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An XL, Xu MR, Pan XF, Cai GJ, Zhao CX, Li H, Ye ZL, Zhu YG, Su JQ. Local environment, surface characteristics and stochastic processes shape the dynamics of urban dustbin surface microbiome. ENVIRONMENT INTERNATIONAL 2023; 177:108004. [PMID: 37295164 DOI: 10.1016/j.envint.2023.108004] [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: 02/22/2023] [Revised: 05/24/2023] [Accepted: 05/29/2023] [Indexed: 06/12/2023]
Abstract
Dustbins function as critical infrastructures for urban sanitation, creating a distinct breeding ground for microbial assemblages. However, there is no information regarding the dynamics of microbial communities and the underlying mechanism for community assembly on dustbin surfaces. Here, surface samples were collected from three sampling zones (business building, commercial street and residential community) with different types (kitchen waste, harmful waste, recyclables, and others) and materials (metallic and plastic); and distribution pattern and assembly of microbial communities were investigated by high-throughput sequencing. Bacterial and fungal communities showed the distinct community variations across sampling zones and waste sorting. Core community and biomarker species were significantly correlated with the spatial distribution of overall community. The detection of pathogens highlighted the potential risk of surface microbiome. Human skin, human feces and soil biomes were the potential source environments of the surface microbiomes. Neutral model prediction suggested that microbial community assembly was significantly driven by stochastic processes. Co-association patterns varied with sampling zones and waste types, and neutral amplicon sequence variants (ASVs) that fall within the 95 % confidence intervals of neutral model were largely involved in the stability of microbial networks. These findings improve our understanding of the distribution pattern and the underlying assembly of microbial community on the dustbin surface, thus enabling prospective prediction and assessment of urban microbiomes and their impacts on human health.
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Affiliation(s)
- Xin-Li An
- Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Mei-Rong Xu
- Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; College of Resource and Environmental Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xiao-Fang Pan
- Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Guan-Jing Cai
- College of Science, Shantou University, Shantou, 515063, China
| | - Cai-Xia Zhao
- Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Hu Li
- Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Zhi-Long Ye
- Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Yong-Guan Zhu
- Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; State Key Lab of Urban and Regional Ecology, Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Jian-Qiang Su
- Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.
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Cloacal microbiota are biogeographically structured in larks from desert, tropical and temperate areas. BMC Microbiol 2023; 23:40. [PMID: 36765278 PMCID: PMC9921332 DOI: 10.1186/s12866-023-02768-2] [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: 03/07/2022] [Accepted: 01/11/2023] [Indexed: 02/12/2023] Open
Abstract
BACKGROUND In contrast with macroorganisms, that show well-documented biogeographical patterns in distribution associated with local adaptation of physiology, behavior and life history, strong biogeographical patterns have not been found for microorganisms, raising questions about what determines their biogeography. Thus far, large-scale biogeographical studies have focused on free-living microbes, paying little attention to host-associated microbes, which play essential roles in physiology, behavior and life history of their hosts. Investigating cloacal gut microbiota of closely-related, ecologically similar free-living songbird species (Alaudidae, larks) inhabiting desert, temperate and tropical regions, we explored influences of geographical location and host species on α-diversity, co-occurrence of amplicon sequence variants (ASVs) and genera, differentially abundant and dominant bacterial taxa, and community composition. We also investigated how geographical distance explained differences in gut microbial community composition among larks. RESULTS Geographic location did not explain variation in richness and Shannon diversity of cloacal microbiota in larks. Out of 3798 ASVs and 799 bacterial genera identified, 17 ASVs (< 0.5%) and 43 genera (5%) were shared by larks from all locations. Desert larks held fewer unique ASVs (25%) than temperate zone (31%) and tropical larks (34%). Five out of 33 detected bacterial phyla dominated lark cloacal gut microbiomes. In tropical larks three bacterial classes were overrepresented. Highlighting the distinctiveness of desert lark microbiota, the relative abundances of 52 ASVs differed among locations, which classified within three dominant and 11 low-abundance phyla. Clear and significant phylogenetic clustering in cloacal microbiota community composition (unweighted UniFrac) showed segregation with geography and host species, where microbiota of desert larks were distinct from those of tropical and temperate regions. Geographic distance was nonlinearly associated with pairwise unweighted UniFrac distances. CONCLUSIONS We conclude that host-associated microbiota are geographically structured in a group of widespread but closely-related bird species, following large-scale macro-ecological patterns and contrasting with previous findings for free-living microbes. Future work should further explore if and to what extent geographic variation in host-associated microbiota can be explained as result of co-evolution between gut microbes and host adaptive traits, and if and how acquisition from the environmental pool of bacteria contributes to explaining host-associated communities.
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Baldo L, Tavecchia G, Rotger A, Igual JM, Riera JL. Insular holobionts: persistence and seasonal plasticity of the Balearic wall lizard ( Podarcis lilfordi) gut microbiota. PeerJ 2023; 11:e14511. [PMID: 36620745 PMCID: PMC9817956 DOI: 10.7717/peerj.14511] [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: 09/16/2022] [Accepted: 11/14/2022] [Indexed: 01/04/2023] Open
Abstract
Background Integrative studies of animals and associated microbial assemblages (i.e., the holobiont) are rapidly changing our perspectives on organismal ecology and evolution. Insular vertebrates provide ideal natural systems to understand patterns of host-gut microbiota coevolution, the resilience and plasticity these microbial communities over temporal and spatial scales, and ultimately their role in the host ecological adaptation. Methods Here we used the endemic Balearic wall lizard Podarcis lilfordi to dissect the drivers of the microbial diversity within and across host allopatric populations/islets. By focusing on three extensively studied populations/islets of Mallorca (Spain) and fecal sampling from individually identified lizards along two years (both in spring and autumn), we sorted out the effect of islet, sex, life stage, year and season on the microbiota composition. We further related microbiota diversity to host genetics, trophic ecology and expected annual metabolic changes. Results All the three populations showed a remarkable conservation of the major microbial taxonomic profile, while carrying their unique microbial signature at finer level of taxonomic resolution (Amplicon Sequence Variants (ASVs)). Microbiota distances across populations were compatible with both host genetics (based on microsatellites) and trophic niche distances (based on stable isotopes and fecal content). Within populations, a large proportion of ASVs (30-50%) were recurrently found along the four sampling dates. The microbial diversity was strongly marked by seasonality, with no sex effect and a marginal life stage and annual effect. The microbiota showed seasonal fluctuations along the two sampled years, primarily due to changes in the relative abundances of fermentative bacteria (mostly families Lachnospiraceae and Ruminococcaceae), without any major compositional turnover. Conclusions These results support a large resilience of the major compositional aspects of the P. lilfordi gut microbiota over the short-term evolutionary divergence of their host allopatric populations (<10,000 years), but also indicate an undergoing process of parallel diversification of the both host and associated gut microbes. Predictable seasonal dynamics in microbiota diversity suggests a role of microbiota plasticity in the lizards' metabolic adaptation to their resource-constrained insular environments. Overall, our study supports the need for longitudinal and integrative studies of host and associated microbes in natural systems.
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Affiliation(s)
- Laura Baldo
- Department of Evolutionary Biology, Ecology and Environmental Sciences, University of Barcelona, Barcelona, Spain,Institute for Research on Biodiversity (IRBio), Barcelona, Spain
| | - Giacomo Tavecchia
- Animal Demography and Ecology Unit, IMEDEA, Consejo Superior de Investigaciones Científicas, Esporles, Spain
| | - Andreu Rotger
- Animal Demography and Ecology Unit, IMEDEA, Consejo Superior de Investigaciones Científicas, Esporles, Spain
| | - José Manuel Igual
- Animal Demography and Ecology Unit, IMEDEA, Consejo Superior de Investigaciones Científicas, Esporles, Spain
| | - Joan Lluís Riera
- Department of Evolutionary Biology, Ecology and Environmental Sciences, University of Barcelona, Barcelona, Spain
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Vasco K, Guevara N, Mosquera J, Zapata S, Zhang L. Characterization of the gut microbiome and resistome of Galapagos marine iguanas (Amblyrhynchus cristatus) from uninhabited islands. Anim Microbiome 2022; 4:65. [PMID: 36517909 PMCID: PMC9749353 DOI: 10.1186/s42523-022-00218-4] [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: 05/19/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Understanding the natural microbiome and resistome of wildlife from remote places is necessary to monitor the human footprint on the environment including antimicrobial use (AU). Marine iguanas are endemic species from the Galapagos Islands where they are highly affected by anthropogenic factors that can alter their microbiota as well as their abundance and diversity of antimicrobial-resistant genes (ARGs). Thus, this study aims to apply culture-independent approaches to characterize the marine iguana's gut metagenomic composition of samples collected from the uninhabited islands Rabida (n = 8) and Fernandina (Cabo Douglas, n = 30; Punta Espinoza, n = 30). Fresh feces from marine iguanas were analyzed through SmartChip RT-PCR, 16S rRNA, and metagenomic next-generation sequencing (mNGS) to identify their microbiome, microbial-metabolic pathways, resistome, mobilome, and virulome. RESULTS The marine iguana's gut microbiome composition was highly conserved despite differences in ecological niches, where 86% of taxa were shared in the three locations. However, site-specific differences were mainly identified in resistome, mobilome, virulorome, and metabolic pathway composition, highlighting the existence of factors that induce microbial adaptations in each location. Functional gut microbiome analyses revealed its role in the biosynthesis and degradation of vitamins, cofactors, proteinogenic amino acids, carbohydrates, nucleosides and nucleotides, fatty acids, lipids, and other compounds necessary for the marine iguanas. The overall bacterial ARG abundance was relatively low (0.006%); nevertheless, the presence of genes encoding resistance to 22 drug classes was identified in the iguana's gut metagenome. ARG-carrying contig and co-occurrence network analyses revealed that commensal bacteria are the main hosts of ARGs. Taxa of public health interest such as Salmonella, Vibrio, and Klebsiella also carried multidrug-resistance genes associated with MGEs which can influence the dissemination of ARGs through horizontal gene transfer. CONCLUSION Marine iguanas depend on the gut microbiome for the biosynthesis and degradation of several compounds through a symbiotic relationship. Niche-specific adaptations were evidenced in the pool of microbial accessory genes (i.e., ARGs, MGEs, and virulence) and metabolic pathways, but not in the microbiome composition. Culture-independent approaches outlined the presence of a diverse resistome composition in the Galapagos marine iguanas from remote islands. The presence of AR pathogens in marine iguanas raises concerns about the dispersion of microbial-resistant threats in pristine areas, highlighting wildlife as sentinel species to identify the impact of AU.
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Affiliation(s)
- Karla Vasco
- grid.17088.360000 0001 2150 1785Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824 USA
| | - Nataly Guevara
- grid.442241.50000 0001 0580 871XDepartamento de Procesos Químicos, Alimentos y Biotecnología, Universidad Técnica de Manabí, 130105 Portoviejo, Ecuador ,grid.412251.10000 0000 9008 4711Galapagos Science Center, Universidad San Francisco de Quito, Quito, Ecuador
| | - Juan Mosquera
- grid.412251.10000 0000 9008 4711Colegio de Ciencias Biológicas y Ambientales, Instituto de Microbiología, Universidad San Francisco de Quito, Quito, Ecuador
| | - Sonia Zapata
- grid.412251.10000 0000 9008 4711Colegio de Ciencias Biológicas y Ambientales, Instituto de Microbiología, Universidad San Francisco de Quito, Quito, Ecuador
| | - Lixin Zhang
- grid.17088.360000 0001 2150 1785Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824 USA ,grid.17088.360000 0001 2150 1785Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI 48824 USA
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Wang Z, Zhang C, Li G, Yi X. The influence of species identity and geographic locations on gut microbiota of small rodents. Front Microbiol 2022; 13:983660. [PMID: 36532505 PMCID: PMC9751661 DOI: 10.3389/fmicb.2022.983660] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 11/10/2022] [Indexed: 10/29/2023] Open
Abstract
Although the correlation between gut microbiota, species identity and geographic locations has long attracted the interest of scientists, to what extent species identity and geographic locations influence the gut microbiota assemblages in granivorous rodents needs further investigation. In this study, we performed a survey of gut microbial communities of four rodent species (Apodemus agrarius, A. peninsulae, Tamias sibiricus and Clethrionomys rufocanus) distributed in two areas with great distance (> 600 km apart), to assess if species identity dominates over geographic locations in shaping gut microbial profiles using 16S rRNA gene sequencing. We found that gut microbiota composition varied significantly across host species and was closely correlated with host genetics. We identified strong species identity effects on gut microbial composition, with a comparatively weaker signal of geographic provenance on the intestinal microbiota. Specifically, microbiota of one species was on average more similar to that of conspecifics living in separate sites than to members of a closely related species living in the same location. Our study suggests that both host genetics and geographical variations influence gut microbial diversity of four rodent species, which merits further investigation to reveal the patterns of phylogenetic correlation of gut microbial community assembly in mammals across multiple habitats.
