbor more similar microbiota than distantly related species. Our findings indicate that gut microbiota of studied orthopteran species is more correlated to host identity and habitat than to the host phylogeny. The higher host specificity in endosymbionts corroborates the idea that-everything else being equal-vertically transmitted microbes harbor stronger host specificity signal, but the absence of phylosymbiosis suggests that host specificity changes quickly on evolutionary time scales.
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Affiliation(s)
- Florent Mazel
- Department of Ecology and Evolution, University of Lausanne, Lausanne 1015, Switzerland
| | - Camille Pitteloud
- Département de la mobilité, du territoire et de l'environnement, Service des forêts, de la nature et du paysage, Sion 1950, Switzerland
- Ecosystems and Landscape Evolution, Department of Environmental Systems Science, ETH Zürich, Zürich 8092, Switzerland
- Swiss Federal Research Institute WSL, Birmensdorf 8903, Switzerland
| | - Antoine Guisan
- Department of Ecology and Evolution, University of Lausanne, Lausanne 1015, Switzerland
- Institute of Earth Surface Dynamics, University of Lausanne, Lausanne 1015, Switzerland
| | - Loïc Pellissier
- Ecosystems and Landscape Evolution, Department of Environmental Systems Science, ETH Zürich, Zürich 8092, Switzerland
- Swiss Federal Research Institute WSL, Birmensdorf 8903, Switzerland
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Härer A, Rennison DJ. The effects of host ecology and phylogeny on gut microbiota (non)parallelism across birds and mammals. mSphere 2023; 8:e0044223. [PMID: 38038446 PMCID: PMC10732045 DOI: 10.1128/msphere.00442-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 10/19/2023] [Indexed: 12/02/2023] Open
Abstract
IMPORTANCE What are the roles of determinism and contingency in evolution? The paleontologist and evolutionary biologist Stephen J. Gould raised this question in his famous thought experiment of "replaying life's tape." Settings where independent lineages have repeatedly adapted to similar ecological niches (i.e., parallel evolution) are well suited to address this question. Here, we quantified whether repeated ecological shifts across 53 mammalian and 50 avian host species are associated with parallel gut microbiota changes. Our results indicate that parallel shifts in host diet are associated with greater gut microbiota parallelism (i.e., more deterministic). While further research will be necessary to obtain a comprehensive picture of the circumstances under which deterministic gut microbiota changes might be expected, our study can be instrumental in motivating the use of more quantitative methods in microbiota research. This, in turn, can help us better understand microbiota dynamics during adaptive evolution of their hosts.
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Affiliation(s)
- Andreas Härer
- Department of Ecology, Behavior & Evolution, School of Biological Sciences , University of California San Diego, La Jolla, California, USA
| | - Diana J. Rennison
- Department of Ecology, Behavior & Evolution, School of Biological Sciences , University of California San Diego, La Jolla, California, USA
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35
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Tang X, Zhang L, Ren S, Zhao Y, Zhang Y. Temporal and geographic distribution of gut microbial enterotypes associated with host thermogenesis characteristics in plateau pikas. Microbiol Spectr 2023; 11:e0002023. [PMID: 37815332 PMCID: PMC10715161 DOI: 10.1128/spectrum.00020-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 08/28/2023] [Indexed: 10/11/2023] Open
Abstract
IMPORTANCE The gut microbiotas of small mammals play an important role in host energy homeostasis. However, it is still unknown whether small mammals with different enterotypes show differences in thermogenesis characteristics. Our study confirmed that plateau pikas with different bacterial enterotypes harbored distinct thermogenesis capabilities and employed various strategies against cold environments. Additionally, we also found that pikas with different fungal enterotypes may display differences in coprophagy.
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Affiliation(s)
- Xianjiang Tang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, China
- University of Chinese Academy of Sciences, College of Life Sciences, Beijing, China
| | - Liangzhi Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, China
| | - Shi'en Ren
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, China
- University of Chinese Academy of Sciences, College of Life Sciences, Beijing, China
| | - Yaqi Zhao
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, China
- University of Chinese Academy of Sciences, College of Life Sciences, Beijing, China
| | - Yanming Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, China
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36
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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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37
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Moeller AH, Sanders JG, Sprockett DD, Landers A. Assessing co-diversification in host-associated microbiomes. J Evol Biol 2023; 36:1659-1668. [PMID: 37750599 PMCID: PMC10843161 DOI: 10.1111/jeb.14221] [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: 01/31/2023] [Revised: 08/08/2023] [Accepted: 08/29/2023] [Indexed: 09/27/2023]
Abstract
When lineages of hosts and microbial symbionts engage in intimate interactions over evolutionary timescales, they can diversify in parallel (i.e., co-diversify), producing associations between the lineages' phylogenetic histories. Tests for co-diversification of individual microbial lineages and their hosts have been developed previously, and these have been applied to discover ancient symbioses in diverse branches of the tree of life. However, most host-microbe relationships are not binary but multipartite, in that a single host-associated microbiota can contain many microbial lineages, generating challenges for assessing co-diversification. Here, we review recent evidence for co-diversification in complex microbiota, highlight the limitations of prior studies, and outline a hypothesis testing approach designed to overcome some of these limitations. We advocate for the use of microbiota-wide scans for co-diversifying symbiont lineages and discuss tools developed for this purpose. Tests for co-diversification for simple host symbiont systems can be extended to entire phylogenies of microbial lineages (e.g., metagenome-assembled or isolate genomes, amplicon sequence variants) sampled from host clades, thereby providing a means for identifying co-diversifying symbionts present within complex microbiota. The relative ages of symbiont clades can corroborate co-diversification, and multi-level permutation tests can account for multiple comparisons and phylogenetic non-independence introduced by repeated sampling of host species. Discovering co-diversifying lineages will generate powerful opportunities for interrogating the molecular evolution and lineage turnover of ancestral, host-species specific symbionts within host-associated microbiota.
