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Baiz MD, Wood AW, Toews DPL. Association between the gut microbiome and carotenoid plumage phenotype in an avian hybrid zone. Proc Biol Sci 2024; 291:20240238. [PMID: 38628125 PMCID: PMC11022011 DOI: 10.1098/rspb.2024.0238] [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: 02/13/2024] [Accepted: 03/18/2024] [Indexed: 04/19/2024] Open
Abstract
Vertebrates host complex microbiomes that impact their physiology. In many taxa, including colourful wood-warblers, gut microbiome similarity decreases with evolutionary distance. This may suggest that as host populations diverge, so do their microbiomes, because of either tight coevolutionary dynamics, or differential environmental influences, or both. Hybridization is common in wood-warblers, but the effects of evolutionary divergence on the microbiome during secondary contact are unclear. Here, we analyse gut microbiomes in two geographically disjunct hybrid zones between blue-winged warblers (Vermivora cyanoptera) and golden-winged warblers (Vermivora chrysoptera). We performed 16S faecal metabarcoding to identify species-specific bacteria and test the hypothesis that host admixture is associated with gut microbiome disruption. Species identity explained a small amount of variation between microbiomes in only one hybrid zone. Co-occurrence of species-specific bacteria was rare for admixed individuals, yet microbiome richness was similar among admixed and parental individuals. Unexpectedly, we found several bacteria that were more abundant among admixed individuals with a broader deposition of carotenoid-based plumage pigments. These bacteria are predicted to encode carotenoid biosynthesis genes, suggesting birds may take advantage of pigments produced by their gut microbiomes. Thus, host admixture may facilitate beneficial symbiotic interactions which contribute to plumage ornaments that function in sexual selection.
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Affiliation(s)
- Marcella D. Baiz
- Department of Biological Sciences, University at Buffalo, Buffalo, NY 14260, USA
| | - Andrew W. Wood
- Department of Biology, Pennylvania State University, University Park, PA 16802, USA
| | - David P. L. Toews
- Department of Biology, Pennylvania State University, University Park, PA 16802, USA
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Wu Y, Zhou T, Yang S, Yin B, Wu R, Wei W. Distinct Gut Microbial Enterotypes and Functional Dynamics in Wild Striped Field Mice ( Apodemus agrarius) across Diverse Populations. Microorganisms 2024; 12:671. [PMID: 38674615 PMCID: PMC11052172 DOI: 10.3390/microorganisms12040671] [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: 03/08/2024] [Revised: 03/22/2024] [Accepted: 03/25/2024] [Indexed: 04/28/2024] Open
Abstract
Rodents, including the striped field mouse (Apodemus agrarius), play vital roles in ecosystem functioning, with their gut microbiota contributing significantly to various ecological processes. Here, we investigated the structure and function of 94 wild A. agrarius individuals from 7 geographic populations (45°57' N, 126°48' E; 45°87' N, 126°37' E; 45°50' N, 125°31' E; 45°59' N, 124°37' E; 46°01' N, 124°88' E; 46°01' N, 124°88' E; 46°01' N, 124°88' E), revealing two distinct enterotypes (Type1 and Type2) for the first time. Each enterotype showed unique microbial diversity, functions, and assembly processes. Firmicutes and Bacteroidetes dominated, with a significant presence of Lactobacillus and Muribaculaceae. Functional analysis highlighted metabolic differences, with Type1 emphasizing nutrient processing and Type2 showing higher energy production capacity. The analysis of the neutral model and the null model revealed a mix of stochastic (drift and homogenizing dispersal) and deterministic processes (homogenous selection) that shape the assembly of the microbiota, with subtle differences in the assembly processes between the two enterotypes. Correlation analysis showed that elevation and BMI were associated with the phylogenetic turnover of microbial communities, suggesting that variations in these factors may influence the composition and diversity of the gut microbiota in A. agrarius. Our study sheds light on gut microbial dynamics in wild A. agrarius populations, highlighting the importance of considering ecological and physiological factors in understanding host-microbiota interactions.
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Affiliation(s)
| | | | | | | | | | - Wanhong Wei
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China; (Y.W.); (T.Z.); (S.Y.); (B.Y.); (R.W.)