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Affiliation(s)
- Zhenyu Wang
- Nanchang Key Laboratory of Microbial Resources Exploitation & Utilization From Poyang Lake Wetland, College of Life Sciences, Jiangxi Normal University, Nanchang, China
| | - Chao Zhang
- Nanchang Key Laboratory of Microbial Resources Exploitation & Utilization From Poyang Lake Wetland, College of Life Sciences, Jiangxi Normal University, Nanchang, China
| | - Guoliang Li
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Xianfeng Yi
- College of Life Sciences, Qufu Normal University, Qufu, China
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Eliades SJ, Colston TJ, Siler CD. Gut microbial ecology of Philippine gekkonids: ecoevolutionary effects on microbiome compositions. FEMS Microbiol Ecol 2022; 98:6763418. [PMID: 36259773 PMCID: PMC9681010 DOI: 10.1093/femsec/fiac124] [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: 03/14/2022] [Revised: 09/20/2022] [Accepted: 10/17/2022] [Indexed: 01/21/2023] Open
Abstract
Given the rapidly changing landscapes of habitats across the globe, a sound understanding of host-associated microbial communities and the ecoevolutionary forces that shape them is needed to assess general organismal adaptability. Knowledge of the symbiotic endogenous microbiomes of most reptilian species worldwide remains limited. We sampled gut microbiomes of geckos spanning nine species and four genera in the Philippines to (i) provide baseline data on gut microbiota in these host species, (ii) test for significant associations between host phylogenetic relationships and observed microbial assemblages, potentially indicative of phylosymbiosis, and (iii) identify correlations between multiple ecoevolutionary factors (e.g. species identity, habitat tendencies, range extents, and maximum body sizes) and gut microbiomes in Philippine gekkonids. We recovered no significant association between interspecific host genetic distances and observed gut microbiomes, providing limited evidence for phylosymbiosis in this group. Philippine gekkonid microbiomes were associated most heavily with host species identity, though marked variation among conspecifics at distinct sampling sites indicates that host locality influences gut microbiomes as well. Interestingly, individuals grouped as widespread and microendemic regardless of host species identity displayed significant differences in alpha and beta diversity metrics examined, likely driven by differences in rare OTU presence between groups. These results provide much needed insight in host-associated microbiomes in wild reptiles and the ecoevolutionary forces that structure such communities.
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Affiliation(s)
- Samuel J Eliades
- Corresponding author: 2401 Chautauqua Avenue, Norman, OK 73072, United States. E-mail:
| | - Timothy J Colston
- Biology Department, University of Puerto Rico at Mayagüez, Call Box 9000, 00681-9000 Mayagüez, Puerto Rico
| | - Cameron D Siler
- Sam Noble Oklahoma Museum of Natural History and Department of Biology, University of Oklahoma, 2401 Chautauqua Avenue, Norman, OK 73072, United States
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Yan B, Jia T, Wang Z, Zhu W. Comparative research of intestinal microbiota diversity and body mass regulation in Eothenomys miletus from different areas of Hengduan mountain regions. Front Microbiol 2022; 13:1026841. [PMID: 36325022 PMCID: PMC9619095 DOI: 10.3389/fmicb.2022.1026841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 09/14/2022] [Indexed: 11/24/2022] Open
Abstract
In order to investigate the effects of different areas on intestinal bacterial diversity and body mass regulation in Eothenomys miletus from Hengduan mountain regions, and to explore the community structure and diversity of intestinal microflora and their role in body mass regulation. E. miletus was collected from five areas including Deqin (DQ), Xianggelila (XGLL), Lijiang (LJ), Jianchuan (JC), and Dali (DL), we used 16S rRNA sequencing technology combined with physiological and morphological methods to study the intestinal microbiota diversity, abundance and community structure of the intestinal bacteria in winter, and to explore the influence of geographical factors, physiological indicators including food intake, resting metabolic rate (RMR), non-shivering thermogenesis (NST), neuropeptide Y (NPY), Agouti-Related Protein (AgRP), proopiomelanocortin (POMC), cocaine and amphetamine regulated transcription peptide (CART), and morphological indicators including body mass, body length and other nine indicators on the intestinal microflora diversity in E. miletus. The results showed that there were significant differences in metabolic indexes such as RMR, NST, NPY, AgRP, and morphological indexes such as body length, tail length and ear length among the five regions. Bacterial community in intestinal tract of E. miletus mainly includes three phyla, of which Firmicutes is the dominant phyla, followed by Bacteroidetes and Tenericutes. At the genus level, the dominant bacterial genera were S24-7(UG), Clostridiales (UG), and Lachnospiraceae (UG), etc. α diversity of intestinal microorganisms in DL and JC were significantly different from that in the other three regions. Genera of intestinal microorganisms in DL and JC were also the most. Moreover, Bacteroides, Ruminococcus, and Treponema could affect energy metabolism in E. miletus, which were closely related to the environment in which they lived. All of these results indicated that different areas in Hengduan Mountain had certain effects on the structure of intestinal microbial community in E. miletus, which were responded positively to changes in food abundance and other environmental factors. Furthermore, Firmicutes and Bacteroidetes play an important role in the body mass regulation in E. miletus.
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Affiliation(s)
- Bowen Yan
- Key Laboratory of Ecological Adaptive Evolution and Conservation on Animals-Plants in Southwest Mountain Ecosystem of Yunnan Province Higher Institutes College, School of Life Sciences, Yunnan Normal University, Kunming, China
| | - Ting Jia
- Yunnan College of Business Management, Kunming, China
| | - Zhengkun Wang
- Key Laboratory of Ecological Adaptive Evolution and Conservation on Animals-Plants in Southwest Mountain Ecosystem of Yunnan Province Higher Institutes College, School of Life Sciences, Yunnan Normal University, Kunming, China
| | - Wanlong Zhu
- Key Laboratory of Ecological Adaptive Evolution and Conservation on Animals-Plants in Southwest Mountain Ecosystem of Yunnan Province Higher Institutes College, School of Life Sciences, Yunnan Normal University, Kunming, China
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming, China
- Key Laboratory of Yunnan Province for Biomass Energy and Environment Biotechnology, Kunming, China
- *Correspondence: Wanlong Zhu,
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Guo R, Zhang S, Chen J, Shen W, Zhang G, Wang J, Zhang F, Pan Q, Xie T, Ai D, Dong J, Suo J, Sun Y, Liu S. Comparison of gut microflora of donkeys in high and low altitude areas. Front Microbiol 2022; 13:964799. [PMID: 36225357 PMCID: PMC9549287 DOI: 10.3389/fmicb.2022.964799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 08/11/2022] [Indexed: 11/13/2022] Open
Abstract
Donkeys’ gut microbe is critical for their health and adaptation to the environment. Little research has been conducted on the donkey gut microbiome compared with other domestic animals. The Tibetan Plateau is an extreme environment. In this study, 6 Qinghai donkeys (QH) from the Tibetan Plateau and 6 Dezhou donkeys (DZ) were investigated, and the contents of 4 parts—stomach, small intestine, cecum, and rectum—were collected. 16S rRNA sequencing and metagenomic sequencing were used to analyze the composition and diversity of gut microbial communities in donkeys. The results showed that the flora diversity and richness of the hindgut were significantly higher than those of the foregut (p < 0.01), with no sex differences, and the community structure and composition of the same or adjacent regions (stomach, small intestine, cecum, and rectum) were similar. Besides, the flora diversity and richness of QH on the Tibetan Plateau were significantly higher than those of DZ (p < 0.05). The major pathways associated with QH were signal transduction mechanisms and carbohydrate transport and metabolism, and Bacteroidales were the major contributors to these functions. Our study provides novel insights into the contribution of microbiomes to the adaptive evolution of donkeys.
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Affiliation(s)
- Rong Guo
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Shuer Zhang
- Shandong Animal Husbandry General Station, Jinan, Shandong, China
| | - Jianxing Chen
- College of Chemistry and Life Science, Chifeng University, Chifeng, Inner Mongolia, China
| | - Wei Shen
- Gene Bank of Equine Genetic Resources, Qingdao, Shandong, China
- College of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Guoliang Zhang
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, Shandong, China
- Gene Bank of Equine Genetic Resources, Qingdao, Shandong, China
| | - Junjie Wang
- Gene Bank of Equine Genetic Resources, Qingdao, Shandong, China
- College of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Fali Zhang
- Gene Bank of Equine Genetic Resources, Qingdao, Shandong, China
- College of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Qingjie Pan
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Taifeng Xie
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Deqiang Ai
- Qinghai Sheep Breeding and Extension Service Center, Gangcha County, Haibei Prefecture, Qinghai, China
| | - Jianbao Dong
- Department of Veterinary Medical Science, Shandong Vocational Animal Science and Veterinary College, Weifang, Shandong, China
| | - Jiajia Suo
- Department of Veterinary Medical Science, Shandong Vocational Animal Science and Veterinary College, Weifang, Shandong, China
| | - Yujiang Sun
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, Shandong, China
- Gene Bank of Equine Genetic Resources, Qingdao, Shandong, China
- Vocational College of Dongying, Dongying, Shandong, China
- *Correspondence: Yujiang Sun,
| | - Shuqin Liu
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, Shandong, China
- Gene Bank of Equine Genetic Resources, Qingdao, Shandong, China
- Shuqin Liu,
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9
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Buglione M, Ricca E, Petrelli S, Baccigalupi L, Troiano C, Saggese A, Rivieccio E, Fulgione D. Gut microbiota plasticity in insular lizards under reversed island syndrome. Sci Rep 2022; 12:12682. [PMID: 35879521 PMCID: PMC9314426 DOI: 10.1038/s41598-022-16955-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 07/19/2022] [Indexed: 11/28/2022] Open
Abstract
Animals living on small islands are more drastically exposed to environmental changes, such as food or water starvation, and rapid temperature shifts. Facing such conditions, and probably thank to adaptive plasticity mechanisms, some animals display a Reversed Island Syndrome (RIS), a suite of traits, including skin pigmentation, voracity, sexual dimorphism, showed differently from mainland relatives. Here, we analyse a so far poorly explored aspect of RIS: the effect of this on the microbiota composition of host Italian wall lizard (Podarcis siculus), strongly influenced by the animal’s lifestyle, and conditioning the same. We compare mainland and island populations, assessing the difference between their microbial communities and their response under unexpected food, experimentally provided. Our observations showed a significant difference in microbiota communities between island and mainland groups, depended mainly from changes in relative abundance of the shared genera (difference due to decrease/increase). Exposure to experimental diet regimes resulted into significative reshaping of bacterial composition of microbiota and a greater variation in body mass only in the island population. Our results could be an evidence that gut microbial community contributes to adaptive plasticity mechanisms of island lizards under RIS to efficiently respond to unexpected changes.
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Affiliation(s)
- Maria Buglione
- Department of Biology, University of Naples Federico II, Via Cinthia 26, 80126, Naples, Italy
| | - Ezio Ricca
- Department of Biology, University of Naples Federico II, Via Cinthia 26, 80126, Naples, Italy.,Task Force of the Federico II University for Microbiome Studies, Naples, Italy
| | - Simona Petrelli
- Department of Biology, University of Naples Federico II, Via Cinthia 26, 80126, Naples, Italy
| | - Loredana Baccigalupi
- Task Force of the Federico II University for Microbiome Studies, Naples, Italy.,Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Claudia Troiano
- Department of Biology, University of Naples Federico II, Via Cinthia 26, 80126, Naples, Italy
| | - Anella Saggese
- Department of Biology, University of Naples Federico II, Via Cinthia 26, 80126, Naples, Italy
| | - Eleonora Rivieccio
- Department of Humanities, University of Naples Federico II, Naples, Italy
| | - Domenico Fulgione
- Department of Biology, University of Naples Federico II, Via Cinthia 26, 80126, Naples, Italy. .,Task Force of the Federico II University for Microbiome Studies, Naples, Italy.
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Hernández M, Ancona S, Díaz De La Vega-Pérez AH, Muñoz-Arenas LC, Hereira-Pacheco SE, Navarro-Noya YE. Is Habitat More Important than Phylogenetic Relatedness for Elucidating the Gut Bacterial Composition in Sister Lizard Species? Microbes Environ 2022; 37. [PMID: 35768277 PMCID: PMC9530725 DOI: 10.1264/jsme2.me21087] [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] [Indexed: 11/12/2022] Open
Abstract
The gut microbiota influences the phenotype and fitness of a host; however, limited information is currently available on the diversity and functions of the gut microbiota in wild animals. Therefore, we herein examined the diversity, composition, and potential functions of the gut microbiota in three Sceloporus lizards: Sceloporus aeneus, S. bicanthalis, and S. grammicus, inhabiting different habitats in a mountainous ecosystem. The gut bacterial community of S. bicanthalis from alpine grasslands at 4,150 m a.s.l. exhibited greater taxonomic, phylogenetic, and functional alpha diversities than its sister species S. aeneus from cornfields and human-induced grasslands at 2,600 m a.s.l. Bacteria of the genus Blautia and metabolic functions related to the degradation of aromatic compounds were more abundant in S. bicanthalis than in S. aeneus, whereas Oscillibacter and predicted functions related to amino acid metabolism and fermentation were more abundant in S. aeneus. The structure of the dominant and most prevalent bacteria, i.e., the core microbiota, was similar between the sister species from different habitats, but differed between S. grammicus and S. aeneus cohabiting at 2,600 m a.s.l. and between S. grammicus and S. bicanthalis cohabiting at 4,150 m a.s.l. These results suggest that phylogenetic relatedness defines the core microbiota, while the transient, i.e., non-core, microbiota is influenced by environmental differences in the habitats. Our comparisons between phylogenetically close species provide further evidence for the specialized and complex associations between hosts and the gut microbiota as well as insights into the roles of phylogeny and ecological factors as drivers of the gut microbiota in wild vertebrates.