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Affiliation(s)
- Andrew H. Moeller
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14850, USA
| | - Jon G. Sanders
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14850, USA
| | - Daniel D. Sprockett
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14850, USA
| | - Abigail Landers
- Department of Microbiology, Cornell University, Ithaca, NY 14850, USA
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38
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Peng L, Hoban J, Joffe J, Smith AH, Carpenter M, Marcelis T, Patel V, Lynn-Bell N, Oliver KM, Russell JA. Cryptic community structure and metabolic interactions among the heritable facultative symbionts of the pea aphid. J Evol Biol 2023; 36:1712-1730. [PMID: 37702036 DOI: 10.1111/jeb.14216] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 06/07/2023] [Accepted: 07/18/2023] [Indexed: 09/14/2023]
Abstract
Most insects harbour influential, yet non-essential heritable microbes in their hemocoel. Communities of these symbionts exhibit low diversity. But their frequent multi-species nature raises intriguing questions on roles for symbiont-symbiont synergies in host adaptation, and on the stability of the symbiont communities, themselves. In this study, we build on knowledge of species-defined symbiont community structure across US populations of the pea aphid, Acyrthosiphon pisum. Through extensive symbiont genotyping, we show that pea aphids' microbiomes can be more precisely defined at the symbiont strain level, with strain variability shaping five out of nine previously reported co-infection trends. Field data provide a mixture of evidence for synergistic fitness effects and symbiont hitchhiking, revealing causes and consequences of these co-infection trends. To test whether within-host metabolic interactions predict common versus rare strain-defined communities, we leveraged the high relatedness of our dominant, community-defined symbiont strains vs. 12 pea aphid-derived Gammaproteobacteria with sequenced genomes. Genomic inference, using metabolic complementarity indices, revealed high potential for cooperation among one pair of symbionts-Serratia symbiotica and Rickettsiella viridis. Applying the expansion network algorithm, through additional use of pea aphid and obligate Buchnera symbiont genomes, Serratia and Rickettsiella emerged as the only symbiont community requiring both parties to expand holobiont metabolism. Through their joint expansion of the biotin biosynthesis pathway, these symbionts may span missing gaps, creating a multi-party mutualism within their nutrient-limited, phloem-feeding hosts. Recent, complementary gene inactivation, within the biotin pathways of Serratia and Rickettsiella, raises further questions on the origins of mutualisms and host-symbiont interdependencies.
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Affiliation(s)
- Linyao Peng
- Department of Biology, Drexel University, Philadelphia, Pennsylvania, USA
| | - Jessica Hoban
- Department of Biology, Drexel University, Philadelphia, Pennsylvania, USA
| | - Jonah Joffe
- Department of Biology, Drexel University, Philadelphia, Pennsylvania, USA
| | - Andrew H Smith
- Department of Biology, Drexel University, Philadelphia, Pennsylvania, USA
| | - Melissa Carpenter
- Department of Biodiversity, Earth, and Environmental Science, Drexel University, Philadelphia, Pennsylvania, USA
| | - Tracy Marcelis
- Department of Biology, Drexel University, Philadelphia, Pennsylvania, USA
| | - Vilas Patel
- Department of Entomology, University of Georgia, Athens, Georgia, USA
| | - Nicole Lynn-Bell
- Department of Entomology, University of Georgia, Athens, Georgia, USA
| | - Kerry M Oliver
- Department of Entomology, University of Georgia, Athens, Georgia, USA
| | - Jacob A Russell
- Department of Biology, Drexel University, Philadelphia, Pennsylvania, USA
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Lee W, Hayakawa T, Kiyono M, Yamabata N, Enari H, Enari HS, Fujita S, Kawazoe T, Asai T, Oi T, Kondo T, Uno T, Seki K, Shimada M, Tsuji Y, Langgeng A, MacIntosh A, Suzuki K, Yamada K, Onishi K, Ueno M, Kubo K, Hanya G. Diet-related factors strongly shaped the gut microbiota of Japanese macaques. Am J Primatol 2023; 85:e23555. [PMID: 37766673 DOI: 10.1002/ajp.23555] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 08/08/2023] [Accepted: 09/17/2023] [Indexed: 09/29/2023]
Abstract
Although knowledge of the functions of the gut microbiome has increased greatly over the past few decades, our understanding of the mechanisms governing its ecology and evolution remains obscure. While host genetic distance is a strong predictor of the gut microbiome in large-scale studies and captive settings, its influence has not always been evident at finer taxonomic scales, especially when considering among the recently diverged animals in natural settings. Comparing the gut microbiome of 19 populations of Japanese macaques Macaca fuscata across the Japanese archipelago, we assessed the relative roles of host genetic distance, geographic distance and dietary factors in influencing the macaque gut microbiome. Our results suggested that the macaques may maintain a core gut microbiome, while each population may have acquired some microbes from its specific habitat/diet. Diet-related factors such as season, forest, and reliance on anthropogenic foods played a stronger role in shaping the macaque gut microbiome. Among closely related mammalian hosts, host genetics may have limited effects on the gut microbiome since the hosts generally have smaller physiological differences. This study contributes to our understanding of the relative roles of host phylogeography and dietary factors in shaping the gut microbiome of closely related mammalian hosts.