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Wu Y, Zhou T, Gu C, Yin B, Yang S, Zhang Y, Wu R, Wei W. Geographical distribution and species variation of gut microbiota in small rodents from the agro-pastoral transition ecotone in northern China. Ecol Evol 2024; 14:e11084. [PMID: 38469048 PMCID: PMC10926059 DOI: 10.1002/ece3.11084] [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: 10/21/2023] [Revised: 02/03/2024] [Accepted: 02/12/2024] [Indexed: 03/13/2024] Open
Abstract
The gut microbiota of rodents is essential for survival and adaptation and is susceptible to various factors, ranging from environmental conditions to genetic predispositions. Nevertheless, few comparative studies have considered the contribution of species identity and geographic spatial distance to variations in the gut microbiota. In this study, a random sampling survey encompassing four rodent species (Apodemus agrarius, Cricetulus barabensis, Tscherskia triton and Rattus norvegicus) was conducted at five sites in northern China's farming-pastoral ecotone. Through a cross-factorial comparison, we aimed to discern whether belonging to the same species or sharing the same capture site predominantly influences the composition of gut microbiota. Notably, the observed variations in microbiome composition among these four rodent species match the host phylogeny at the family level but not at the species level. The gut microbiota of these four rodent species exhibited typical mammalian characteristics, predominantly characterized by the Firmicutes and Bacteroidetes phyla. As the geographic distance between populations increased, the number of shared microbial taxa among conspecific populations decreased. We observed that within a relatively small geographical range, even different species exhibited convergent α-diversity due to their inhabitation within the same environmental microbial pool. In contrast, the composition and structure of the intestinal microbiota in the allopatric populations of A. agrarius demonstrated marked differences, similar to those of C. barabensis. Additionally, geographical environmental elements exhibited significant correlations with diversity indices. Conversely, host-related factors had minimal influence on microbial abundance. Our findings indicated that the similarity of the microbial compositions was not determined primarily by the host species, and the location of the sampling explained a greater amount of variation in the microbial composition, indicating that the local environment played a crucial role in shaping the microbial composition.
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Affiliation(s)
- Yongzhen Wu
- College of Bioscience and BiotechnologyYangzhou UniversityYangzhouJiangsuChina
| | - Taoxiu Zhou
- College of Bioscience and BiotechnologyYangzhou UniversityYangzhouJiangsuChina
| | - Chen Gu
- College of Bioscience and BiotechnologyYangzhou UniversityYangzhouJiangsuChina
| | - Baofa Yin
- College of Bioscience and BiotechnologyYangzhou UniversityYangzhouJiangsuChina
| | - Shengmei Yang
- College of Bioscience and BiotechnologyYangzhou UniversityYangzhouJiangsuChina
| | - Yunzeng Zhang
- College of Bioscience and BiotechnologyYangzhou UniversityYangzhouJiangsuChina
| | - Ruiyong Wu
- College of Bioscience and BiotechnologyYangzhou UniversityYangzhouJiangsuChina
| | - Wanhong Wei
- College of Bioscience and BiotechnologyYangzhou UniversityYangzhouJiangsuChina
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Nielsen DP, Harrison JG, Byer NW, Faske TM, Parchman TL, Simison WB, Matocq MD. The gut microbiome reflects ancestry despite dietary shifts across a hybrid zone. Ecol Lett 2023; 26:63-75. [PMID: 36331164 DOI: 10.1111/ele.14135] [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: 05/24/2022] [Revised: 09/06/2022] [Accepted: 10/03/2022] [Indexed: 11/06/2022]
Abstract
The microbiome is critical to an organism's phenotype, and its composition is shaped by, and a driver of, eco-evolutionary interactions. We investigated how host ancestry, habitat and diet shape gut microbial composition in a mammalian hybrid zone between Neotoma lepida and N. bryanti that occurs across an ecotone between distinct vegetation communities. We found that habitat is the primary determinant of diet, while host genotype is the primary determinant of the gut microbiome-a finding further supported by intermediate microbiome composition in first-generation hybrids. Despite these distinct primary drivers, microbial richness was correlated with diet richness, and individuals that maintained higher dietary richness had greater gut microbial community stability. Both relationships were stronger in the relative dietary generalist of the two parental species. Our findings show that host ancestry interacts with dietary habits to shape the microbiome, ultimately resulting in the phenotypic plasticity that host-microbial interactions allow.
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Affiliation(s)
- Danny P Nielsen
- Department of Natural Resources and Environmental Science, University of Nevada, Reno, Nevada, USA.,Program in Ecology, Evolution and Conservation Biology, Reno, Nevada, USA
| | | | - Nathan W Byer
- Department of Natural Resources and Environmental Science, University of Nevada, Reno, Nevada, USA
| | - Trevor M Faske
- Program in Ecology, Evolution and Conservation Biology, Reno, Nevada, USA.,Department of Biology, University of Nevada, Reno, Nevada, USA
| | - Thomas L Parchman
- Program in Ecology, Evolution and Conservation Biology, Reno, Nevada, USA.,Department of Biology, University of Nevada, Reno, Nevada, USA
| | - W Brian Simison
- Center for Comparative Genomics, California Academy of Sciences, San Francisco, California, USA
| | - Marjorie D Matocq
- Department of Natural Resources and Environmental Science, University of Nevada, Reno, Nevada, USA.,Program in Ecology, Evolution and Conservation Biology, Reno, Nevada, USA
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Liu P, Yang S, Yang S. KTU: K‐mer Taxonomic Units improve the biological relevance of amplicon sequence variant microbiota data. Methods Ecol Evol 2021. [DOI: 10.1111/2041-210x.13758] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Po‐Yu Liu
- Department of Internal Medicine National Taiwan University College of Medicine Taipei Taiwan
- Department of Pathobiology and Population Sciences Royal Veterinary CollegeUniversity of London Hatfield UK
| | - Shan‐Hua Yang
- Institute of Fisheries Science National Taiwan University Taipei Taiwan
| | - Sung‐Yin Yang
- Shimoda Marine Research Center University of Tsukuba Shimoda Japan
- National Museum of Marine Biology and Aquarium Pingtung Taiwan
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