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Affiliation(s)
- Mauricio Hernández
- Doctorado en Ciencias Biológicas, Centro Tlaxcala de Biología de la Conducta, Universidad Autónoma de Tlaxcala
| | - Sergio Ancona
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México
| | | | | | - Stephanie E Hereira-Pacheco
- Estación Científica La Malinche, Centro Tlaxcala de Biología de la Conducta, Universidad Autónoma de Tlaxcala
| | - Yendi E Navarro-Noya
- Laboratorio de Interacciones Bióticas, Centro de Investigación en Ciencias Biológicas, Universidad Autónoma de Tlaxcala
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11
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Marsh KJ, Raulo AM, Brouard M, Troitsky T, English HM, Allen B, Raval R, Venkatesan S, Pedersen AB, Webster JP, Knowles SCL. Synchronous Seasonality in the Gut Microbiota of Wild Mouse Populations. Front Microbiol 2022; 13:809735. [PMID: 35547129 PMCID: PMC9083407 DOI: 10.3389/fmicb.2022.809735] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 03/08/2022] [Indexed: 12/03/2022] Open
Abstract
The gut microbiome performs many important functions in mammalian hosts, with community composition shaping its functional role. However, the factors that drive individual microbiota variation in wild animals and to what extent these are predictable or idiosyncratic across populations remains poorly understood. Here, we use a multi-population dataset from a common rodent species (the wood mouse, Apodemus sylvaticus), to test whether a consistent “core” gut microbiota is identifiable in this species, and to what extent the predictors of microbiota variation are consistent across populations. Between 2014 and 2018 we used capture-mark-recapture and 16S rRNA profiling to intensively monitor two wild wood mouse populations and their gut microbiota, as well as characterising the microbiota from a laboratory-housed colony of the same species. Although the microbiota was broadly similar at high taxonomic levels, the two wild populations did not share a single bacterial amplicon sequence variant (ASV), despite being only 50km apart. Meanwhile, the laboratory-housed colony shared many ASVs with one of the wild populations from which it is thought to have been founded decades ago. Despite not sharing any ASVs, the two wild populations shared a phylogenetically more similar microbiota than either did with the colony, and the factors predicting compositional variation in each wild population were remarkably similar. We identified a strong and consistent pattern of seasonal microbiota restructuring that occurred at both sites, in all years, and within individual mice. While the microbiota was highly individualised, some seasonal convergence occurred in late winter/early spring. These findings reveal highly repeatable seasonal gut microbiota dynamics in multiple populations of this species, despite different taxa being involved. This provides a platform for future work to understand the drivers and functional implications of such predictable seasonal microbiome restructuring, including whether it might provide the host with adaptive seasonal phenotypic plasticity.
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Affiliation(s)
- Kirsty J Marsh
- Department of Pathobiology and Population Sciences, The Royal Veterinary College, University of London, Hatfield, United Kingdom.,College of Life and Environmental Sciences, University of Exeter, Cornwall, United Kingdom
| | - Aura M Raulo
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Marc Brouard
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Tanya Troitsky
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Holly M English
- Department of Pathobiology and Population Sciences, The Royal Veterinary College, University of London, Hatfield, United Kingdom.,Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Bryony Allen
- Department of Life Sciences, Imperial College London, Silwood Park, Ascot, United Kingdom
| | - Rohan Raval
- Department of Life Sciences, Imperial College London, Silwood Park, Ascot, United Kingdom
| | - Saudamini Venkatesan
- Institute of Evolutionary Biology, School of Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Amy B Pedersen
- Institute of Evolutionary Biology, School of Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Joanne P Webster
- Department of Pathobiology and Population Sciences, The Royal Veterinary College, University of London, Hatfield, United Kingdom
| | - Sarah C L Knowles
- Department of Pathobiology and Population Sciences, The Royal Veterinary College, University of London, Hatfield, United Kingdom.,Department of Zoology, University of Oxford, Oxford, United Kingdom
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12
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Host microbiome responses to the Snake Fungal Disease pathogen (Ophidiomyces ophidiicola) are driven by changes in microbial richness. Sci Rep 2022; 12:3078. [PMID: 35197501 PMCID: PMC8866498 DOI: 10.1038/s41598-022-07042-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 02/07/2022] [Indexed: 11/24/2022] Open
Abstract
Dermatophytic pathogens are a source of disturbance to the host microbiome, but the temporal progression of these disturbances is unclear. Here, we determined how Snake Fungal Disease, caused by Ophidiomyces ophidiicola, resulted in disturbance to the host microbiome. To assess disease effects on the microbiome, 22 Common Watersnakes (Nerodia sipedon) were collected and half were inoculated with O. ophidiicola. Epidermal swabs were collected weekly for use in microbiome and pathogen load characterization. For the inoculated treatment only, we found a significant effect of disease progression on microbial richness and Shannon diversity consistent with the intermediate disturbance hypothesis. When explicitly accounting for differences in assemblage richness, we found that β-diversity among snakes was significantly affected by the interaction of time and treatment group, with assemblages becoming more dissimilar across time in the inoculated, but not the control group. Also, differences between treatments in average microbiome composition became greater with time, but this interactive effect was not evident when accounting for assemblage richness. These results suggest that changes in composition of the host microbiome associated with disease largely occur due to changes in microbial richness related to disease progression.
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13
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Schulz D, Pšenková-Profousová I, Červená B, Procter M, Neba TF, Modrý D, Petrželková KJ, Qablan MA. Occurrence and diversity of anaerobic gut fungi in wild forest elephants and buffaloes inhabiting two separated forest ecosystems in Central West Africa. JOURNAL OF VERTEBRATE BIOLOGY 2021. [DOI: 10.25225/jvb.21033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Doreen Schulz
- Department of Pathology and Parasitology, University of Veterinary Sciences Brno, Brno, Czech Republic
| | - Ilona Pšenková-Profousová
- Department of Pathology and Parasitology, University of Veterinary Sciences Brno, Brno, Czech Republic
| | - Barbora Červená
- Department of Pathology and Parasitology, University of Veterinary Sciences Brno, Brno, Czech Republic
| | - Miranda Procter
- Department of Veterinary Medicine, United Arab Emirates University, College of Agriculture and Veterinary Medicine, Al Ain, Abu Dhabi, United Arab Emirates; e-mail: ,
| | - Terence Fuh Neba
- World Wildlife Fund, Primate Habituation Project, Dzanga-Sangha Protected Areas, Bangui, Central African Republic; e-mail:
| | - David Modrý
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic; e-mail: ,
| | - Klára J. Petrželková
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic; e-mail: ,
| | - Moneeb A. Qablan
- Department of Veterinary Medicine, United Arab Emirates University, College of Agriculture and Veterinary Medicine, Al Ain, Abu Dhabi, United Arab Emirates; e-mail: ,
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14
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Weinstein SB, Martínez-Mota R, Stapleton TE, Klure DM, Greenhalgh R, Orr TJ, Dale C, Kohl KD, Dearing MD. Microbiome stability and structure is governed by host phylogeny over diet and geography in woodrats ( Neotoma spp.). Proc Natl Acad Sci U S A 2021; 118:e2108787118. [PMID: 34799446 PMCID: PMC8617456 DOI: 10.1073/pnas.2108787118] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/23/2021] [Indexed: 01/17/2023] Open
Abstract
The microbiome is critical for host survival and fitness, but gaps remain in our understanding of how this symbiotic community is structured. Despite evidence that related hosts often harbor similar bacterial communities, it is unclear whether this pattern is due to genetic similarities between hosts or to common ecological selection pressures. Here, using herbivorous rodents in the genus Neotoma, we quantify how geography, diet, and host genetics, alongside neutral processes, influence microbiome structure and stability under natural and captive conditions. Using bacterial and plant metabarcoding, we first characterized dietary and microbiome compositions for animals from 25 populations, representing seven species from 19 sites across the southwestern United States. We then brought wild animals into captivity, reducing the influence of environmental variation. In nature, geography, diet, and phylogeny collectively explained ∼50% of observed microbiome variation. Diet and microbiome diversity were correlated, with different toxin-enriched diets selecting for distinct microbial symbionts. Although diet and geography influenced natural microbiome structure, the effects of host phylogeny were stronger for both wild and captive animals. In captivity, gut microbiomes were altered; however, responses were species specific, indicating again that host genetic background is the most significant predictor of microbiome composition and stability. In captivity, diet effects declined and the effects of host genetic similarity increased. By bridging a critical divide between studies in wild and captive animals, this work underscores the extent to which genetics shape microbiome structure and stability in closely related hosts.
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Affiliation(s)
- Sara B Weinstein
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112;
| | - Rodolfo Martínez-Mota
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112
- Centro de Investigaciones Tropicales, Universidad Veracruzana, Veracruz, 91000, Mexico
| | - Tess E Stapleton
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112
| | - Dylan M Klure
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112
| | - Robert Greenhalgh
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112
| | - Teri J Orr
- Department of Biology, New Mexico State University, Las Cruces, NM 88003
| | - Colin Dale
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112
| | - Kevin D Kohl
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15217
| | - M Denise Dearing
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112
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15
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Correa F, Torti V, Spiezio C, Checcucci A, Modesto M, Borruso L, Cavani L, Mimmo T, Cesco S, Luise D, Randrianarison RM, Gamba M, Rarojoson NJ, Sanguinetti M, Di Vito M, Bugli F, Mattarelli P, Trevisi P, Giacoma C, Sandri C. Disentangling the Possible Drivers of Indri indri Microbiome: A Threatened Lemur Species of Madagascar. Front Microbiol 2021; 12:668274. [PMID: 34421838 PMCID: PMC8378179 DOI: 10.3389/fmicb.2021.668274] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 07/08/2021] [Indexed: 01/04/2023] Open
Abstract
Research on the gut microbiome may help with increasing our understanding of primate health with species' ecology, evolution, and behavior. In particular, microbiome-related information has the potential to clarify ecology issues, providing knowledge in support of wild primates conservation and their associated habitats. Indri (Indri indri) is the largest extant living lemur of Madagascar. This species is classified as "critically endangered" by the IUCN Red List of Threatened Species, representing one of the world's 25 most endangered primates. Indris diet is mainly folivorous, but these primates frequently and voluntarily engage in geophagy. Indris have never been successfully bred under human care, suggesting that some behavioral and/or ecological factors are still not considered from the ex situ conservation protocols. Here, we explored gut microbiome composition of 18 indris belonging to 5 different family groups. The most represented phyla were Proteobacteria 40.1 ± 9.5%, Bacteroidetes 28.7 ± 2.8%, Synergistetes 16.7 ± 4.5%, and Firmicutes 11.1 ± 1.9%. Further, our results revealed that bacterial alpha and beta diversity were influenced by indri family group and sex. In addition, we investigated the chemical composition of geophagic soil to explore the possible ecological value of soil as a nutrient supply. The quite acidic pH and high levels of secondary oxide-hydroxides of the soils could play a role in the folivorous diet's gut detoxification activity. In addition, the high contents of iron and manganese found the soils could act as micronutrients in the indris' diet. Nevertheless, the concentration of a few elements (i.e., calcium, sulfur, boron, nickel, sodium, and chromium) was higher in non-geophagic than in geophagic soils. In conclusion, the data presented herein provide a baseline for outlining some possible drivers responsible for the gut microbiome diversity in indris, thus laying the foundations for developing further strategies involved in indris' conservation.
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Affiliation(s)
- Federico Correa
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Valeria Torti
- Department of Life Sciences and Systems Biology, University of Torino, Turin, Italy
| | - Caterina Spiezio
- Department of Animal Health Care and Management, Parco Natura Viva – Garda Zoological Park, Verona, Italy
| | - Alice Checcucci
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Monica Modesto
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Luigimaria Borruso
- Faculty of Science and Technology, Free University of Bolzano-Bozen, Bolzano, Italy
| | - Luciano Cavani
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Tanja Mimmo
- Faculty of Science and Technology, Free University of Bolzano-Bozen, Bolzano, Italy
| | - Stefano Cesco
- Faculty of Science and Technology, Free University of Bolzano-Bozen, Bolzano, Italy
| | - Diana Luise
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Rose M. Randrianarison
- Groupe d’Étude et de Recherche sur les Primates de Madagascar, Antananarivo, Madagascar
- Mention d’Anthropobiologie et de Deìveloppement Durable, Université de Antananarivo, Antananarivo, Madagascar
| | - Marco Gamba
- Department of Life Sciences and Systems Biology, University of Torino, Turin, Italy
| | | | - Maurizio Sanguinetti
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Rome, Italy
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Maura Di Vito
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Francesca Bugli
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Rome, Italy
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Paola Mattarelli
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Paolo Trevisi
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Cristina Giacoma
- Department of Life Sciences and Systems Biology, University of Torino, Turin, Italy
| | - Camillo Sandri
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
- Department of Animal Health Care and Management, Parco Natura Viva – Garda Zoological Park, Verona, Italy
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16
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Kim PS, Shin NR, Lee JB, Kim MS, Whon TW, Hyun DW, Yun JH, Jung MJ, Kim JY, Bae JW. Host habitat is the major determinant of the gut microbiome of fish. MICROBIOME 2021; 9:166. [PMID: 34332628 PMCID: PMC8325807 DOI: 10.1186/s40168-021-01113-x] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 06/14/2021] [Indexed: 05/09/2023]
Abstract
BACKGROUND Our understanding of the gut microbiota of animals is largely based on studies of mammals. To better understand the evolutionary basis of symbiotic relationships between animal hosts and indigenous microbes, it is necessary to investigate the gut microbiota of non-mammalian vertebrate species. In particular, fish have the highest species diversity among groups of vertebrates, with approximately 33,000 species. In this study, we comprehensively characterized gut bacterial communities in fish. RESULTS We analyzed 227 individual fish representing 14 orders, 42 families, 79 genera, and 85 species. The fish gut microbiota was dominated by Proteobacteria (51.7%) and Firmicutes (13.5%), different from the dominant taxa reported in terrestrial vertebrates (Firmicutes and Bacteroidetes). The gut microbial community in fish was more strongly shaped by host habitat than by host taxonomy or trophic level. Using a machine learning approach trained on the microbial community composition or predicted functional profiles, we found that the host habitat exhibited the highest classification accuracy. Principal coordinate analysis revealed that the gut bacterial community of fish differs significantly from those of other vertebrate classes (reptiles, birds, and mammals). CONCLUSIONS Collectively, these data provide a reference for future studies of the gut microbiome of aquatic animals as well as insights into the relationship between fish and their gut bacteria, including the key role of host habitat and the distinct compositions in comparison with those of mammals, reptiles, and birds. Video Abstract.