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Affiliation(s)
- Wanyi Lee
- Center for Ecological Research, Kyoto University, Inuyama, Japan
- Japan Society for the Promotion of Science, Tokyo, Japan
- Primate Research Institute, Kyoto University, Inuyama, Japan
| | - Takashi Hayakawa
- Faculty of Environmental Earth Science, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Mieko Kiyono
- Graduate School of Human Development and Environment, Kobe University, Kobe, Hyogo, Japan
| | - Naoto Yamabata
- Institute of Natural and Environmental Sciences, University of Hyogo, Sanda, Hyogo, Japan
| | - Hiroto Enari
- Faculty of Agriculture, Yamagata University, Wakabamachi, Tsuruoka, Yamagata, Japan
| | - Haruka S Enari
- Faculty of Agriculture, Yamagata University, Wakabamachi, Tsuruoka, Yamagata, Japan
| | - Shiho Fujita
- Department of Behavioral Physiology and Ecology, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima, Japan
| | - Tatsuro Kawazoe
- Research Institute for Languages and Cultures of Asia and Africa, Tokyo University of Foreign Studies, Tokyo, Japan
| | - Takayuki Asai
- South Kyushu Wildlife Management Center, Kagoshima, Japan
| | - Toru Oi
- Faculty of Bioresources and Environmental Science, Ishikawa Prefectural University, Nonoichi, Ishikawa, Japan
| | | | - Takeharu Uno
- Tohoku Monkey and Mammal Management Center, Sendai, Miyagi, Japan
| | - Kentaro Seki
- Tohoku Monkey and Mammal Management Center, Sendai, Miyagi, Japan
| | - Masaki Shimada
- Department of Animal Sciences, Teikyo University of Science, Uenohara, Yamanashi, Japan
| | - Yamato Tsuji
- Department of Science and Engineering, Ishinomaki Senshu University, Ishinomaki, Miyagi, Japan
| | - Abdullah Langgeng
- Primate Research Institute, Kyoto University, Inuyama, Japan
- Wildlife Research Center, Kyoto University, Kanrin, Inuyama, Japan
| | - Andrew MacIntosh
- Primate Research Institute, Kyoto University, Inuyama, Japan
- Wildlife Research Center, Kyoto University, Kanrin, Inuyama, Japan
| | | | - Kazunori Yamada
- Graduate School of Human Sciences, Osaka University, Suita, Osaka, Japan
| | - Kenji Onishi
- Department of Early Childhood Education, Nara University of Education, Nara, Japan
| | - Masataka Ueno
- Faculty of Applied Sociology, Kindai University, Higashiosaka, Osaka, Japan
| | - Kentaro Kubo
- Cultural Asset Management Division, Board of Education, Oita-City, Japan
| | - Goro Hanya
- Center for Ecological Research, Kyoto University, Inuyama, Japan
- Primate Research Institute, Kyoto University, Inuyama, Japan
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40
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Brunetti AE, Lyra ML, Monteiro JPC, Zurano JP, Baldo D, Haddad CFB, Moeller AH. Convergence of gut microbiota in myrmecophagous amphibians. Proc Biol Sci 2023; 290:20232223. [PMID: 37964521 PMCID: PMC10646458 DOI: 10.1098/rspb.2023.2223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Accepted: 10/20/2023] [Indexed: 11/16/2023] Open
Abstract
The gut microbiome composition of terrestrial vertebrates is known to converge in response to common specialized dietary strategies, like leaf-eating (folivory) or ant- and termite-eating (myrmecophagy). To date, such convergence has been studied in mammals and birds, but has been neglected in amphibians. Here, we analysed 15 anuran species (frogs and toads) representing five Neotropical families and demonstrated the compositional convergence of the gut microbiomes of distantly related myrmecophagous species. Specifically, we found that the gut microbial communities of bufonids and microhylids, which have independently evolved myrmecophagy, were significantly more similar than expected based on their hosts' evolutionary divergence. Conversely, we found that gut microbiome composition was significantly associated with host evolutionary history in some cases. For instance, the microbiome composition of Xenohyla truncata, one of the few known amphibians that eat fruits, was not different from those of closely related tree frogs with an arthropod generalist diet. Bacterial taxa overrepresented in myrmecophagous species relative to other host families include Paludibacter, Treponema, and Rikenellaceae, suggesting diet-mediated selection and prey-to-predator transmission likely driving the observed compositional convergence. This study provides a basis for examining the roles of the gut microbiome in host tolerance and sequestration of toxic alkaloids from ants and termites.
