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Poquérusse J, Brown CL, Gaillard C, Doughty C, Dalén L, Gallagher AJ, Wooller M, Zimov N, Church GM, Lamm B, Hysolli E. Assessing contemporary Arctic habitat availability for a woolly mammoth proxy. Sci Rep 2024; 14:9804. [PMID: 38684726 PMCID: PMC11058768 DOI: 10.1038/s41598-024-60442-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 04/23/2024] [Indexed: 05/02/2024] Open
Abstract
Interest continues to grow in Arctic megafaunal ecological engineering, but, since the mass extinction of megafauna ~ 12-15 ka, key physiographic variables and available forage continue to change. Here we sought to assess the extent to which contemporary Arctic ecosystems are conducive to the rewilding of megaherbivores, using a woolly mammoth (M. primigenius) proxy as a model species. We first perform a literature review on woolly mammoth dietary habits. We then leverage Oak Ridge National Laboratories Distributive Active Archive Center Global Aboveground and Belowground Biomass Carbon Density Maps to generate aboveground biomass carbon density estimates in plant functional types consumed by the woolly mammoth at 300 m resolution on Alaska's North Slope. We supplement these analyses with a NASA Arctic Boreal Vulnerability Experiment dataset to downgrade overall biomass estimates to digestible levels. We further downgrade available forage by using a conversion factor representing the relationship between total biomass and net primary productivity (NPP) for arctic vegetation types. Integrating these estimates with the forage needs of woolly mammoths, we conservatively estimate Alaska's North Slope could support densities of 0.0-0.38 woolly mammoth km-2 (mean 0.13) across a variety of habitats. These results may inform innovative rewilding strategies.
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Affiliation(s)
| | | | - Camille Gaillard
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Chris Doughty
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Love Dalén
- Department of Zoology, Stockholm University, Stockholm, Sweden
- Centre for Palaeogenetics, Svante Arrhenius Väg 20C, Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | | | - Matthew Wooller
- College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, Fairbanks, AK, 99775, USA
| | - Nikita Zimov
- North-East Science Station, Pacific Institute of Geography, Russian Academy of Sciences, Chersky, Russia
| | - George M Church
- Colossal Biosciences Inc, Austin, TX, 78701, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Harvard-MIT Program in Health Sciences and Technology, Cambridge, MA, 02139, USA
| | - Ben Lamm
- Colossal Biosciences Inc, Austin, TX, 78701, USA.
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2
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Kamenova S, de Muinck EJ, Veiberg V, Utsi TA, Steyaert SMJG, Albon SD, Loe LE, Trosvik P. Gut microbiome biogeography in reindeer supersedes millennia of ecological and evolutionary separation. FEMS Microbiol Ecol 2023; 99:fiad157. [PMID: 38031339 DOI: 10.1093/femsec/fiad157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 10/17/2023] [Accepted: 11/28/2023] [Indexed: 12/01/2023] Open
Abstract
Ruminants are dependent on their gut microbiomes for nutrient extraction from plant diets. However, knowledge about the composition, diversity, function, and spatial structure of gut microbiomes, especially in wild ruminants, is limited, largely because analysis has been restricted to faeces or the rumen. In two geographically separated reindeer subspecies, 16S rRNA gene amplicon sequencing revealed strong spatial structuring, and pronounced differences in microbial diversity of at least 33 phyla across the stomach, small intestine, and large intestine (including faeces). The main structural feature was the Bacteroidota to Firmicutes ratio, which declined from the stomach to the large intestine, likely reflecting functional adaptation. Metagenome shotgun sequencing also revealed highly significant structuring in the relative occurrence of carbohydrate-active enzymes (CAZymes). CAZymes were enriched in the rumen relative to the small and large intestines. Interestingly, taxonomic diversity was highest in the large intestine, suggesting an important and understudied role for this organ. Despite the two study populations being separated by an ocean and six millennia of evolutionary history, gut microbiome structuring was remarkably consistent. Our study suggests a strong selection for gut microbiome biogeography along the gastrointestinal tract in reindeer subspecies.