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Affiliation(s)
- Pil Soo Kim
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Dongdaemun-gu, Seoul, 02447 Republic of Korea
| | - Na-Ri Shin
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Dongdaemun-gu, Seoul, 02447 Republic of Korea
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, Jeollabuk-do 56212 Republic of Korea
| | - Jae-Bong Lee
- Distant-water Fisheries Resources Division, National Institute of Fisheries Science, Gijang-eup, Busan, 46083 Republic of Korea
| | - Min-Soo Kim
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Dongdaemun-gu, Seoul, 02447 Republic of Korea
| | - Tae Woong Whon
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Dongdaemun-gu, Seoul, 02447 Republic of Korea
| | - Dong-Wook Hyun
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Dongdaemun-gu, Seoul, 02447 Republic of Korea
| | - Ji-Hyun Yun
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Dongdaemun-gu, Seoul, 02447 Republic of Korea
| | - Mi-Ja Jung
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Dongdaemun-gu, Seoul, 02447 Republic of Korea
| | - Joon Yong Kim
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Dongdaemun-gu, Seoul, 02447 Republic of Korea
| | - Jin-Woo Bae
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Dongdaemun-gu, Seoul, 02447 Republic of Korea
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17
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Doña J, Virrueta Herrera S, Nyman T, Kunnasranta M, Johnson KP. Patterns of Microbiome Variation Among Infrapopulations of Permanent Bloodsucking Parasites. Front Microbiol 2021; 12:642543. [PMID: 33935998 PMCID: PMC8085356 DOI: 10.3389/fmicb.2021.642543] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 03/26/2021] [Indexed: 12/22/2022] Open
Abstract
While interspecific variation in microbiome composition can often be readily explained by factors such as host species identity, there is still limited knowledge of how microbiomes vary at scales lower than the species level (e.g., between individuals or populations). Here, we evaluated variation in microbiome composition of individual parasites among infrapopulations (i.e., populations of parasites of the same species living on a single host individual). To address this question, we used genome-resolved and shotgun metagenomic data of 17 infrapopulations (balanced design) of the permanent, bloodsucking seal louse Echinophthirius horridus sampled from individual Saimaa ringed seals Pusa hispida saimensis. Both genome-resolved and read-based metagenomic classification approaches consistently show that parasite infrapopulation identity is a significant factor that explains both qualitative and quantitative patterns of microbiome variation at the intraspecific level. This study contributes to the general understanding of the factors driving patterns of intraspecific variation in microbiome composition, especially of bloodsucking parasites, and has implications for understanding how well-known processes occurring at higher taxonomic levels, such as phylosymbiosis, might arise in these systems.
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Affiliation(s)
- Jorge Doña
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, Champaign, IL, United States.,Departamento de Biología Animal, Universidad de Granada, Granada, Spain
| | - Stephany Virrueta Herrera
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, Champaign, IL, United States
| | - Tommi Nyman
- Department of Ecosystems in the Barents Region, Norwegian Institute of Bioeconomy Research, Svanvik, Norway
| | - Mervi Kunnasranta
- Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland.,Natural Resources Institute Finland, Joensuu, Finland
| | - Kevin P Johnson
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, Champaign, IL, United States
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18
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Locally adapted gut microbiomes mediate host stress tolerance. ISME JOURNAL 2021; 15:2401-2414. [PMID: 33658622 PMCID: PMC8319338 DOI: 10.1038/s41396-021-00940-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 01/29/2021] [Accepted: 02/11/2021] [Indexed: 01/04/2023]
Abstract
While evidence for the role of the microbiome in shaping host stress tolerance is becoming well-established, to what extent this depends on the interaction between the host and its local microbiome is less clear. Therefore, we investigated whether locally adapted gut microbiomes affect host stress tolerance. In the water flea Daphnia magna, we studied if the host performs better when receiving a microbiome from their source region than from another region when facing a stressful condition, more in particular exposure to the toxic cyanobacteria Microcystis aeruginosa. Therefore, a reciprocal transplant experiment was performed in which recipient, germ-free D. magna, isolated from different ponds, received a donor microbiome from sympatric or allopatric D. magna that were pre-exposed to toxic cyanobacteria or not. We tested for effects on host life history traits and gut microbiome composition. Our data indicate that Daphnia interact with particular microbial strains mediating local adaptation in host stress tolerance. Most recipient D. magna individuals performed better when inoculated with sympatric than with allopatric microbiomes. This effect was most pronounced when the donors were pre-exposed to the toxic cyanobacteria, but this effect was also pond and genotype dependent. We discuss how this host fitness benefit is associated with microbiome diversity patterns.
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19
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Ibáñez A, Bletz MC, Quezada G, Geffers R, Jarek M, Vences M, Steinfartz S. No impact of a short-term climatic "El Niño" fluctuation on gut microbial diversity in populations of the Galápagos marine iguana (Amblyrhynchus cristatus). Naturwissenschaften 2021; 108:7. [PMID: 33528676 PMCID: PMC7854437 DOI: 10.1007/s00114-020-01714-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 11/26/2020] [Accepted: 11/29/2020] [Indexed: 01/05/2023]
Abstract
Gut microorganisms are crucial for many biological functions playing a pivotal role in the host's well-being. We studied gut bacterial community structure of marine iguana populations across the Galápagos archipelago. Marine iguanas depend heavily on their specialized gut microbiome for the digestion of dietary algae, a resource whose growth was strongly reduced by severe "El Niño"-related climatic fluctuations in 2015/2016. As a consequence, marine iguana populations showed signs of starvation as expressed by a poor body condition. Body condition indices (BCI) varied between island populations indicating that food resources (i.e., algae) are affected differently across the archipelago during 'El Niño' events. Though this event impacted food availability for marine iguanas, we found that reductions in body condition due to "El Niño"-related starvation did not result in differences in bacterial gut community structure. Species richness of gut microorganisms was instead correlated with levels of neutral genetic diversity in the distinct host populations. Our data suggest that marine iguana populations with a higher level of gene diversity and allelic richness may harbor a more diverse gut microbiome than those populations with lower genetic diversity. Since low values of these diversity parameters usually correlate with small census and effective population sizes, we use our results to propose a novel hypothesis according to which small and genetically less diverse host populations might be characterized by less diverse microbiomes. Whether such genetically depauperate populations may experience additional threats from reduced dietary flexibility due to a limited intestinal microbiome is currently unclear and calls for further investigation.
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Affiliation(s)
- Alejandro Ibáñez
- Zoological Institute, Technische Universität Braunschweig, Braunschweig, Germany. .,Department of Comparative Anatomy, Institute of Zoology and Biomedical Research, Jagiellonian University, ul. Gronostajowa 9, 30-387, Kraków, Poland.
| | - Molly C Bletz
- Zoological Institute, Technische Universität Braunschweig, Braunschweig, Germany.,Department of Biology, University of Massachusetts Boston, Boston, MA, USA
| | - Galo Quezada
- Dirección Parque Nacional Galápagos, Puerto Ayora, Santa Cruz, Galápagos, Ecuador
| | - Robert Geffers
- Department of Genome Analytics, Helmholtz Centre for Infection Research, 38124, Braunschweig, Germany
| | - Michael Jarek
- Department of Genome Analytics, Helmholtz Centre for Infection Research, 38124, Braunschweig, Germany
| | - Miguel Vences
- Zoological Institute, Technische Universität Braunschweig, Braunschweig, Germany
| | - Sebastian Steinfartz
- Zoological Institute, Technische Universität Braunschweig, Braunschweig, Germany. .,Institute of Biology, Molecular Evolution and Systematics of Animals, University of Leipzig, Talstrasse 33, 04103, Leipzig, Germany.
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20
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Qu YF, Wu YQ, Zhao YT, Lin LH, Du Y, Li P, Li H, Ji X. The invasive red-eared slider turtle is more successful than the native Chinese three-keeled pond turtle: evidence from the gut microbiota. PeerJ 2020; 8:e10271. [PMID: 33194431 PMCID: PMC7603792 DOI: 10.7717/peerj.10271] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 10/08/2020] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND The mutualistic symbiosis between the gut microbial communities (microbiota) and their host animals has attracted much attention. Many factors potentially affect the gut microbiota, which also varies among host animals. The native Chinese three-keeled pond turtle (Chinemys reevesii) and the invasive red-eared slider turtle (Trachemys scripta elegans) are two common farm-raised species in China, with the latter generally considered a more successful species. However, supporting evidence from the gut microbiota has yet to be collected. METHODS We collected feces samples from these two turtle species raised in a farm under identical conditions, and analyzed the composition and relative abundance of the gut microbes using bacterial 16S rRNA sequencing on the Roach/454 platform. RESULTS The gut microbiota was mainly composed of Bacteroidetes and Firmicutes at the phylum level, and Porphyromonadaceae, Bacteroidaceae and Lachnospiraceae at the family level in both species. The relative abundance of the microbes and gene functions in the gut microbiota differed between the two species, whereas alpha or beta diversity did not. Microbes of the families Bacteroidaceae, Clostridiaceae and Lachnospiraceae were comparatively more abundant in C. reevesii, whereas those of the families Porphyromonadaceae and Fusobacteriaceae were comparatively more abundant in T. s. elegans. In both species the gut microbiota had functional roles in enhancing metabolism, genetic information processing and environmental information processing according to the Kyoto Encyclopedia of Genes and Genomes database. The potential to gain mass is greater in T. s. elegans than in C. reevesii, as revealed by the fact that the Firmicutes/Bacteroidetes ratio was lower in the former species. The percentage of human disease-related functional genes was lower in T. s. elegans than in C. reevesii, presumably suggesting an enhanced potential to colonize new habitats in the former species.
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Affiliation(s)
- Yan-Fu Qu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
| | - Yan-Qing Wu
- National Key Laboratory of Environmental Protection and Biosafety, Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing, Jiangsu, China
| | - Yu-Tian Zhao
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
| | - Long-Hui Lin
- Hangzhou Key Laboratory for Ecosystem Protection and Restoration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Yu Du
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
- Hainan Key Laboratory of Herpetological Research, College of Fisheries and Life Science, Hainan Tropical Ocean University, Sanya, Hainan, China
| | - Peng Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
| | - Hong Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
| | - Xiang Ji
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
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21
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Speare L, Davies SW, Balmonte JP, Baumann J, Castillo KD. Patterns of environmental variability influence coral-associated bacterial and algal communities on the Mesoamerican Barrier Reef. Mol Ecol 2020; 29:2334-2348. [PMID: 32497352 DOI: 10.1111/mec.15497] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 05/11/2020] [Accepted: 05/26/2020] [Indexed: 02/06/2023]
Abstract
A coral's capacity to alter its microbial symbionts may enhance its fitness in the face of climate change. Recent work predicts exposure to high environmental variability may increase coral resilience and adaptability to future climate conditions. However, how this heightened environmental variability impacts coral-associated microbial communities remains largely unexplored. Here, we examined the bacterial and algal symbionts associated with two coral species of the genus Siderastrea with distinct life history strategies from three reef sites on the Belize Mesoamerican Barrier Reef System with low or high environmental variability. Our results reveal bacterial community structure, as well as alpha- and beta-diversity patterns, vary by host species. Differences in bacterial communities between host species were partially explained by high abundance of Deltaproteobacteria and Rhodospirillales and high bacterial diversity in Siderastrea radians. Our findings also suggest Siderastrea spp. have dynamic core bacterial communities that likely drive differences observed in the entire bacterial community, which may play a critical role in rapid acclimatization to environmental change. Unlike the bacterial community, Symbiodiniaceae composition was only distinct between host species at high thermal variability sites, suggesting that different factors shape bacterial versus algal communities within the coral holobiont. Our findings shed light on how domain-specific shifts in dynamic microbiomes may allow for unique methods of enhanced host fitness.