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Affiliation(s)
- Andrés E. Brunetti
- Laboratorio de Genética Evolutiva, Instituto de Biología Subtropical (IBS, UNaM-CONICET), Posadas, Misiones 3300, Argentina
- Department of Insect Symbiosis, Max Planck Institute for Chemical Ecology, Jena 07745, Germany
| | - Mariana L. Lyra
- New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, United Arab Emirates
| | - Juliane P. C. Monteiro
- Departamento de Biodiversidade e Centro de Aquicultura da UNESP (CAUNESP), Instituto de Biociências, UNESP-Universidade Estadual Paulista, Rio Claro, SP 13506-900, Brazil
| | - Juan P. Zurano
- Instituto de Biología Subtropical (IBS, UNaM-CONICET), Puerto Iguazú, Misiones 3370, Argentina
| | - Diego Baldo
- Laboratorio de Genética Evolutiva, Instituto de Biología Subtropical (IBS, UNaM-CONICET), Posadas, Misiones 3300, Argentina
| | - Celio F. B. Haddad
- Departamento de Biodiversidade e Centro de Aquicultura da UNESP (CAUNESP), Instituto de Biociências, UNESP-Universidade Estadual Paulista, Rio Claro, SP 13506-900, Brazil
| | - Andrew H. Moeller
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14850, USA
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Switzer AD, Callahan BJ, Costello EK, Bik EM, Fontaine C, Gulland FM, Relman DA. Rookery through rehabilitation: Microbial community assembly in newborn harbour seals after maternal separation. Environ Microbiol 2023; 25:2182-2202. [PMID: 37329141 PMCID: PMC11180496 DOI: 10.1111/1462-2920.16444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 05/22/2023] [Indexed: 06/18/2023]
Abstract
Microbial community assembly remains largely unexplored in marine mammals, despite its potential importance for conservation and management. Here, neonatal microbiota assembly was studied in harbour seals (Phoca vitulina richardii) at a rehabilitation facility soon after maternal separation, through weaning, to the time of release back to their native environment. We found that the gingival and rectal communities of rehabilitated harbour seals were distinct from the microbiotas of formula and pool water, and became increasingly diverse and dissimilar over time, ultimately resembling the gingival and rectal communities of local wild harbour seals. Harbour seal microbiota assembly was compared to that of human infants, revealing the rapid emergence of host specificity and evidence of phylosymbiosis even though these harbour seals had been raised by humans. Early life prophylactic antibiotics were associated with changes in the composition of the harbour seal gingival and rectal communities and surprisingly, with transient increases in alpha diversity, perhaps because of microbiota sharing during close cohabitation with other harbour seals. Antibiotic-associated effects dissipated over time. These results suggest that while early life maternal contact may provide seeding for microbial assembly, co-housing of conspecifics during rehabilitation may help neonatal mammals achieve a healthy host-specific microbiota with features of resilience.
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Affiliation(s)
- Alexandra D. Switzer
- Department of Medicine, School of Medicine, Stanford University, Stanford, CA, United States
- Department of Microbiology and Immunology, School of Medicine, Stanford University, Stanford, CA, United States
| | - Benjamin J. Callahan
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, United States
- Department of Statistics, Stanford University, Stanford, CA, United States
| | - Elizabeth K. Costello
- Department of Medicine, School of Medicine, Stanford University, Stanford, CA, United States
| | | | | | - Frances M.D. Gulland
- The Marine Mammal Center, Sausalito, CA, United States
- Wildlife Health Center, School of Veterinary Medicine, University of California at Davis, Davis, CA, United States
| | - David A. Relman
- Department of Medicine, School of Medicine, Stanford University, Stanford, CA, United States
- Department of Microbiology and Immunology, School of Medicine, Stanford University, Stanford, CA, United States
- Infectious Diseases Section, VA Palo Alto Health Care System, Palo Alto, CA, United States
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Hoffbeck C, Middleton DMRL, Nelson NJ, Taylor MW. 16S rRNA gene-based meta-analysis of the reptile gut microbiota reveals environmental effects, host influences and a limited core microbiota. Mol Ecol 2023; 32:6044-6058. [PMID: 37795930 DOI: 10.1111/mec.17153] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 09/05/2023] [Accepted: 09/20/2023] [Indexed: 10/06/2023]
Abstract
An animal's gut microbiota plays an important role in host health, reproduction and digestion. However, many studies focus on only a few individuals or a single species, limiting our ability to recognize emergent patterns across a wider taxonomic grouping. Here, we compiled and reanalysed published 16S rRNA gene sequence data for 745 gut microbiota samples from 91 reptile species using a uniform bioinformatics pipeline to draw broader conclusions about the taxonomy of the reptile gut microbiota and the forces shaping it. Our meta-analysis revealed the significant differences in alpha- and beta-diversity across host order, environment, diet, habitat and conservation status, with host diet and order contributing the most to these differences. We identified the principal bacterial phyla present in the reptile gut microbiota as Bacteroidota, Proteobacteria (mostly Gamma class), and Firmicutes, and detected the bacterial genus Bacteroides in most reptile individuals, thus representing a putative 'core' microbiota. Our study provides novel insights into key drivers of the reptile gut microbiota, highlights existing knowledge gaps and lays the groundwork for future research on these fascinating hosts and their associated microbes.