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Affiliation(s)
- Stefaniya Kamenova
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, 0371 Oslo, Norway
- Departments of Ecology and Natural Resource Management, Norwegian University of Life Sciences, 1433 Ås, Norway
- National Museum of Natural History, Bulgarian Academy of Sciences, 1000 Sofia, Bulgaria
| | - Eric J de Muinck
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, 0371 Oslo, Norway
- Department of Pharmacy, University of Oslo, 0371 Oslo, Norway
| | - Vebjørn Veiberg
- Norwegian Institute for Nature Research, 7034 Trondheim, Norway
| | - Tove Aagnes Utsi
- Department of Arctic and Marine Biology, Faculty of Biosciences, Fisheries, and Economics, UiT The Arctic University of Norway, 9510 Alta, Norway
| | - Sam M J G Steyaert
- Faculty of Biosciences and Aquaculture, Nord University, 7713 Steinkjer, Norway
| | - Steve D Albon
- The James Hutton Institute, Craigiebuckler, Aberdeen AB15 8QH, United Kingdom
| | - Leif Egil Loe
- Departments of Ecology and Natural Resource Management, Norwegian University of Life Sciences, 1433 Ås, Norway
| | - Pål Trosvik
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, 0371 Oslo, Norway
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3
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Du T, Li P, Niu Q, Pu G, Wang B, Liu G, Li P, Niu P, Zhang Z, Wu C, Hou L, Hedemann MS, Zhao Q, Huang R. Effects of Varying Levels of Wheat Bran Dietary Fiber on Growth Performance, Fiber Digestibility and Gut Microbiota in Erhualian and Large White Pigs. Microorganisms 2023; 11:2474. [PMID: 37894132 PMCID: PMC10609096 DOI: 10.3390/microorganisms11102474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 09/28/2023] [Accepted: 09/29/2023] [Indexed: 10/29/2023] Open
Abstract
To evaluate the tolerance of a high-fiber diet in Erhualian pigs (Er-HL), the present investigation systematically investigated the ramifications of varying wheat bran fiber levels, specified as total dietary fiber (TDF) values of 14.07%, 16.32%, 17.99%, and 18.85%, on growth performance, fiber digestibility and gut microbiota in Er-HL, large Large White pigs (L-LW, the same physiological stage as the Er-HL) and small Large White pigs (S-LW, the same body weight as the Er-HL). Our results revealed that fiber levels exerted no discernable impact on growth performance (average daily feed intake (ADFI), and average daily gain (ADG)) of Er-HL (p > 0.05). Conversely, L-LW exhibited a decrease in ADFI and ADG with increasing fiber levels (p < 0.05). Notably, the apparent total tract digestibility (ATTD) of various fiber components, including neutral detergent fiber (NDF), acid detergent fiber (ADF), hemicellulose, TDF and insoluble dietary fiber (IDF), in Er-HL were significantly higher than those in S-LW and L-LW irrespective of diets (p < 0.05). The ATTD of cellulose and hemicellulose in Er-HL significantly decreased with increasing fiber levels (p < 0.05), yet remained statistically indifferent when comparing the 7%-wheat-bran-replaced diet (7% WRB, TDF 16.32%) to the basal diet (TDF 14.07%) (p > 0.05). The cecal microbiota of Er-HL had higher richness estimators (Chao1 and ACE) than those of S-LW and L-LW irrespective of diets (p < 0.01). Breed serves as a pivotal determinant in shaping swine gut microbiota. Thirteen genera were selected as the key bacteria related to high fiber digestibility of Er-HL. Further functional examination of these key genera elucidated an enrichment of pathways pertinent to carbohydrate metabolism in Er-HL samples compared with S-LW and L-LW samples. In summary, Er-HL exhibited high-fiber tolerance both in terms of growth performance and fiber digestibility compared with Large White pigs. Specifically, the ATTD of NDF, ADF, hemicellulose, IDF and TDF were significantly higher in Er-HL compared with L-LW and S-LW, irrespective of diets. Fiber level exerted no discernable impact on growth performance (ADFI, ADG) and the ATTD of fiber (NDF, ADF, IDF and TDF) in Er-HL. The optimum fiber level of the Er-HL was identified as 7% WRB (TDF 16.32%). Thirteen genera were ascertained to significantly contribute to high fiber digestibility of Er-HL, correlating with an enhancement of carbohydrate metabolism pathways.