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Affiliation(s)
- Lauren Speare
- Department of Marine Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Sarah W Davies
- Department of Marine Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Department of Biology, Boston University, Boston, MA, USA
| | - John P Balmonte
- Department of Marine Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Department of Ecology and Genetics - Limnology, Uppsala University, Uppsala, Sweden
| | - Justin Baumann
- Department of Marine Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Karl D Castillo
- Department of Marine Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Environment, Ecology, and Energy Program, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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22
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Budd K, Gunn JC, Finch T, Klymus K, Sitati N, Eggert LS. Effects of diet, habitat, and phylogeny on the fecal microbiome of wild African savanna ( Loxodonta africana) and forest elephants ( L. cyclotis). Ecol Evol 2020; 10:5637-5650. [PMID: 32607180 PMCID: PMC7319146 DOI: 10.1002/ece3.6305] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 04/02/2020] [Accepted: 04/03/2020] [Indexed: 01/05/2023] Open
Abstract
The gut microbiome, or the community of microorganisms inhabiting the digestive tract, is often unique to its symbiont and, in many animal taxa, is highly influenced by host phylogeny and diet. In this study, we characterized the gut microbiome of the African savanna elephant (Loxodonta africana) and the African forest elephant (Loxodonta cyclotis), sister taxa separated by 2.6-5.6 million years of independent evolution. We examined the effect of host phylogeny on microbiome composition. Additionally, we examined the influence of habitat types (forest versus savanna) and diet types (crop-raiding versus noncrop-raiding) on the microbiome within L. africana. We found 58 bacterial orders, representing 16 phyla, across all African elephant samples. The most common phyla were Firmicutes, Proteobacteria, and Bacteroidetes. The microbiome of L. africana was dominated by Firmicutes, similar to other hindgut fermenters, while the microbiome of L. cyclotis was dominated by Proteobacteria, similar to more frugivorous species. Alpha diversity did not differ across species, habitat type, or diet, but beta diversity indicated that microbial communities differed significantly among species, diet types, and habitat types. Based on predicted KEGG metabolic pathways, we also found significant differences between species, but not habitat or diet, in amino acid metabolism, energy metabolism, and metabolism of terpenoids and polyketides. Understanding the digestive capabilities of these elephant species could aid in their captive management and ultimately their conservation.
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Affiliation(s)
- Kris Budd
- Division of Biological SciencesUniversity of MissouriColumbiaMOUSA
| | - Joe C. Gunn
- Division of Biological SciencesUniversity of MissouriColumbiaMOUSA
| | - Tabitha Finch
- Division of Biological SciencesUniversity of MissouriColumbiaMOUSA
- Vermont Genetics NetworkUniversity of VermontBurlingtonVTUSA
| | - Katy Klymus
- Division of Biological SciencesUniversity of MissouriColumbiaMOUSA
- Columbia Environmental Research CenterUnited States Geological SurveyColumbiaMOUSA
| | - Noah Sitati
- World Wide Fund for NatureDar es SalaamTanzania
| | - Lori S. Eggert
- Division of Biological SciencesUniversity of MissouriColumbiaMOUSA
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23
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Interactions between social groups of colobus monkeys (Colobus vellerosus) explain similarities in their gut microbiomes. Anim Behav 2020. [DOI: 10.1016/j.anbehav.2020.02.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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24
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An Z, Guo F, Chen Y, Bai G, Chen Z. Rhizosphere bacterial and fungal communities during the growth of Angelica sinensis seedlings cultivated in an Alpine uncultivated meadow soil. PeerJ 2020; 8:e8541. [PMID: 32257632 PMCID: PMC7103203 DOI: 10.7717/peerj.8541] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 01/09/2020] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Angelica sinensis seedlings are grown in alpine uncultivated meadow soil with rainfed agroecosystems to ensure the quality of A. sinensis after seedling transplantation. The aim was to investigate the rhizosphere bacterial and fungal communities during the growth stages of A. sinensis seedlings. METHODS The bacterial and fungal communities were investigated by HiSeq sequencing of 16S and 18S rDNA, respectively. RESULTS Proteobacteria and Bacteroidetes were bacterial dominant phyla throughout growth stages. Fungal dominant phyla varied with growth stages, dominant phyla Ascomycota and Chytridiomycota in AM5, dominant phyla Basidiomycota, Ascomycota and Zygomycota in BM5, and dominant phyla Basidiomycota and Ascomycota in CM5. There was no significant variation in the alpha-diversity of the bacterial and fungal communities, but significant variation was in the beta-diversity. We found that the variation of microbial community composition was accompanied by the changes in community function. The relative abundance of fungal pathogens increased with plant growth. We also identified the core microbes, significant-changing microbes, stage-specific microbes, and host-specific microbes. Plant weight, root length, root diameter, soil pH, rainfall, and climate temperature were the key divers to microbial community composition. CONCLUSIONS Our findings reported the variation and environmental drivers of rhizosphere bacterial and fungal communities during the growth of A. sinensis seedlings, which enhance the understanding of the rhizosphere microbial community in this habitat.
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Affiliation(s)
- Zhigang An
- College of Life Science and Technology, College of Agronomy, Gansu Provincial Key Lab of Good Agricultural Production for Traditional Chinese Medicine, Gansu Provincial Engineering Research Centre for Medical Plant Cultivation and Breeding, Provincial Key Lab of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- Pharmacy Department, Gansu University of Chinese Medicine, Dingxi, China
| | - Fengxia Guo
- College of Life Science and Technology, College of Agronomy, Gansu Provincial Key Lab of Good Agricultural Production for Traditional Chinese Medicine, Gansu Provincial Engineering Research Centre for Medical Plant Cultivation and Breeding, Provincial Key Lab of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
| | - Yuan Chen
- College of Life Science and Technology, College of Agronomy, Gansu Provincial Key Lab of Good Agricultural Production for Traditional Chinese Medicine, Gansu Provincial Engineering Research Centre for Medical Plant Cultivation and Breeding, Provincial Key Lab of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- Gansu Engineering Lab of Resource Reservation and Utilization for Characteristic Chinese Medicine, Gansu Tasly Zhongtian Pharmaceutical Co., Ltd., Dingxi, China
| | - Gang Bai
- College of Life Science and Technology, College of Agronomy, Gansu Provincial Key Lab of Good Agricultural Production for Traditional Chinese Medicine, Gansu Provincial Engineering Research Centre for Medical Plant Cultivation and Breeding, Provincial Key Lab of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
| | - Zhengjun Chen
- College of Life Science and Technology, College of Agronomy, Gansu Provincial Key Lab of Good Agricultural Production for Traditional Chinese Medicine, Gansu Provincial Engineering Research Centre for Medical Plant Cultivation and Breeding, Provincial Key Lab of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
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25
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Grieneisen LE, Charpentier MJE, Alberts SC, Blekhman R, Bradburd G, Tung J, Archie EA. Genes, geology and germs: gut microbiota across a primate hybrid zone are explained by site soil properties, not host species. Proc Biol Sci 2020; 286:20190431. [PMID: 31014219 DOI: 10.1098/rspb.2019.0431] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Gut microbiota in geographically isolated host populations are often distinct. These differences have been attributed to between-population differences in host behaviours, environments, genetics and geographical distance. However, which factors are most important remains unknown. Here, we fill this gap for baboons by leveraging information on 13 environmental variables from 14 baboon populations spanning a natural hybrid zone. Sampling across a hybrid zone allowed us to additionally test whether phylosymbiosis (codiversification between hosts and their microbiota) is detectable in admixed, closely related primates. We found little evidence of genetic effects: none of host genetic ancestry, host genetic relatedness nor genetic distance between host populations were strong predictors of baboon gut microbiota. Instead, gut microbiota were best explained by the baboons' environments, especially the soil's geologic history and exchangeable sodium. Indeed, soil effects were 15 times stronger than those of host-population FST, perhaps because soil predicts which foods are present, or because baboons are terrestrial and consume soil microbes incidentally with their food. Our results support an emerging picture in which environmental variation is the dominant predictor of host-associated microbiomes. We are the first to show that such effects overshadow host species identity among members of the same primate genus.
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Affiliation(s)
- Laura E Grieneisen
- 1 Department of Genetics, Cell Biology, and Development, University of Minnesota , Minneapolis, MN 55455 , USA.,2 Department of Biology, University of Notre Dame , Notre Dame, IN 46556 , USA
| | - Marie J E Charpentier
- 3 Institut des Sciences de l'Evolution de Montpellier, Université Montpellier, CNRS, IRD, EPHE , Montpellier , France
| | - Susan C Alberts
- 4 Department of Biology, Duke University , Durham, NC 27708 , USA.,5 Department of Evolutionary Anthropology, Duke University , Durham, NC 27708 , USA.,6 Institute for Primate Research, National Museums of Kenya , Nairobi 00502 , Kenya
| | - Ran Blekhman
- 1 Department of Genetics, Cell Biology, and Development, University of Minnesota , Minneapolis, MN 55455 , USA.,7 Department of Ecology, Evolution, and Behavior, University of Minnesota , Minneapolis, MN 55455 , USA
| | - Gideon Bradburd
- 8 Department of Integrative Biology, Michigan State University , East Lansing, MI 48824 , USA
| | - Jenny Tung
- 4 Department of Biology, Duke University , Durham, NC 27708 , USA.,5 Department of Evolutionary Anthropology, Duke University , Durham, NC 27708 , USA.,6 Institute for Primate Research, National Museums of Kenya , Nairobi 00502 , Kenya
| | - Elizabeth A Archie
- 2 Department of Biology, University of Notre Dame , Notre Dame, IN 46556 , USA.,6 Institute for Primate Research, National Museums of Kenya , Nairobi 00502 , Kenya
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26
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Mioduchowska M, Zając K, Bartoszek K, Madanecki P, Kur J, Zając T. 16S rRNA
gene‐based metagenomic analysis of the gut microbial community associated with the DUI species
Unio crassus
(Bivalvia: Unionidae). J ZOOL SYST EVOL RES 2020. [DOI: 10.1111/jzs.12377] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Monika Mioduchowska
- Department of Genetics and Biosystematics Faculty of Biology University of Gdańsk Gdańsk Poland
| | - Katarzyna Zając
- Institute of Nature Conservation Polish Academy of Sciences Kraków Poland
| | - Krzysztof Bartoszek
- Department of Computer and Information Science Division of Statistics and Machine Learning Linköping University Linköping Sweden
| | - Piotr Madanecki
- Department of Biology and Pharmaceutical Botany Faculty of Pharmacy Medical University of Gdańsk Gdańsk Poland
| | | | - Tadeusz Zając
- Institute of Nature Conservation Polish Academy of Sciences Kraków Poland
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27
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Li P, Liu J, Jiang C, Wu M, Liu M, Li Z. Distinct Successions of Common and Rare Bacteria in Soil Under Humic Acid Amendment - A Microcosm Study. Front Microbiol 2019; 10:2271. [PMID: 31632376 PMCID: PMC6779779 DOI: 10.3389/fmicb.2019.02271] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 09/18/2019] [Indexed: 01/08/2023] Open
Abstract
Humic acid (HA) is widely used for soil quality improvement, yet little is known how bacterial communities, especially common and rare bacteria, respond to HA amendment, which is crucial to understand biodiversity and function in agroecosystem. Therefore, a manipulated microcosm experiment with a gradient of HA amendment was conducted to unveil this. The results showed that common and rare taxa had similar patterns in species richness, while rare taxa exhibited a higher turnover, which caused their higher structural dissimilarity. Common species with wider niche breadths were more strongly influenced by deterministic filtering when compared to rare taxa, which occupied narrow niches and were primarily controlled by stochastic processes. Generally, species with wider niche breadths were always more strongly influenced by deterministic selection. The analysis of predicted functions revealed that rare taxa occupied more unique predicted functional traits than common taxa, suggesting that rare taxa played a key role in maintaining the functional diversity. In addition, there was a significant positive correlation between species richness and predicted functional diversity in rare taxa rather than common taxa. Our findings highlight the distinct structural and predicted functional successions of common and rare bacteria in soil under HA amendment.
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Affiliation(s)
- Pengfa Li
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jia Liu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China.,Soil and Fertilizer & Resources and Environment Institute, Jiangxi Academy of Agricultural Sciences, Nanchang, China
| | - Chunyu Jiang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Meng Wu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Ming Liu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Zhongpei Li
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China.,University of Chinese Academy of Sciences, Beijing, China
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28
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Baldo L, Riera JL, Mitsi K, Pretus JL. Processes shaping gut microbiota diversity in allopatric populations of the endemic lizard Podarcis lilfordi from Menorcan islets (Balearic Islands). FEMS Microbiol Ecol 2019; 94:4780271. [PMID: 29294010 DOI: 10.1093/femsec/fix186] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 12/22/2017] [Indexed: 12/22/2022] Open
Abstract
Compositional variation of the gut microbiota across host allopatric populations can reflect both adaptation and stochasticity since the time of separation. Major factors shaping this variation include the host phylogeographic and demographic history, the microbiota inheritance, environmental inputs and dispersal of bacteria. Here we explored the impact of these factors in driving gut community diversity in seven allopatric populations of the omnivorous lizard Podarcis lilfordi from the Menorcan coastal islets, all descending from an ancestral mainland population. Using 16S rRNA Illumina sequencing, we showed that 'islet' and 'age' (time since islet separation from mainland) were the only significant variables in microbial community clustering, suggesting a partial islet-restricted diversification following these lizards phylogeography. Despite a significant variation, islets/populations were characterized by a remarkably low bacterial uniqueness (2.4% of total OTUs) and a minor differential enrichment of taxa, indicating a negligible impact of local inputs and important host common constraints. Overall, the extant pattern of similarity/dissimilarity among islets is compatible with partial retention of the ancestral mainland microbial pool, with differences among islets potentially explained by a differential loss of bacteria following population fragmentation and bottlenecks (i.e. ecological drift). While more quantitative data are needed to validate this hypothesis, this study unveils the importance of considering both neutral and niche-driven processes in driving contemporary patterns of gut metacommunity diversity.