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Affiliation(s)
- Carmen Hoffbeck
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | | | - Nicola J Nelson
- School of Biological Sciences, Victoria University of Wellington, New Zealand
| | - Michael W Taylor
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
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43
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Qin M, Jiang L, Qiao G, Chen J. Phylosymbiosis: The Eco-Evolutionary Pattern of Insect-Symbiont Interactions. Int J Mol Sci 2023; 24:15836. [PMID: 37958817 PMCID: PMC10650905 DOI: 10.3390/ijms242115836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 10/27/2023] [Accepted: 10/30/2023] [Indexed: 11/15/2023] Open
Abstract
Insects harbor diverse assemblages of bacterial and fungal symbionts, which play crucial roles in host life history. Insects and their various symbionts represent a good model for studying host-microbe interactions. Phylosymbiosis is used to describe an eco-evolutionary pattern, providing a new cross-system trend in the research of host-associated microbiota. The phylosymbiosis pattern is characterized by a significant positive correlation between the host phylogeny and microbial community dissimilarities. Although host-symbiont interactions have been demonstrated in many insect groups, our knowledge of the prevalence and mechanisms of phylosymbiosis in insects is still limited. Here, we provide an order-by-order summary of the phylosymbiosis patterns in insects, including Blattodea, Coleoptera, Diptera, Hemiptera, Hymenoptera, and Lepidoptera. Then, we highlight the potential contributions of stochastic effects, evolutionary processes, and ecological filtering in shaping phylosymbiotic microbiota. Phylosymbiosis in insects can arise from a combination of stochastic and deterministic mechanisms, such as the dispersal limitations of microbes, codiversification between symbionts and hosts, and the filtering of phylogenetically conserved host traits (incl., host immune system, diet, and physiological characteristics).
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Affiliation(s)
- Man Qin
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; (M.Q.); (L.J.)
| | - Liyun Jiang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; (M.Q.); (L.J.)
| | - Gexia Qiao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; (M.Q.); (L.J.)
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jing Chen
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; (M.Q.); (L.J.)
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Teullet S, Tilak MK, Magdeleine A, Schaub R, Weyer NM, Panaino W, Fuller A, Loughry WJ, Avenant NL, de Thoisy B, Borrel G, Delsuc F. Metagenomics uncovers dietary adaptations for chitin digestion in the gut microbiota of convergent myrmecophagous mammals. mSystems 2023; 8:e0038823. [PMID: 37650612 PMCID: PMC10654083 DOI: 10.1128/msystems.00388-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 06/19/2023] [Indexed: 09/01/2023] Open
Abstract
IMPORTANCE Myrmecophagous mammals are specialized in the consumption of ants and/or termites. They do not share a direct common ancestor and evolved convergently in five distinct placental orders raising questions about the underlying adaptive mechanisms involved and the relative contribution of natural selection and phylogenetic constraints. Understanding how these species digest their prey can help answer these questions. More specifically, the role of their gut microbial symbionts in the digestion of the insect chitinous exoskeleton has not been investigated in all myrmecophagous orders. We generated 29 new gut metagenomes from nine myrmecophagous species to reconstruct more than 300 bacterial genomes in which we identified chitin-degrading enzymes. Studying the distribution of these chitinolytic bacteria among hosts revealed both shared and specific bacteria between ant-eating species. Overall, our results highlight the potential role of gut symbionts in the convergent dietary adaptation of myrmecophagous mammals and the evolutionary mechanisms shaping their gut microbiota.