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Affiliation(s)
- Taoran Du
- Key Laboratory of Evaluation and Utilization of Livestock and Poultry Resources (Pig) of Ministry of Agriculture and Rural Affairs, Institute of Swine Science, College of Animal Science & Technology, Nanjing Agricultural University, Nanjing 210095, China; (T.D.); (P.L.)
| | - Pinghua Li
- Key Laboratory of Evaluation and Utilization of Livestock and Poultry Resources (Pig) of Ministry of Agriculture and Rural Affairs, Institute of Swine Science, College of Animal Science & Technology, Nanjing Agricultural University, Nanjing 210095, China; (T.D.); (P.L.)
- Huaian Academy, Nanjing Agricultural University, Huaian 223005, China
| | - Qing Niu
- Key Laboratory of Evaluation and Utilization of Livestock and Poultry Resources (Pig) of Ministry of Agriculture and Rural Affairs, Institute of Swine Science, College of Animal Science & Technology, Nanjing Agricultural University, Nanjing 210095, China; (T.D.); (P.L.)
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Guang Pu
- Key Laboratory of Evaluation and Utilization of Livestock and Poultry Resources (Pig) of Ministry of Agriculture and Rural Affairs, Institute of Swine Science, College of Animal Science & Technology, Nanjing Agricultural University, Nanjing 210095, China; (T.D.); (P.L.)
| | - Binbin Wang
- Key Laboratory of Evaluation and Utilization of Livestock and Poultry Resources (Pig) of Ministry of Agriculture and Rural Affairs, Institute of Swine Science, College of Animal Science & Technology, Nanjing Agricultural University, Nanjing 210095, China; (T.D.); (P.L.)
| | - Gensheng Liu
- Key Laboratory of Evaluation and Utilization of Livestock and Poultry Resources (Pig) of Ministry of Agriculture and Rural Affairs, Institute of Swine Science, College of Animal Science & Technology, Nanjing Agricultural University, Nanjing 210095, China; (T.D.); (P.L.)
| | - Pinghui Li
- Key Laboratory of Evaluation and Utilization of Livestock and Poultry Resources (Pig) of Ministry of Agriculture and Rural Affairs, Institute of Swine Science, College of Animal Science & Technology, Nanjing Agricultural University, Nanjing 210095, China; (T.D.); (P.L.)
| | - Peipei Niu
- Huaian Academy, Nanjing Agricultural University, Huaian 223005, China
| | - Zongping Zhang
- Huaian Academy, Nanjing Agricultural University, Huaian 223005, China
| | - Chengwu Wu
- Huaian Academy, Nanjing Agricultural University, Huaian 223005, China
| | - Liming Hou
- Key Laboratory of Evaluation and Utilization of Livestock and Poultry Resources (Pig) of Ministry of Agriculture and Rural Affairs, Institute of Swine Science, College of Animal Science & Technology, Nanjing Agricultural University, Nanjing 210095, China; (T.D.); (P.L.)
- Huaian Academy, Nanjing Agricultural University, Huaian 223005, China
| | | | - Qingbo Zhao
- Key Laboratory of Evaluation and Utilization of Livestock and Poultry Resources (Pig) of Ministry of Agriculture and Rural Affairs, Institute of Swine Science, College of Animal Science & Technology, Nanjing Agricultural University, Nanjing 210095, China; (T.D.); (P.L.)
| | - Ruihua Huang
- Key Laboratory of Evaluation and Utilization of Livestock and Poultry Resources (Pig) of Ministry of Agriculture and Rural Affairs, Institute of Swine Science, College of Animal Science & Technology, Nanjing Agricultural University, Nanjing 210095, China; (T.D.); (P.L.)