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Affiliation(s)
- Laura Baldo
- Department of Evolutionary Biology, Ecology and Environmental Sciences, University of Barcelona, 08028 Barcelona, Spain.,Institute for Research on Biodiversity (IRBio), University of Barcelona, 08028 Barcelona, Spain
| | - Joan Lluís Riera
- Department of Evolutionary Biology, Ecology and Environmental Sciences, University of Barcelona, 08028 Barcelona, Spain
| | - Konstantina Mitsi
- Department of Evolutionary Biology, Ecology and Environmental Sciences, University of Barcelona, 08028 Barcelona, Spain
| | - Joan Lluís Pretus
- Department of Evolutionary Biology, Ecology and Environmental Sciences, University of Barcelona, 08028 Barcelona, Spain.,Institute for Research on Biodiversity (IRBio), University of Barcelona, 08028 Barcelona, Spain
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29
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Schmidt E, Mykytczuk N, Schulte-Hostedde AI. Effects of the captive and wild environment on diversity of the gut microbiome of deer mice (Peromyscus maniculatus). ISME JOURNAL 2019; 13:1293-1305. [PMID: 30664674 DOI: 10.1038/s41396-019-0345-8] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 12/09/2018] [Accepted: 12/20/2018] [Indexed: 02/07/2023]
Abstract
Vertebrate gastrointestinal tracts have co-existed with microbes over millennia. These microbial communities provide their host with numerous benefits. However, the extent to which different environmental factors contribute to the assemblage of gut microbial communities is not fully understood. The purpose of this study was to determine how the external environment influences the development of gut microbiome communities (GMCs). Faecal samples were collected from deer mice (Peromyscus maniculatus) born and raised in captivity and the wild at approximately 3-5 weeks of age. Additional samples were collected 2 weeks later, with a subset of individuals being translocated between captive and wild environments. Microbial data were analysed using 16S rRNA next-generation Illumina HiSeq sequencing methods. GMCs of deer mice were more similar between neighbours who shared the same environment, regardless of where an individual was born, demonstrating that GMCs are significantly influenced by the surrounding environment and can rapidly change over time. Mice in natural environments contained more diverse GMCs with higher relative abundances of Ruminoccocaceae, Helicobacteraceae and Lachnospiraceae spp. Future studies should examine the fitness consequences associated with the presence/absence of microbes that are characteristic of GMCs of wild populations to gain a better understanding of environment-microbe-host evolutionary and ecological relationships.
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Affiliation(s)
- Elliott Schmidt
- Department of Biology, Laurentian University, Sudbury, ON, P3E 2C6, Canada.
| | - Nadia Mykytczuk
- Vale Living with Lakes Centre, Laurentian University, Sudbury, ON, P3E 2C6, Canada
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30
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Michel AJ, Ward LM, Goffredi SK, Dawson KS, Baldassarre DT, Brenner A, Gotanda KM, McCormack JE, Mullin SW, O'Neill A, Tender GS, Uy JAC, Yu K, Orphan VJ, Chaves JA. The gut of the finch: uniqueness of the gut microbiome of the Galápagos vampire finch. MICROBIOME 2018; 6:167. [PMID: 30231937 PMCID: PMC6146768 DOI: 10.1186/s40168-018-0555-8] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 09/05/2018] [Indexed: 05/13/2023]
Abstract
BACKGROUND Darwin's finches are a clade of 19 species of passerine birds native to the Galápagos Islands, whose biogeography, specialized beak morphologies, and dietary choices-ranging from seeds to blood-make them a classic example of adaptive radiation. While these iconic birds have been intensely studied, the composition of their gut microbiome and the factors influencing it, including host species, diet, and biogeography, has not yet been explored. RESULTS We characterized the microbial community associated with 12 species of Darwin's finches using high-throughput 16S rRNA sequencing of fecal samples from 114 individuals across nine islands, including the unusual blood-feeding vampire finch (Geospiza septentrionalis) from Darwin and Wolf Islands. The phylum-level core gut microbiome for Darwin's finches included the Firmicutes, Gammaproteobacteria, and Actinobacteria, with members of the Bacteroidetes at conspicuously low abundance. The gut microbiome was surprisingly well conserved across the diversity of finch species, with one exception-the vampire finch-which harbored bacteria that were either absent or extremely rare in other finches, including Fusobacterium, Cetobacterium, Ureaplasma, Mucispirillum, Campylobacter, and various members of the Clostridia-bacteria known from the guts of carnivorous birds and reptiles. Complementary stable isotope analysis of feathers revealed exceptionally high δ15N isotope values in the vampire finch, resembling top marine predators. The Galápagos archipelago is also known for extreme wet and dry seasons, and we observed a significant seasonal shift in the gut microbial community of five additional finch species sampled during both seasons. CONCLUSIONS This study demonstrates the overall conservatism of the finch gut microbiome over short (< 1 Ma) divergence timescales, except in the most extreme case of dietary specialization, and elevates the evolutionary importance of seasonal shifts in driving not only species adaptation, but also gut microbiome composition.
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Affiliation(s)
- Alice J Michel
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Lewis M Ward
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Shana K Goffredi
- Department of Biology, Occidental College, Los Angeles, CA, 90041, USA
| | - Katherine S Dawson
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, 91125, USA
- School of Environmental and Biological Sciences, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Daniel T Baldassarre
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Alec Brenner
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Kiyoko M Gotanda
- Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ, England
| | - John E McCormack
- Department of Biology, Occidental College, Los Angeles, CA, 90041, USA
| | - Sean W Mullin
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Ariel O'Neill
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Gabrielle S Tender
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, 91125, USA
| | - J Albert C Uy
- Department of Biology, University of Miami, Coral Gables, FL, 33146, USA
| | - Kristie Yu
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Victoria J Orphan
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, 91125, USA.
| | - Jaime A Chaves
- Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Diego de Robles y Pampite, Quito, Ecuador.
- Galápagos Science Center, Puerto Baquerizo Moreno, Galápagos, Ecuador.
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31
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Reich I, Ijaz UZ, Gormally M, Smith CJ. 16S rRNA sequencing reveals likely beneficial core microbes within faecal samples of the EU protected slug Geomalacus maculosus. Sci Rep 2018; 8:10402. [PMID: 29991804 PMCID: PMC6039444 DOI: 10.1038/s41598-018-28720-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 06/25/2018] [Indexed: 01/20/2023] Open
Abstract
The EU-protected slug Geomalacus maculosus Allman occurs only in the West of Ireland and in northern Spain and Portugal. We explored the microbial community found within the faeces of Irish specimens with a view to determining whether a core microbiome existed among geographically isolated slugs which could give insight into the adaptations of G. maculosus to the available food resources within its habitat. Faecal samples of 30 wild specimens were collected throughout its Irish range and the V3 region of the bacterial 16S rRNA gene was sequenced using Illumina MiSeq. To investigate the influence of diet on the microbial composition, faecal samples were taken and sequenced from six laboratory reared slugs which were raised on two different foods. We found a widely diverse microbiome dominated by Enterobacteriales with three core OTUs shared between all specimens. While the reared specimens appeared clearly separated by diet in NMDS plots, no significant difference between the slugs fed on the two different diets was found. Our results indicate that while the majority of the faecal microbiome of G. maculosus is probably dependent on the microhabitat of the individual slugs, parts of it are likely selected for by the host.
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Affiliation(s)
- Inga Reich
- Applied Ecology Unit, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland.
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR, 97331, USA.
| | - Umer Zeeshan Ijaz
- School of Engineering, University of Glasgow, Glasgow, Scotland, UK.
| | - Mike Gormally
- Applied Ecology Unit, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Cindy J Smith
- School of Engineering, University of Glasgow, Glasgow, Scotland, UK.
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Varudkar A, Ramakrishnan U. Gut microflora may facilitate adaptation to anthropic habitat: A comparative study in Rattus. Ecol Evol 2018; 8:6463-6472. [PMID: 30038748 PMCID: PMC6053588 DOI: 10.1002/ece3.4040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 02/14/2018] [Accepted: 02/17/2018] [Indexed: 01/14/2023] Open
Abstract
Anthropophilic species ("commensal" species) that are completely dependent upon anthropic habitats experience different selective pressures particularly in terms of food than their noncommensal counterparts. Using a next-generation sequencing approach, we characterized and compared the gut microflora community of 53 commensal Rattus rattus and 59 noncommensal Rattus satarae captured in 10 locations in the Western Ghats, India. We observed that, while species identity was important in characterizing the microflora communities of the two Rattus hosts, environmental factors also had a significant effect. While there was significant geographic variation in the microflora of the noncommensal R. satarae, there was no effect of geographic distance on gut microflora of the commensal R. rattus. Interestingly, host genetic distance did not significantly influence the community in either Rattus hosts. Collectively, these results indicate that a shift in habitat is likely to result in a change in the gut microflora community and imply that the gut microflora is a complex trait, influenced by various parameters in different habitats.
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Zhang W, Li N, Tang X, Liu N, Zhao W. Changes in intestinal microbiota across an altitudinal gradient in the lizard Phrynocephalus vlangalii. Ecol Evol 2018; 8:4695-4703. [PMID: 29760909 PMCID: PMC5938461 DOI: 10.1002/ece3.4029] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 02/24/2018] [Accepted: 03/01/2018] [Indexed: 12/21/2022] Open
Abstract
High altitude is an important driving force in animal evolution. However, the effect of altitude on gut microbial communities in reptiles has not been examined in detail. Here, we investigated the intestinal microbiota of three populations of the lizard Phrynocephalus vlangalii living at different altitudes using 16S rRNA gene sequencing. Bacteroidetes, Firmicutes, and Proteobacteria were the most abundant phyla. Bacteroides, Odoribacter, and Parabacteroides were the most abundant genera. Significant differences in the intestinal microbiota composition were found among the three populations from different altitudes. The proportions of Verrucomicrobia and Akkermansia decreased, whereas Bacteroides increased significantly with altitude. Greater abundance of Bacteroides at higher altitude led to the fractional increase in the phylum Bacteroides relative to other phyla. Hypoxia may be the main factor that caused intestinal microbiota variation in P. vlangalii along the altitude gradient. Overall, our study suggested that the community composition and structure of intestinal microbiota of the lizard P. vlangalii varied along altitudes, and such differences likely play a certain role in highland adaptation. Our findings warrant a further study that would determine whether ambient and body temperatures play a key role in the modulation of intestinal microbiota in reptiles.
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Affiliation(s)
- Wenya Zhang
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution School of Life Sciences Lanzhou University Lanzhou China
| | - Na Li
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution School of Life Sciences Lanzhou University Lanzhou China
| | - Xiaolong Tang
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution School of Life Sciences Lanzhou University Lanzhou China
| | - Naifa Liu
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution School of Life Sciences Lanzhou University Lanzhou China
| | - Wei Zhao
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution School of Life Sciences Lanzhou University Lanzhou China
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Interhost dispersal alters microbiome assembly and can overwhelm host innate immunity in an experimental zebrafish model. Proc Natl Acad Sci U S A 2017; 114:11181-11186. [PMID: 28973938 DOI: 10.1073/pnas.1702511114] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The diverse collections of microorganisms associated with humans and other animals, collectively referred to as their "microbiome," are critical for host health, but the mechanisms that govern their assembly are poorly understood. This has made it difficult to identify consistent host factors that explain variation in microbiomes across hosts, despite large-scale sampling efforts. While ecological theory predicts that the movement, or dispersal, of individuals can have profound and predictable consequences on community assembly, its role in the assembly of animal-associated microbiomes remains underexplored. Here, we show that dispersal of microorganisms among hosts can contribute substantially to microbiome variation, and is able to overwhelm the effects of individual host factors, in an experimental test of ecological theory. We manipulated dispersal among wild-type and immune-deficient myd88 knockout zebrafish and observed that interhost dispersal had a large effect on the diversity and composition of intestinal microbiomes. Interhost dispersal was strong enough to overwhelm the effects of host factors, largely eliminating differences between wild-type and immune-deficient hosts, regardless of whether dispersal occurred within or between genotypes, suggesting dispersal can independently alter the ecology of microbiomes. Our observations are consistent with a predictive model that assumes metacommunity dynamics and are likely mediated by dispersal-related microbial traits. These results illustrate the importance of microbial dispersal to animal microbiomes and motivate its integration into the study of host-microbe systems.
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35
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Risely A, Waite D, Ujvari B, Klaassen M, Hoye B. Gut microbiota of a long-distance migrant demonstrates resistance against environmental microbe incursions. Mol Ecol 2017; 26:5842-5854. [PMID: 28815767 DOI: 10.1111/mec.14326] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 08/05/2017] [Indexed: 12/21/2022]
Abstract
Migratory animals encounter suites of novel microbes as they move between disparate sites during their migrations, and are frequently implicated in the global spread of pathogens. Although wild animals have been shown to source a proportion of their gut microbiota from their environment, the susceptibility of migrants to enteric infections may be dependent upon the capacity of their gut microbiota to resist incorporating encountered microbes. To evaluate migrants' susceptibility to microbial invasion, we determined the extent of microbial sourcing from the foraging environment and examined how this influenced gut microbiota dynamics over time and space in a migratory shorebird, the Red-necked stint Calidris ruficollis. Contrary to previous studies on wild, nonmigratory hosts, we found that stint on their nonbreeding grounds obtained very little of their microbiota from their environment, with most individuals sourcing only 0.1% of gut microbes from foraging sediment. This microbial resistance was reflected at the population level by only weak compositional differences between stint flocks occupying ecologically distinct sites, and by our finding that stint that had recently migrated 10,000 km did not differ in diversity or taxonomy from those that had inhabited the same site for a full year. However, recent migrants had much greater abundances of the genus Corynebacterium, suggesting a potential microbial response to either migration or exposure to a novel environment. We conclude that the gut microbiota of stint is largely resistant to invasion from ingested microbes and that this may have implications for their susceptibility to enteric infections during migration.