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Affiliation(s)
- Sophie Teullet
- Institut des Sciences de l’Evolution de Montpellier (ISEM), Univ Montpellier, CNRS, IRD, Montpellier, France
| | - Marie-Ka Tilak
- Institut des Sciences de l’Evolution de Montpellier (ISEM), Univ Montpellier, CNRS, IRD, Montpellier, France
| | - Amandine Magdeleine
- Institut des Sciences de l’Evolution de Montpellier (ISEM), Univ Montpellier, CNRS, IRD, Montpellier, France
| | - Roxane Schaub
- CIC AG/Inserm 1424, Centre Hospitalier de Cayenne Andrée Rosemon, Cayenne, French Guiana, France
- Tropical Biome and immunopathology, Université de Guyane, Labex CEBA, DFR Santé, Cayenne, French Guiana, France
| | - Nora M. Weyer
- Brain Function Research Group, School of Physiology, University of the Witwatersrand, Johannesburg, South Africa
| | - Wendy Panaino
- Brain Function Research Group, School of Physiology, University of the Witwatersrand, Johannesburg, South Africa
- Centre for African Ecology, School of Animals, Plant, and Environmental Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Andrea Fuller
- Brain Function Research Group, School of Physiology, University of the Witwatersrand, Johannesburg, South Africa
| | - W. J. Loughry
- Department of Biology, Valdosta State University, Valdosta, Georgia, USA
| | - Nico L. Avenant
- National Museum and Centre for Environmental Management, University of the Free State, Bloemfontein, South Africa
| | - Benoit de Thoisy
- Institut Pasteur de la Guyane, Cayenne, French Guiana, France
- Kwata NGO, Cayenne, French Guiana, France
| | - Guillaume Borrel
- Evolutionary Biology of the Microbial Cell, Institut Pasteur, Université Paris Cité, Paris, France
| | - Frédéric Delsuc
- Institut des Sciences de l’Evolution de Montpellier (ISEM), Univ Montpellier, CNRS, IRD, Montpellier, France
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Klinsawat W, Uthaipaisanwong P, Jenjaroenpun P, Sripiboon S, Wongsurawat T, Kusonmano K. Microbiome variations among age classes and diets of captive Asian elephants (Elephas maximus) in Thailand using full-length 16S rRNA nanopore sequencing. Sci Rep 2023; 13:17685. [PMID: 37848699 PMCID: PMC10582034 DOI: 10.1038/s41598-023-44981-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 10/14/2023] [Indexed: 10/19/2023] Open
Abstract
Asian elephant (Elephas maximus) is the national symbol of Thailand and linked to Thai history and culture for centuries. The elephant welfare improvement is one of the major components to achieve sustainable captive management. Microbiome inhabiting digestive tracts have been shown with symbiotic relations to host health. This work provided high-resolution microbiome profiles of 32 captive elephants at a species level by utilizing full-length 16S rRNA gene nanopore sequencing. Eleven common uncultured bacterial species were found across elephants fed with solid food including uncultured bacterium Rikenellaceae RC9 gut group, Kiritimatiellae WCHB1-41, Phascolarctobacterium, Oscillospiraceae NK4A214 group, Christensenellaceae R-7 group, Oribacterium, Oscillospirales UCG-010, Lachnospiraceae, Bacteroidales F082, uncultured rumen Rikenellaceae RC9 gut group, and Lachnospiraceae AC2044 group. We observed microbiome shifts along the age classes of baby (0-2 years), juvenile (2-10 years), and adult (> 10 years). Interestingly, we found distinct microbiome profiles among adult elephants fed with a local palm, Caryota urens, as a supplement. Potential beneficial microbes have been revealed according to the age classes and feed diets. The retrieved microbiome data could be provided as good baseline microbial profiles for monitoring elephant health, suggesting further studies towards dietary selection suitable for each age class and the use of local supplementary diets.
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Affiliation(s)
- Worata Klinsawat
- Conservation Ecology Program, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Pichahpuk Uthaipaisanwong
- Systems Biology and Bioinformatics Research Group, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Piroon Jenjaroenpun
- Division of Medical Bioinformatics, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Supaphen Sripiboon
- Department of Large Animal and Wildlife Clinical Science, Faculty of Veterinary Medicine, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom, Thailand
| | - Thidathip Wongsurawat
- Division of Medical Bioinformatics, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.
| | - Kanthida Kusonmano
- Systems Biology and Bioinformatics Research Group, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, Thailand.
- Bioinformatics and Systems Biology Program, Schools of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, Thailand.
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46
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Huang G, Shi W, Wang L, Qu Q, Zuo Z, Wang J, Zhao F, Wei F. PandaGUT provides new insights into bacterial diversity, function, and resistome landscapes with implications for conservation. MICROBIOME 2023; 11:221. [PMID: 37805557 PMCID: PMC10559513 DOI: 10.1186/s40168-023-01657-0] [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: 12/31/2022] [Accepted: 08/23/2023] [Indexed: 10/09/2023]
Abstract
BACKGROUND The gut microbiota play important roles in host adaptation and evolution, but are understudied in natural population of wild mammals. To address host adaptive evolution and improve conservation efforts of threatened mammals from a metagenomic perspective, we established a high-quality gut microbiome catalog of the giant panda (pandaGUT) to resolve the microbiome diversity, functional, and resistome landscapes using approximately 7 Tbp of long- and short-read sequencing data from 439 stool samples. RESULTS The pandaGUT catalog comprises 820 metagenome-assembled genomes, including 40 complete closed genomes, and 64.5% of which belong to species that have not been previously reported, greatly expanding the coverage of most prokaryotic lineages. The catalog contains 2.37 million unique genes, with 74.8% possessing complete open read frames, facilitating future mining of microbial functional potential. We identified three microbial enterotypes across wild and captive panda populations characterized by Clostridium, Pseudomonas, and Escherichia, respectively. We found that wild pandas exhibited host genetic-specific microbial structures and functions, suggesting host-gut microbiota phylosymbiosis, while the captive cohorts encoded more multi-drug resistance genes. CONCLUSIONS Our study provides largely untapped resources for biochemical and biotechnological applications as well as potential intervention avenues via the rational manipulation of microbial diversity and reducing antibiotic usage for future conservation management of wildlife. Video Abstract.