- Huaian Academy, Nanjing Agricultural University, Huaian 223005, China
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4
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Prewer E, Vilaça ST, Bird S, Kutz S, Leclerc L, Kyle CJ. Metabarcoding of fecal pellets in wild muskox populations reveals negative relationships between microbiome and diet alpha diversity. Ecol Evol 2023; 13:e10192. [PMID: 37325724 PMCID: PMC10261903 DOI: 10.1002/ece3.10192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 05/24/2023] [Accepted: 06/01/2023] [Indexed: 06/17/2023] Open
Abstract
Microbiome diversity and diet composition concomitantly influence species health, fitness, immunity, and digestion. In environments where diet varies spatially and temporally, microbiome plasticity may promote rapid host adaptation to available resources. For northern ungulates in particular, metabarcoding of noninvasively collected fecal pellets presents unprecedented insights into their diverse ecological requirements and niches by clarifying the interrelationships of microbiomes, key to deriving nutrients, in context of altered forage availability in changing climates. Muskoxen (Ovibos moschatus) are Arctic-adapted species that experience fluctuating qualities and quantities of vegetation. Geography and seasonality have been noted to influence microbiome composition and diversity in muskoxen, yet it is unclear how their microbiomes intersect with diet. Following observations from other species, we hypothesized increasing diet diversity would result in higher microbiome diversity in muskoxen. We assessed diet composition in muskoxen using three common plant metabarcoding markers and explored correlations with microbiome data. Patterns of dietary diversity and composition were not fully concordant among the markers used, yet all reflected the primary consumption of willows and sedges. Individuals with similar diets had more similar microbiomes, yet in contrast to most literature, yielded negative relationships between microbiome and diet alpha diversity. This negative correlation may reflect the unique capacities of muskoxen to survive solely on high-fiber Arctic forage and provide insight into their resiliency to exploit changing dietary resources in a rapidly warming Arctic altering vegetation diversity.
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Affiliation(s)
- Erin Prewer
- Environmental and Life Sciences Graduate ProgramTrent UniversityPeterboroughOntarioCanada
| | - Sibelle T. Vilaça
- Environmental and Life Sciences Graduate ProgramTrent UniversityPeterboroughOntarioCanada
| | - Samantha Bird
- Forensic Science DepartmentTrent UniversityPeterboroughOntarioCanada
| | - Susan Kutz
- Department of Ecosystem and Public Health, Faculty of Veterinary MedicineUniversity of CalgaryCalgaryAlbertaCanada
| | | | - Christopher J. Kyle
- Environmental and Life Sciences Graduate ProgramTrent UniversityPeterboroughOntarioCanada
- Forensic Science DepartmentTrent UniversityPeterboroughOntarioCanada
- Natural Resources DNA Profiling and Forensic CentrePeterboroughOntarioCanada
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5
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Liu H, Li Z, Pei C, Degen A, Hao L, Cao X, Liu H, Zhou J, Long R. A comparison between yaks and Qaidam cattle in in vitro rumen fermentation, methane emission, and bacterial community composition with poor quality substrate. Anim Feed Sci Technol 2022. [DOI: 10.1016/j.anifeedsci.2022.115395] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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6
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Aggerbeck MR, Nielsen TK, Mosbacher JB, Schmidt NM, Hansen LH. Muskoxen homogenise soil microbial communities and affect the abundance of methanogens and methanotrophs. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 827:153877. [PMID: 35218841 DOI: 10.1016/j.scitotenv.2022.153877] [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: 12/06/2021] [Revised: 02/09/2022] [Accepted: 02/10/2022] [Indexed: 06/14/2023]
Abstract
Grazing herbivores may affect soil microbial communities indirectly by impacting soil structure and vegetation composition. In high arctic environments, this impact is poorly elucidated, while having potentially wide-reaching effects on the ecosystem. This study examines how a key arctic herbivore, the muskox Ovibos moschatus, affects the soil microbial community in a high arctic fen. Environmental DNA was extracted from soil samples taken from grazed control plots and from muskox exclosures established 5 years prior. We sequenced amplicons of the 16S rRNA gene to provide insight into the microbial communities. We found that in the grazed control plots, microbial communities exhibited high evenness and displayed highly similar overall diversity. In plots where muskoxen had been excluded, microbial diversity was significantly reduced, and had more uneven intra-sample populations and overall lower ecological richness and evenness. We observed that the composition of microbial communities in grazed soils were significantly affected by the presence of muskoxen, as seen by elevated relative abundances of Bacteroides and Firmicutes, two major phyla found in muskox faeces. Furthermore, an increase in relative abundance of bacteria involved in degradation of recalcitrant carbohydrates and cycling of nitrogen was observed in grazed soil. Ungrazed soils displayed increased abundances of bacteria potentially involved in anaerobic oxidation of methane, whereas some methanogens were more abundant in grazed soils. This corroborates a previous finding that methane emissions are higher in arctic fens under muskox grazing. Our results show that the presence of large herbivores stimulates soil microbial diversity and has a homogenizing influence on the inter-species dynamics in soil microbial communities. The findings of this study, thus, improve our understanding of the effect of herbivore grazing on arctic ecosystems and the derived methane cycling.