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Affiliation(s)
- Alice Risely
- Centre for Integrative Ecology, Deakin University, Geelong, Vic., Australia
| | - David Waite
- Australian Centre for Ecogenomics, University of Queensland, Brisbane, QLD, Australia
| | - Beata Ujvari
- Centre for Integrative Ecology, Deakin University, Geelong, Vic., Australia
| | - Marcel Klaassen
- Centre for Integrative Ecology, Deakin University, Geelong, Vic., Australia
| | - Bethany Hoye
- Centre for Integrative Ecology, Deakin University, Geelong, Vic., Australia.,School of Biological Sciences, University of Wollongong, Wollongong, NSW, Australia
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Romano M. Gut Microbiota as a Trigger of Accelerated Directional Adaptive Evolution: Acquisition of Herbivory in the Context of Extracellular Vesicles, MicroRNAs and Inter-Kingdom Crosstalk. Front Microbiol 2017; 8:721. [PMID: 28473829 PMCID: PMC5397478 DOI: 10.3389/fmicb.2017.00721] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Accepted: 04/06/2017] [Indexed: 11/17/2022] Open
Abstract
According to a traditional view, the specific diet in vertebrates is one of the key factors structuring the composition of the gut microbiota. In this interpretation, the microbiota assumes a subordinate position, where the larger host shapes, through evolution and its fitness, the taxonomical composition of the hosted microbiota. The present contribution shows how the evolution of herbivory, framed within the new concept of holobiont, the possibility of inter-kingdom crosstalk and its epigenetic effects, could pave the way to a completely reversed interpretation: instead of being passively shaped, the microbiota can mold and shape the general host body structure to increase its fitness. Central elements to consider in this context are the inter-kingdom crosstalk, the possibility of transporting RNAs through nanovesicles in feces from parents to offspring, and the activation of epigenetic processes passed on vertically from generation to generation. The new hypothesis is that the gut microbiota could play a great role in the macroevolutionary dynamics of herbivorous vertebrates, causing directly through host-microbiota dialog of epigenetic nature (i.e., methylation, histone acetylation, etc.), major changes in the organisms phenotype. The vertical exchange of the same microbial communities from parents to offspring, the interaction of these microbes with fairly uniform genotypes, and the socially restricted groups where these processes take place, could all explain the reasons why herbivory has appeared several time (and independently) during the evolution of vertebrates. The new interpretation could also represent a key factor in understanding the convergent evolution of analogous body structures in very distant lineages.
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Affiliation(s)
- Marco Romano
- Museum für Naturkunde, Leibniz-Institut für Evolutions- und BiodiversitätsforschungBerlin, Germany.,Dipartimento di Scienze della Terra, Sapienza Universita di RomaRome, Italy
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37
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Kohl KD, Brun A, Magallanes M, Brinkerhoff J, Laspiur A, Acosta JC, Caviedes-Vidal E, Bordenstein SR. Gut microbial ecology of lizards: insights into diversity in the wild, effects of captivity, variation across gut regions and transmission. Mol Ecol 2016; 26:1175-1189. [PMID: 27862531 DOI: 10.1111/mec.13921] [Citation(s) in RCA: 116] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 10/24/2016] [Accepted: 11/01/2016] [Indexed: 12/13/2022]
Abstract
Animals maintain complex associations with a diverse microbiota living in their guts. Our understanding of the ecology of these associations is extremely limited in reptiles. Here, we report an in-depth study into the microbial ecology of gut communities in three syntopic and viviparous lizard species (two omnivores: Liolaemus parvus and Liolaemus ruibali and an herbivore: Phymaturus williamsi). Using 16S rRNA gene sequencing to inventory various bacterial communities, we elucidate four major findings: (i) closely related lizard species harbour distinct gut bacterial microbiota that remain distinguishable in captivity; a considerable portion of gut bacterial diversity (39.1%) in nature overlap with that found on plant material, (ii) captivity changes bacterial community composition, although host-specific communities are retained, (iii) faecal samples are largely representative of the hindgut bacterial community and thus represent acceptable sources for nondestructive sampling, and (iv) lizards born in captivity and separated from their mothers within 24 h shared 34.3% of their gut bacterial diversity with their mothers, suggestive of maternal or environmental transmission. Each of these findings represents the first time such a topic has been investigated in lizard hosts. Taken together, our findings provide a foundation for comparative analyses of the faecal and gastrointestinal microbiota of reptile hosts.
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Affiliation(s)
- Kevin D Kohl
- Department of Biological Sciences, Vanderbilt University, 465 21st Ave South, Nashville, TN, 37235, USA.,Laboratorio de Biología Integrativa, Instituto Multidisciplinario de Investigaciones Biológicas de San Luis, Consejo Nacional de Investigaciones Científicas y Técnicas, San Luis, 5700, Argentina.,Departamento de Bioquímica y Ciencias Biológicas, Universidad Nacional de San Luis, Chacabuco 917, San Luis, 5700, Argentina
| | - Antonio Brun
- Laboratorio de Biología Integrativa, Instituto Multidisciplinario de Investigaciones Biológicas de San Luis, Consejo Nacional de Investigaciones Científicas y Técnicas, San Luis, 5700, Argentina.,Departamento de Bioquímica y Ciencias Biológicas, Universidad Nacional de San Luis, Chacabuco 917, San Luis, 5700, Argentina
| | - Melisa Magallanes
- Laboratorio de Biología Integrativa, Instituto Multidisciplinario de Investigaciones Biológicas de San Luis, Consejo Nacional de Investigaciones Científicas y Técnicas, San Luis, 5700, Argentina.,Departamento de Bioquímica y Ciencias Biológicas, Universidad Nacional de San Luis, Chacabuco 917, San Luis, 5700, Argentina
| | - Joshua Brinkerhoff
- Laboratorio de Biología Integrativa, Instituto Multidisciplinario de Investigaciones Biológicas de San Luis, Consejo Nacional de Investigaciones Científicas y Técnicas, San Luis, 5700, Argentina.,Departamento de Bioquímica y Ciencias Biológicas, Universidad Nacional de San Luis, Chacabuco 917, San Luis, 5700, Argentina
| | - Alejandro Laspiur
- Centro de Investigaciones de la Geósfera y la Biósfera (CIGEOBIO-CONICET) - Departamento de Biología, Facultad de Ciencias Exactas, Físicas y Naturales, Universidad Nacional de San Juan, Av. José I. de la Roza 590 Oeste, J5402DCS, San Juan, Argentina
| | - Juan Carlos Acosta
- Centro de Investigaciones de la Geósfera y la Biósfera (CIGEOBIO-CONICET) - Departamento de Biología, Facultad de Ciencias Exactas, Físicas y Naturales, Universidad Nacional de San Juan, Av. José I. de la Roza 590 Oeste, J5402DCS, San Juan, Argentina
| | - Enrique Caviedes-Vidal
- Laboratorio de Biología Integrativa, Instituto Multidisciplinario de Investigaciones Biológicas de San Luis, Consejo Nacional de Investigaciones Científicas y Técnicas, San Luis, 5700, Argentina.,Departamento de Bioquímica y Ciencias Biológicas, Universidad Nacional de San Luis, Chacabuco 917, San Luis, 5700, Argentina
| | - Seth R Bordenstein
- Department of Biological Sciences, Vanderbilt University, 465 21st Ave South, Nashville, TN, 37235, USA.,Department of Pathology, Microbiology, and Immunology, Vanderbilt University, 465 21st Ave South, Nashville, TN, 37235, USA
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38
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Ren T, Kahrl AF, Wu M, Cox RM. Does adaptive radiation of a host lineage promote ecological diversity of its bacterial communities? A test using gut microbiota of Anolis lizards. Mol Ecol 2016; 25:4793-804. [PMID: 27497270 DOI: 10.1111/mec.13796] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 07/08/2016] [Accepted: 07/11/2016] [Indexed: 12/22/2022]
Abstract
Adaptive radiations provide unique opportunities to test whether and how recent ecological and evolutionary diversification of host species structures the composition of entire bacterial communities. We used 16S rRNA gene sequencing of faecal samples to test for differences in the gut microbiota of six species of Puerto Rican Anolis lizards characterized by the evolution of distinct 'ecomorphs' related to differences in habitat use. We found substantial variation in the composition of the microbiota within each species and ecomorph (trunk-crown, trunk-ground, grass-bush), but no differences in bacterial alpha diversity among species or ecomorphs. Beta diversity analyses revealed subtle but significant differences in bacterial composition related to host phylogeny and species, but these differences were not consistently associated with Anolis ecomorph. Comparison of a trunk-ground species from this clade (A. cristatellus) with a distantly related member of the same ecomorph class (A. sagrei) where the two species have been introduced and are now sympatric in Florida revealed pronounced differences in the alpha diversity and beta diversity of their microbiota despite their ecological similarity. Comparisons of these populations with allopatric conspecifics also revealed geographic differences in bacterial alpha diversity and beta diversity within each species. Finally, we observed high intraindividual variation over time and strong effects of a simplified laboratory diet on the microbiota of A. sagrei. Collectively, our results indicate that bacterial communities are only weakly shaped by the diversification of their lizard hosts due to the strikingly high levels of bacterial diversity and variation observed within Anolis species.
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Affiliation(s)
- Tiantian Ren
- Department of Biology, University of Virginia, PO Box 400328, Charlottesville, VA, 22904, USA
| | - Ariel F Kahrl
- Department of Biology, University of Virginia, PO Box 400328, Charlottesville, VA, 22904, USA
| | - Martin Wu
- Department of Biology, University of Virginia, PO Box 400328, Charlottesville, VA, 22904, USA
| | - Robert M Cox
- Department of Biology, University of Virginia, PO Box 400328, Charlottesville, VA, 22904, USA.
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39
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Colston TJ, Jackson CR. Microbiome evolution along divergent branches of the vertebrate tree of life: what is known and unknown. Mol Ecol 2016; 25:3776-800. [DOI: 10.1111/mec.13730] [Citation(s) in RCA: 223] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Revised: 05/25/2016] [Accepted: 05/30/2016] [Indexed: 02/06/2023]
Affiliation(s)
- Timothy J. Colston
- Department of Biology The University of Mississippi University MS 38677 USA
| | - Colin R. Jackson
- Department of Biology The University of Mississippi University MS 38677 USA
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40
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Burns AR, Stephens WZ, Stagaman K, Wong S, Rawls JF, Guillemin K, Bohannan BJM. Contribution of neutral processes to the assembly of gut microbial communities in the zebrafish over host development. THE ISME JOURNAL 2016; 10:655-64. [PMID: 26296066 PMCID: PMC4817674 DOI: 10.1038/ismej.2015.142] [Citation(s) in RCA: 413] [Impact Index Per Article: 51.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Revised: 06/19/2015] [Accepted: 07/05/2015] [Indexed: 01/22/2023]
Abstract
Despite their importance to host health and development, the communities of microorganisms associated with humans and other animals are characterized by a large degree of unexplained variation across individual hosts. The processes that drive such inter-individual variation are not well understood. To address this, we surveyed the microbial communities associated with the intestine of the zebrafish, Danio rerio, over developmental time. We compared our observations of community composition and distribution across hosts with that predicted by a neutral assembly model, which assumes that community assembly is driven solely by chance and dispersal. We found that as hosts develop from larvae to adults, the fit of the model to observed microbial distributions decreases, suggesting that the relative importance of non-neutral processes, such as microbe-microbe interactions, active dispersal, or selection by the host, increases as hosts mature. We also observed that taxa which depart in their distributions from the neutral prediction form ecologically distinct sub-groups, which are phylogenetically clustered with respect to the full metacommunity. These results demonstrate that neutral processes are sufficient to generate substantial variation in microbiota composition across individual hosts, and suggest that potentially unique or important taxa may be identified by their divergence from neutral distributions.
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Affiliation(s)
- Adam R Burns
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
| | - W Zac Stephens
- Department of Pathology, University of Utah, Salt Lake City, UT, USA
| | - Keaton Stagaman
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
| | - Sandi Wong
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - John F Rawls
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA
| | - Karen Guillemin
- Institute of Molecular Biology, University of Oregon, Eugene, OR, USA
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41
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Habitat fragmentation is associated to gut microbiota diversity of an endangered primate: implications for conservation. Sci Rep 2015; 5:14862. [PMID: 26445280 PMCID: PMC4595646 DOI: 10.1038/srep14862] [Citation(s) in RCA: 130] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 09/07/2015] [Indexed: 02/08/2023] Open
Abstract
The expansion of agriculture is shrinking pristine forest areas worldwide, jeopardizing the persistence of their wild inhabitants. The Udzungwa red colobus monkey (Procolobus gordonorum) is among the most threatened primate species in Africa. Primarily arboreal and highly sensitive to hunting and habitat destruction, they provide a critical model to understanding whether anthropogenic disturbance impacts gut microbiota diversity. We sampled seven social groups inhabiting two forests (disturbed vs. undisturbed) in the Udzungwa Mountains of Tanzania. While Ruminococcaceae and Lachnospiraceae dominated in all individuals, reflecting their role in extracting energy from folivorous diets, analysis of genus composition showed a marked diversification across habitats, with gut microbiota α-diversity significantly higher in the undisturbed forest. Functional analysis suggests that such variation may be associated with food plant diversity in natural versus human-modified habitats, requiring metabolic pathways to digest xenobiotics. Thus, the effects of changes in gut microbiota should not be ignored to conserve endangered populations.