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Affiliation(s)
- Guangping Huang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wenyu Shi
- Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Le Wang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Qingyue Qu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhenqiang Zuo
- Laboratory for Computational Genomics, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jinfeng Wang
- Laboratory for Computational Genomics, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China
| | - Fangqing Zhao
- Laboratory for Computational Genomics, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Fuwen Wei
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- College of Forestry, Jiangxi Agricultural University, Nanchang, 330045, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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47
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Graciette AGC, Hoopes LA, Clauss T, Stewart FJ, Pratte ZA. The microbiome of African penguins (Spheniscus demersus) under managed care resembles that of wild marine mammals and birds. Sci Rep 2023; 13:16679. [PMID: 37794122 PMCID: PMC10551019 DOI: 10.1038/s41598-023-43899-w] [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: 02/07/2023] [Accepted: 09/29/2023] [Indexed: 10/06/2023] Open
Abstract
Animals under managed care in zoos and aquariums are ideal surrogate study subjects for endangered species that are difficult to obtain in the wild. We compared the fecal and oral microbiomes of healthy, managed African penguins (Spheniscus demersus) to those of other domestic and wild vertebrate hosts to determine how host identity, diet, and environment shape the penguin microbiome. The African penguin oral microbiome was more similar to that of piscivorous marine mammals, suggesting that diet and a marine environment together play a strong role in shaping the oral microbiome. Conversely, the penguin cloaca/fecal microbiome was more similar to that of other birds, suggesting that host phylogeny plays a significant role in shaping the gut microbiome. Although the penguins were born under managed care, they had a gut microbiome more similar to that of wild bird species compared to domesticated (factory-farmed) birds, suggesting that the managed care environment and diet resemble those experienced by wild birds. Finally, the microbiome composition at external body sites was broadly similar to that of the habitat, suggesting sharing of microbes between animals and their environment. Future studies should link these results to microbial functional capacity and host health, which will help inform conservation efforts.
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Affiliation(s)
- Ana G Clavere Graciette
- School of Biological Sciences, Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, USA
| | | | | | - Frank J Stewart
- School of Biological Sciences, Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, USA
- Department of Microbiology & Cell Biology, Montana State University, Bozeman, MT, USA
| | - Zoe A Pratte
- School of Biological Sciences, Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, USA.
- Department of Microbiology & Cell Biology, Montana State University, Bozeman, MT, USA.
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48
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Pisaniello A, Handley KM, White WL, Angert ER, Boey JS, Clements KD. Host individual and gut location are more important in gut microbiota community composition than temporal variation in the marine herbivorous fish Kyphosus sydneyanus. BMC Microbiol 2023; 23:275. [PMID: 37773099 PMCID: PMC10540440 DOI: 10.1186/s12866-023-03025-2] [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: 03/23/2023] [Accepted: 09/19/2023] [Indexed: 09/30/2023] Open
Abstract
BACKGROUND Gut microbiota play a key role in the nutrition of many marine herbivorous fishes through hindgut fermentation of seaweed. Gut microbiota composition in the herbivorous fish Kyphosus sydneyanus (family Kyphosidae) varies between individuals and gut sections, raising two questions: (i) is community composition stable over time, especially given seasonal shifts in storage metabolites of dietary brown algae, and (ii) what processes influence community assembly in the hindgut? RESULTS We examined variation in community composition in gut lumen and mucosa samples from three hindgut sections of K. sydneyanus collected at various time points in 2020 and 2021 from reefs near Great Barrier Island, New Zealand. 16S rRNA gene analysis was used to characterize microbial community composition, diversity and estimated density. Differences in community composition between gut sections remained relatively stable over time, with little evidence of temporal variation. Clostridia dominated the proximal hindgut sections and Bacteroidia the most distal section. Differences were detected in microbial composition between lumen and mucosa, especially at genus level. CONCLUSIONS High variation in community composition and estimated bacterial density among individual fish combined with low variation in community composition temporally suggests that initial community assembly involved environmental selection and random sampling/neutral effects. Community stability following colonisation could also be influenced by historical contingency, where early colonizing members of the community may have a selective advantage. The impact of temporal changes in the algae may be limited by the dynamics of substrate depletion along the gut following feeding, i.e. the depletion of storage metabolites in the proximal hindgut. Estimated bacterial density, showed that Bacteroidota has the highest density (copies/mL) in distal-most lumen section V, where SCFA concentrations are highest. Bacteroidota genera Alistipes and Rikenella may play important roles in the breakdown of seaweed into useful compounds for the fish host.
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Affiliation(s)
- Alessandro Pisaniello
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand.
| | - Kim M Handley
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
| | - W Lindsey White
- School of Science, Auckland University of Technology, Private Bag 92006, Auckland, New Zealand
| | - Esther R Angert
- Department of Microbiology, Cornell University, 123 Wing Drive, Ithaca, NY, 14853, USA
| | - Jian Sheng Boey
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
| | - Kendall D Clements
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand.