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Affiliation(s)
| | - Tue Kjærgaard Nielsen
- Department of Plant and Environmental Science, University of Copenhagen, 1871 Copenhagen, Denmark
| | - Jesper Bruun Mosbacher
- Department of Ecoscience, Aarhus University, 4000 Roskilde, Denmark; Arctic Research Centre, Aarhus University, 8000 Aarhus, Denmark
| | - Niels Martin Schmidt
- Department of Ecoscience, Aarhus University, 4000 Roskilde, Denmark; Arctic Research Centre, Aarhus University, 8000 Aarhus, Denmark
| | - Lars Hestbjerg Hansen
- Department of Plant and Environmental Science, University of Copenhagen, 1871 Copenhagen, Denmark.
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7
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Hecker LJ, Edwards MA, Nielsen SE. Assessing the nutritional consequences of switching foraging behavior in wood bison. Ecol Evol 2021; 11:16165-16176. [PMID: 34824819 PMCID: PMC8601871 DOI: 10.1002/ece3.8298] [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: 06/08/2021] [Revised: 10/17/2021] [Accepted: 10/19/2021] [Indexed: 12/02/2022] Open
Abstract
Diet is one of the most common traits used to organize species of animals into niches. For ruminant herbivores, the breadth and uniqueness of their dietary niche are placed on a spectrum from browsers that consume woody (i.e., browse) and herbaceous (i.e., forbs) plants, to grazers with graminoid-rich diets. However, seasonal changes in plant availability and quality can lead to switching of their dietary niche, even within species. In this study, we examined whether a population of wood bison (Bison bison athabascae) in northeast Alberta, Canada, seasonally switched their foraging behavior, and if so, whether this was associated with changes in nutrient acquisition. We hypothesized that bison should switch foraging behaviors from grazing in the winter when standing, dead graminoids are the only foliar plants readily available to browsing during spring and summer as nutritious and digestible foliar parts of browse and forbs become available. If bison are switching foraging strategy to maximize protein consumption, then there should be a corresponding shift in the nutritional niche. Alternatively, if bison are eating different plants, but consuming similar amounts of nutrients, then bison are switching their dietary niche to maintain a particular nutrient composition. We found wood bison were grazers in the winter and spring, but switch to a browsing during summer. However, only winter nutrient consumption of consumed plants differed significantly among seasons. Between spring and summer, bison maintained a specific nutritional composition in their diet despite compositional differences in the consumed plants. Our evidence suggests that bison are selecting plants to maintain a target macronutrient composition. We posit that herbivore's can and will switch their dietary niche to maintain a target nutrient composition.
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Affiliation(s)
- Lee J. Hecker
- University of AlbertaEdmontonAlbertaCanada
- Royal Alberta MuseumEdmontonAlbertaCanada
| | - Mark A. Edwards
- University of AlbertaEdmontonAlbertaCanada
- Royal Alberta MuseumEdmontonAlbertaCanada
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8
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Special Issue: Wildlife Microbiology. Microorganisms 2021; 9:microorganisms9091968. [PMID: 34576861 PMCID: PMC8469691 DOI: 10.3390/microorganisms9091968] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 09/14/2021] [Indexed: 11/25/2022] Open
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9
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Isolation and characterization of anaerobic bacteria with fiber degradation potential from faeces of Boselaphus tragocamelus grazing on semi arid Indian conditions. Arch Microbiol 2021; 203:5105-5116. [PMID: 34304303 DOI: 10.1007/s00203-021-02477-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 06/14/2021] [Accepted: 07/04/2021] [Indexed: 10/20/2022]
Abstract
Hindgut of wild ruminants harbours diversified anaerobic bacteria with promising fiber degrading ability. Fibrolytic enzyme activity is strongly influenced by diet and host species which till date remains unexplored for harnessing their optimum benefits. The present study was conducted to isolate and characterize fiber degrading anaerobic bacteria from faeces of wild blue bull (Boselaphus tragocamelus) inhabiting in semiarid regions. A total of 167 isolates were obtained from 85 faecal samples using M-10 medium, on the basis of clear zones formed on Congo red plates 20 isolates were selected and designated as NLG1-20 for microscopic and biochemical characterization. Further, molecular confirmation was done by PCR analysis with universal 16S rDNA primers. All isolates were obligatory anaerobes except, NLG4, NLG19 and NLG20. Majority of the sugars tested were utilized by most of the isolates except arabinose. Fibrolytic enzyme activities revealed that NLG1 had highest endoglucanase activity, NLG13 had highest exoglucanase activity while NLG8 showed maximum xylanase activity. In case of FPase assay, highest and lowest values were observed in isolate NLG11 (8.96 U/mL) and NLG8 (5.58 U/mL), respectively. Phylogenetic analysis of the isolates revealed a highly diverse group of microbes mainly belonging to the family Paenibacillaceae which have not been previously characterized in ruminants for fiber degradation. Therefore, results obtained in the present study indicated that the screened isolates showed promising fiber degrading potential in terms of filter paper assay and fibrolytic enzyme activity which can be explored further for improving lignocellulose digestibility in ruminants as an additive.