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42
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Gut Microbiota Dynamics during Dietary Shift in Eastern African Cichlid Fishes. PLoS One 2015; 10:e0127462. [PMID: 25978452 PMCID: PMC4433246 DOI: 10.1371/journal.pone.0127462] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 04/15/2015] [Indexed: 12/20/2022] Open
Abstract
The gut microbiota structure reflects both a host phylogenetic history and a signature of adaptation to the host ecological, mainly trophic niches. African cichlid fishes, with their array of closely related species that underwent a rapid dietary niche radiation, offer a particularly interesting system to explore the relative contribution of these two factors in nature. Here we surveyed the host intra- and interspecific natural variation of the gut microbiota of five cichlid species from the monophyletic tribe Perissodini of lake Tanganyika, whose members transitioned from being zooplanktivorous to feeding primarily on fish scales. The outgroup riverine species Astatotilapia burtoni, largely omnivorous, was also included in the study. Fusobacteria, Firmicutes and Proteobacteria represented the dominant components in the gut microbiota of all 30 specimens analysed according to two distinct 16S rRNA markers. All members of the Perissodini tribe showed a homogenous pattern of microbial alpha and beta diversities, with no significant qualitative differences, despite changes in diet. The recent diet shift between zooplantkon- and scale-eaters simply reflects on a significant enrichment of Clostridium taxa in scale-eaters where they might be involved in the scale metabolism. Comparison with the omnivorous species A. burtoni suggests that, with increased host phylogenetic distance and/or increasing herbivory, the gut microbiota begins differentiating also at qualitative level. The cichlids show presence of a large conserved core of taxa and a small set of core OTUs (average 13–15%), remarkably stable also in captivity, and putatively favoured by both restricted microbial transmission among related hosts (putatively enhanced by mouthbrooding behavior) and common host constraints. This study sets the basis for a future large-scale investigation of the gut microbiota of cichlids and its adaptation in the process of the host adaptive radiation.
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43
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Yuan ML, Dean SH, Longo AV, Rothermel BB, Tuberville TD, Zamudio KR. Kinship, inbreeding and fine-scale spatial structure influence gut microbiota in a hindgut-fermenting tortoise. Mol Ecol 2015; 24:2521-36. [PMID: 25809385 DOI: 10.1111/mec.13169] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Revised: 03/11/2015] [Accepted: 03/19/2015] [Indexed: 12/12/2022]
Abstract
Herbivorous vertebrates rely on complex communities of mutualistic gut bacteria to facilitate the digestion of celluloses and hemicelluloses. Gut microbes are often convergent based on diet and gut morphology across a phylogenetically diverse group of mammals. However, little is known about microbial communities of herbivorous hindgut-fermenting reptiles. Here, we investigate how factors at the individual level might constrain the composition of gut microbes in an obligate herbivorous reptile. Using multiplexed 16S rRNA gene sequencing, we characterized the faecal microbial community of a population of gopher tortoises (Gopherus polyphemus) and examined how age, genetic diversity, spatial structure and kinship influence differences among individuals. We recovered phylotypes associated with known cellulolytic function, including candidate phylum Termite Group 3, suggesting their importance for gopher tortoise digestion. Although host genetic structure did not explain variation in microbial composition and community structure, we found that fine-scale spatial structure, inbreeding, degree of relatedness and possibly ontogeny shaped patterns of diversity in faecal microbiomes of gopher tortoises. Our findings corroborate widespread convergence of faecal-associated microbes based on gut morphology and diet and demonstrate the role of spatial and demographic structure in driving differentiation of gut microbiota in natural populations.
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Affiliation(s)
- Michael L Yuan
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14853-2701, USA; Archbold Biological Station, Venus, FL, 33960, USA
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Keenan SW, Elsey RM. The Good, the Bad, and the Unknown: Microbial Symbioses of the American Alligator. Integr Comp Biol 2015; 55:972-85. [DOI: 10.1093/icb/icv006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
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45
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Application of a neutral community model to assess structuring of the human lung microbiome. mBio 2015. [PMID: 25604788 DOI: 10.1128/mbio.02 284-14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
UNLABELLED DNA from phylogenetically diverse microbes is routinely recovered from healthy human lungs and used to define the lung microbiome. The proportion of this DNA originating from microbes adapted to the lungs, as opposed to microbes dispersing to the lungs from other body sites and the atmosphere, is not known. We use a neutral model of community ecology to distinguish members of the lung microbiome whose presence is consistent with dispersal from other body sites and those that deviate from the model, suggesting a competitive advantage to these microbes in the lungs. We find that the composition of the healthy lung microbiome is consistent with predictions of the neutral model, reflecting the overriding role of dispersal of microbes from the oral cavity in shaping the microbial community in healthy lungs. In contrast, the microbiome of diseased lungs was readily distinguished as being under active selection. We also assessed the viability of microbes from lung samples by cultivation with a variety of media and incubation conditions. Bacteria recovered by cultivation from healthy lungs represented species that comprised 61% of the 16S rRNA-encoding gene sequences derived from bronchoalveolar lavage samples. IMPORTANCE Neutral distribution of microbes is a distinguishing feature of the microbiome in healthy lungs, wherein constant dispersal of bacteria from the oral cavity overrides differential growth of bacteria. No bacterial species consistently deviated from the model predictions in healthy lungs, although representatives of many of the dispersed species were readily cultivated. In contrast, bacterial populations in diseased lungs were identified as being under active selection. Quantification of the relative importance of selection and neutral processes such as dispersal in shaping the healthy lung microbiome is a first step toward understanding its impacts on host health.
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Abstract
UNLABELLED DNA from phylogenetically diverse microbes is routinely recovered from healthy human lungs and used to define the lung microbiome. The proportion of this DNA originating from microbes adapted to the lungs, as opposed to microbes dispersing to the lungs from other body sites and the atmosphere, is not known. We use a neutral model of community ecology to distinguish members of the lung microbiome whose presence is consistent with dispersal from other body sites and those that deviate from the model, suggesting a competitive advantage to these microbes in the lungs. We find that the composition of the healthy lung microbiome is consistent with predictions of the neutral model, reflecting the overriding role of dispersal of microbes from the oral cavity in shaping the microbial community in healthy lungs. In contrast, the microbiome of diseased lungs was readily distinguished as being under active selection. We also assessed the viability of microbes from lung samples by cultivation with a variety of media and incubation conditions. Bacteria recovered by cultivation from healthy lungs represented species that comprised 61% of the 16S rRNA-encoding gene sequences derived from bronchoalveolar lavage samples. IMPORTANCE Neutral distribution of microbes is a distinguishing feature of the microbiome in healthy lungs, wherein constant dispersal of bacteria from the oral cavity overrides differential growth of bacteria. No bacterial species consistently deviated from the model predictions in healthy lungs, although representatives of many of the dispersed species were readily cultivated. In contrast, bacterial populations in diseased lungs were identified as being under active selection. Quantification of the relative importance of selection and neutral processes such as dispersal in shaping the healthy lung microbiome is a first step toward understanding its impacts on host health.
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Abstract
Recent research has expanded our understanding of microbial community assembly. However, the field of community ecology is inaccessible to many microbial ecologists because of inconsistent and often confusing terminology as well as unnecessarily polarizing debates. Thus, we review recent literature on microbial community assembly, using the framework of Vellend (Q. Rev. Biol. 85:183-206, 2010) in an effort to synthesize and unify these contributions. We begin by discussing patterns in microbial biogeography and then describe four basic processes (diversification, dispersal, selection, and drift) that contribute to community assembly. We also discuss different combinations of these processes and where and when they may be most important for shaping microbial communities. The spatial and temporal scales of microbial community assembly are also discussed in relation to assembly processes. Throughout this review paper, we highlight differences between microbes and macroorganisms and generate hypotheses describing how these differences may be important for community assembly. We end by discussing the implications of microbial assembly processes for ecosystem function and biodiversity.
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Giessler S, Wolinska J. Capturing the population structure of microparasites: using ITS-sequence data and a pooled DNA approach. Mol Ecol Resour 2014; 13:918-28. [PMID: 23937576 DOI: 10.1111/1755-0998.12144] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2012] [Revised: 05/23/2013] [Accepted: 06/18/2013] [Indexed: 11/28/2022]
Abstract
The internal transcribed spacer (ITS) region of nuclear ribosomal DNA is a common marker not only for the molecular identification of different taxa and strains, but also for the analysis of population structure of wild microparasite communities. Importantly, the multicopy nature of this region allows the amplification of low-quantity samples of the target DNA, a common problem in studies on unicellular, unculturable microparasites. We analysed ITS sequences from the protozoan parasite Caullerya mesnili (class Ichthyosporea) infecting waterflea (Daphnia) hosts, across several host population samples. We showed that analysing representative ITS-types [as identified by statistical parsimony network analysis (SPN)] is a suitable method to address relevant polymorphism. The spatial patterns were consistent regardless of whether parasite DNA was extracted from individual hosts or pooled host samples. Remarkably, the efficiency in detecting different sequence types was even higher after sample pooling. As shown by simulations, an easily manageable number of sequences from pooled DNA samples are sufficient to resolve the spatial population structure in this system. In summary, the ITS region analysed from pooled DNA samples can provide valuable insights into the spatial and temporal dynamics of microparasites. Moreover, the application of SPN analysis is a good alternative to the well-established neighbour-joining method (NJ) for the identification of representative ITS-types. SPN can even outperform NJ by joining most of the singleton sequences to representative sequence clusters.
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Affiliation(s)
- Sabine Giessler
- Department of Biology II, Ludwig-Maximilians-University Munich, Grosshaderner Str. 2, 82152, Planegg-Martinsried, Germany.
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Delsuc F, Metcalf JL, Wegener Parfrey L, Song SJ, González A, Knight R. Convergence of gut microbiomes in myrmecophagous mammals. Mol Ecol 2013; 23:1301-1317. [PMID: 24118574 DOI: 10.1111/mec.12501] [Citation(s) in RCA: 204] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2013] [Revised: 08/14/2013] [Accepted: 08/15/2013] [Indexed: 12/19/2022]
Abstract
Mammals have diversified into many dietary niches. Specialized myrmecophagous (ant- and termite-eating) placental mammals represent a textbook example of evolutionary convergence driven by extreme diet specialization. Armadillos, anteaters, aardvarks, pangolins and aardwolves thus provide a model system for understanding the potential role of gut microbiota in the convergent adaptation to myrmecophagy. Here, we expand upon previous mammalian gut microbiome studies by using high-throughput barcoded Illumina sequencing of the 16S rRNA gene to characterize the composition of gut microbiota in 15 species representing all placental myrmecophagous lineages and their close relatives from zoo- and field-collected samples. We confirm that both diet and phylogeny drive the evolution of mammalian gut microbiota, with cases of convergence in global composition, but also examples of phylogenetic inertia. Our results reveal specialized placental myrmecophages as a spectacular case of large-scale convergence in gut microbiome composition. Indeed, neighbour-net networks and beta-diversity plots based on UniFrac distances show significant clustering of myrmecophagous species (anteaters, aardvarks and aardwolves), even though they belong to phylogenetically distant lineages representing different orders. The aardwolf, which diverged from carnivorous hyenas only in the last 10 million years, experienced a convergent shift in the composition of its gut microbiome to become more similar to other myrmecophages. These results confirm diet adaptation to be a major driving factor of convergence in gut microbiome composition over evolutionary timescales. This study sets the scene for future metagenomic studies aiming at evaluating potential convergence in functional gene content in the microbiomes of specialized mammalian myrmecophages.
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Affiliation(s)
- Frédéric Delsuc
- Institut des Sciences de l'Evolution, UMR 5554-CNRS-IRD, Université Montpellier 2, Montpellier, France; Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO, 80309, USA; Biofrontiers Institute, University of Colorado, Boulder, CO, 80309, USA
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Linnenbrink M, Wang J, Hardouin EA, Künzel S, Metzler D, Baines JF. The role of biogeography in shaping diversity of the intestinal microbiota in house mice. Mol Ecol 2013; 22:1904-16. [PMID: 23398547 DOI: 10.1111/mec.12206] [Citation(s) in RCA: 138] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2012] [Revised: 12/06/2012] [Accepted: 12/11/2012] [Indexed: 12/17/2022]
Abstract
The microbial communities inhabiting the mammalian intestinal tract play an important role in diverse aspects of host biology. However, little is known regarding the forces shaping variation in these communities and their influence on host fitness. To shed light on the contributions of host genetics, transmission and geography to diversity in microbial communities between individuals, we performed a survey of intestinal microbial communities in a panel of 121 house mice derived from eight locations across Western Europe using pyrosequencing of the bacterial 16S rRNA gene. The host factors studied included population structure estimated by microsatellite loci and mitochondrial DNA, genetic distance and geography. To determine whether host tissue (mucosa)-associated communities display properties distinct from those of the lumen, both the caecal mucosa and contents were examined. We identified Bacteroides, Robinsoniella and Helicobacter as the most abundant genera in both the caecal content and mucosa-associated communities of wild house mice. Overall, we found geography to be the most significant factor explaining patterns of diversity in the intestinal microbiota, with a comparatively weaker influence of host population structure and genetic distance. Furthermore, the influence of host genetic distance was limited to the mucosa communities, consistent with this environment being more intimately coupled to the host.
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