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49
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Hyde J, Brackney DE, Steven B. Three species of axenic mosquito larvae recruit a shared core of bacteria in a common garden experiment. Appl Environ Microbiol 2023; 89:e0077823. [PMID: 37681948 PMCID: PMC10537770 DOI: 10.1128/aem.00778-23] [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: 05/08/2023] [Accepted: 07/05/2023] [Indexed: 09/09/2023] Open
Abstract
In this study, we describe the generation of two new species of axenic mosquito, Aedes albopictus and Aedes triseriatus. Along with Aedes aegypti, axenic larvae of these three species were exposed to an environmental water source to document the assembly of the microbiome in a common garden experiment. Additionally, the larvae were reared either individually or combinatorially with the other species to characterize the effects of co-rearing on the composition of the microbiome. We found that the microbiome of the larvae was composed of a relatively low-diversity collection of bacteria from the colonizing water. The abundance of bacteria in the water was a poor predictor of their abundance in the larvae, suggesting the larval microbiome is made up of a subset of relatively rare aquatic bacteria. We found 11 bacterial 16S rRNA gene amplicon sequence variants (ASVs) that were conserved among ≥90% of the mosquitoes sampled, including 2 found in 100% of the larvae, pointing to a conserved core of bacteria capable of colonizing all three species of mosquito. Yet, the abundance of these ASVs varied widely between larvae, suggesting individuals harbored largely unique microbiome structures, even if they overlapped in membership. Finally, larvae reared in a tripartite mix of the host-species consistently showed a convergence in the structure of their microbiome, indicating that multi-species interactions between hosts potentially lead to shifts in the composition of their respective microbiomes. IMPORTANCE This study is the first report of the axenic (free of external microbes) rearing of two species of mosquito, Aedes albopictus and Aedes triseriatus. Our previous report of axenic Aedes aegypti brings the number of axenic species to three. We designed a method to perform a common garden experiment to characterize the bacteria the three species of axenic larvae assemble from their surroundings. Furthermore, species could be reared in isolation or in multi-species combinations to assess how host-species interactions influence the composition of the microbiome. We found all three species recruited a common core of bacteria from their rearing water, with a large contingent of rare and sporadically detected bacteria. Finally, we also show that co-rearing of mosquito larvae leads to a coalescence in the composition of their microbiome, indicating that host-species interactions potentially influence the composition of the microbiome.
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Affiliation(s)
- Josephine Hyde
- Department of Environmental Science and Forestry, Connecticut Agricultural Experiment Station, New Haven, Connecticut, USA
| | - Doug E. Brackney
- Department of Entomology, Center for Vector Biology and Zoonotic Diseases, Connecticut Agricultural Experiment Station, New Haven, Connecticut, USA
| | - Blaire Steven
- Department of Environmental Science and Forestry, Connecticut Agricultural Experiment Station, New Haven, Connecticut, USA
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50
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Malukiewicz J, D'arc M, Dias CA, Cartwright RA, Grativol AD, Moreira SB, Souza AR, Tavares MCH, Pissinatti A, Ruiz-Miranda CR, Santos AFA. Bifidobacteria define gut microbiome profiles of golden lion tamarin (Leontopithecus rosalia) and marmoset (Callithrix sp.) metagenomic shotgun pools. Sci Rep 2023; 13:15679. [PMID: 37735195 PMCID: PMC10514281 DOI: 10.1038/s41598-023-42059-4] [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: 08/01/2022] [Accepted: 09/05/2023] [Indexed: 09/23/2023] Open
Abstract
Gut microbiome disruptions may lead to adverse effects on wildlife fitness and viability, thus maintaining host microbiota biodiversity needs to become an integral part of wildlife conservation. The highly-endangered callitrichid golden lion tamarin (GLT-Leontopithecus rosalia) is a rare conservation success, but allochthonous callitrichid marmosets (Callithrix) serve as principle ecological GLT threats. However, incorporation of microbiome approaches to GLT conservation is impeded by limited gut microbiome studies of Brazilian primates. Here, we carried out analysis of gut metagenomic pools from 114 individuals of wild and captive GLTs and marmosets. More specifically, we analyzed the bacterial component of ultra filtered samples originally collected as part of a virome profiling study. The major findings of this study are consistent with previous studies in showing that Bifidobacterium, a bacterial species important for the metabolism of tree gums consumed by callitrichids, is an important component of the callitrichid gut microbiome - although GTLs and marmosets were enriched for different species of Bifidobacterium. Additionally, the composition of GLT and marmoset gut microbiota is sensitive to host environmental factors. Overall, our data expand baseline gut microbiome data for callitrichids to allow for the development of new tools to improve their management and conservation.
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Affiliation(s)
- Joanna Malukiewicz
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen, 37077, Germany.
- Instituto de Medicina Tropical de São Paulo, Universidade de São Paulo, São Paulo, SP, 05403-000, Brazil.
| | - Mirela D'arc
- Laboratório de Diversidade e Doenças Virais, Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Cecilia A Dias
- Centro de Primatologia, Universidade de Brasília, Brasília, Brazil
| | - Reed A Cartwright
- School of Life Sciences and the Biodesign Institute, Arizona State University, Tempe, AZ, 85281, USA
| | | | - Silvia Bahadian Moreira
- Centro de Primatologia do Rio de Janeiro, Instituto Estadual do Ambiente, Rio de Janeiro, Brazil
| | | | | | - Alcides Pissinatti
- Centro de Primatologia do Rio de Janeiro, Instituto Estadual do Ambiente, Rio de Janeiro, Brazil
| | - Carlos R Ruiz-Miranda
- Laboratorio das Ciencias Ambientais, Centro de Biociencias e Biotecnologia, Universidade Estadual do Norte Fluminense, Campos dos Goytacazes, RJ, 28013-602, Brazil
| | - André F A Santos
- Laboratório de Diversidade e Doenças Virais, Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
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