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10
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Rojas CA, Ramírez-Barahona S, Holekamp KE, Theis KR. Host phylogeny and host ecology structure the mammalian gut microbiota at different taxonomic scales. Anim Microbiome 2021; 3:33. [PMID: 33892813 PMCID: PMC8063394 DOI: 10.1186/s42523-021-00094-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 04/04/2021] [Indexed: 12/13/2022] Open
Abstract
The gut microbiota is critical for host function. Among mammals, host phylogenetic relatedness and diet are strong drivers of gut microbiota structure, but one factor may be more influential than the other. Here, we used 16S rRNA gene sequencing to determine the relative contributions of host phylogeny and host diet in structuring the gut microbiotas of 11 herbivore species from 5 families living sympatrically in southwest Kenya. Herbivore species were classified as grazers, browsers, or mixed-feeders and dietary data (% C4 grasses in diet) were compiled from previously published sources. We found that herbivore gut microbiotas were highly species-specific, and that host taxonomy accounted for more variation in the gut microbiota (30%) than did host dietary guild (10%) or sample month (8%). Overall, similarity in the gut microbiota increased with host phylogenetic relatedness (r = 0.74) across the 11 species of herbivores, but among 7 closely related Bovid species, dietary %C4 grass values more strongly predicted gut microbiota structure (r = 0.64). Additionally, within bovids, host dietary guild explained more of the variation in the gut microbiota (17%) than did host species (12%). Lastly, while we found that the gut microbiotas of herbivores residing in southwest Kenya converge with those of distinct populations of conspecifics from central Kenya, fine-scale differences in the abundances of bacterial amplicon sequence variants (ASVs) between individuals from the two regions were also observed. Overall, our findings suggest that host phylogeny and taxonomy strongly structure the gut microbiota across broad host taxonomic scales, but these gut microbiotas can be further modified by host ecology (i.e., diet, geography), especially among closely related host species.
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Affiliation(s)
- Connie A. Rojas
- Department of Integrative Biology, Michigan State University, East Lansing, MI USA
- Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI USA
- BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI USA
| | - Santiago Ramírez-Barahona
- Departament of Botany, Institute of Biology, Universidad Nacional Autónoma de México, Mexico City, MX Mexico
| | - Kay E. Holekamp
- Department of Integrative Biology, Michigan State University, East Lansing, MI USA
- Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI USA
- BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI USA
| | - Kevin R. Theis
- BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI USA
- Department of Biochemistry, Microbiology and Immunology, Wayne State University School of Medicine, Detroit, MI USA
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11
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Barboza PS, Shively RD, Gustine DD, Addison JA. Winter Is Coming: Conserving Body Protein in Female Reindeer, Caribou, and Muskoxen. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00150] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
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12
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Lin D, Lacey EA, Bach BH, Bi K, Conroy CJ, Suvorov A, Bowie RCK. Gut microbial diversity across a contact zone for California voles: Implications for lineage divergence of hosts and mitonuclear mismatch in the assembly of the mammalian gut microbiome. Mol Ecol 2020; 29:1873-1889. [PMID: 32282951 DOI: 10.1111/mec.15443] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Accepted: 03/27/2020] [Indexed: 12/29/2022]
Abstract
Gut microbial diversity is thought to reflect the co-evolution of microbes and their hosts as well as current host-specific attributes such as genetic background and environmental setting. To explore interactions among these parameters, we characterized variation in gut microbiome composition of California voles (Microtus californicus) across a contact zone between two recently diverged lineages of this species. Because this contact zone contains individuals with mismatched mitochondrial-nuclear genomes (cybrids), it provides an important opportunity to explore how different components of the genotype contribute to gut microbial diversity. Analyses of bacterial 16S rRNA sequences and joint species distribution modelling revealed that host genotypes and genetic differentiation among host populations together explained more than 50% of microbial community variation across our sampling transect. The ranked importance (most to least) of factors contributing to gut microbial diversity in our study populations were: genome-wide population differentiation, local environmental conditions, and host genotypes. However, differences in microbial communities among vole populations (β-diversity) did not follow patterns of lineage divergence (i.e., phylosymbiosis). Instead, among-population variation was best explained by the spatial distribution of hosts, as expected if the environment is a primary source of gut microbial diversity (i.e., dispersal limitation hypothesis). Across the contact zone, several bacterial taxa differed in relative abundance between the two parental lineages as well as among individuals with mismatched mitochondrial and nuclear genomes. Thus, genetic divergence among host lineages and mitonuclear genomic mismatches may also contribute to microbial diversity by altering interactions between host genomes and gut microbiota (i.e., hologenome speciation hypothesis).
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Affiliation(s)
- Dana Lin
- Department of Integrative Biology, University of California, Berkeley, CA, USA.,Museum of Vertebrate Zoology, University of California, Berkeley, CA, USA
| | - Eileen A Lacey
- Department of Integrative Biology, University of California, Berkeley, CA, USA.,Museum of Vertebrate Zoology, University of California, Berkeley, CA, USA
| | - Bryan H Bach
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, USA.,Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA
| | - Ke Bi
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, USA.,Computational Genomics Resource Laboratory, California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA
| | | | - Anton Suvorov
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Rauri C K Bowie
- Department of Integrative Biology, University of California, Berkeley, CA, USA.,Museum of Vertebrate Zoology, University of California, Berkeley, CA, USA
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Bird S, Prewer E, Kutz S, Leclerc L, Vilaça ST, Kyle CJ. Geography, seasonality, and host-associated population structure influence the fecal microbiome of a genetically depauparate Arctic mammal. Ecol Evol 2019; 9:13202-13217. [PMID: 31871639 PMCID: PMC6912892 DOI: 10.1002/ece3.5768] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 09/19/2019] [Accepted: 09/25/2019] [Indexed: 12/17/2022] Open
Abstract
The Canadian Arctic is an extreme environment with low floral and faunal diversity characterized by major seasonal shifts in temperature, moisture, and daylight. Muskoxen (Ovibos moschatus) are one of few large herbivores able to survive this harsh environment. Microbiome research of the gastrointestinal tract may hold clues as to how muskoxen exist in the Arctic, but also how this species may respond to rapid environmental changes. In this study, we investigated the effects of season (spring/summer/winter), year (2007-2016), and host genetic structure on population-level microbiome variation in muskoxen from the Canadian Arctic. We utilized 16S rRNA gene sequencing to characterize the fecal microbial communities of 78 male muskoxen encompassing two population genetic clusters. These clusters are defined by Arctic Mainland and Island populations, including the following: (a) two mainland sampling locations of the Northwest Territories and Nunavut and (b) four locations of Victoria Island. Between these geographic populations, we found that differences in the microbiome reflected host-associated genetic cluster with evidence of migration. Within populations, seasonality influenced bacterial diversity with no significant differences between years of sampling. We found evidence of pathogenic bacteria, with significantly higher presence in mainland samples. Our findings demonstrate the effects of seasonality and the role of host population-level structure in driving fecal microbiome differences in a large Arctic mammal.
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Affiliation(s)
- Samantha Bird
- Forensic Science ProgramTrent UniversityPeterboroughONCanada
| | - Erin Prewer
- Environmental and Life Sciences Graduate ProgramTrent UniversityPeterboroughONCanada
| | - Susan Kutz
- Faculty of Veterinary MedicineUniversity of CalgaryCalgaryABCanada
- Canadian Wildlife Health CooperativeAlberta NodeFaculty of Veterinary MedicineUniversity of CalgaryCalgaryABCanada
| | | | - Sibelle T. Vilaça
- Environmental and Life Sciences Graduate ProgramTrent UniversityPeterboroughONCanada
- Biology DepartmentTrent UniversityPeterboroughONCanada
| | - Christopher J. Kyle
- Forensic Science ProgramTrent UniversityPeterboroughONCanada
- Environmental and Life Sciences Graduate ProgramTrent UniversityPeterboroughONCanada
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