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Moraïs S, Winkler S, Zorea A, Levin L, Nagies FSP, Kapust N, Lamed E, Artan-Furman A, Bolam DN, Yadav MP, Bayer EA, Martin WF, Mizrahi I. Cryptic diversity of cellulose-degrading gut bacteria in industrialized humans. Science 2024; 383:eadj9223. [PMID: 38484069 PMCID: PMC7615765 DOI: 10.1126/science.adj9223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 02/08/2024] [Indexed: 03/19/2024]
Abstract
Humans, like all mammals, depend on the gut microbiome for digestion of cellulose, the main component of plant fiber. However, evidence for cellulose fermentation in the human gut is scarce. We have identified ruminococcal species in the gut microbiota of human populations that assemble functional multienzymatic cellulosome structures capable of degrading plant cell wall polysaccharides. One of these species, which is strongly associated with humans, likely originated in the ruminant gut and was subsequently transferred to the human gut, potentially during domestication where it underwent diversification and diet-related adaptation through the acquisition of genes from other gut microbes. Collectively, these species are abundant and widespread among ancient humans, hunter-gatherers, and rural populations but are rare in populations from industrialized societies thus indicating potential disappearance in response to the westernized lifestyle.
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Affiliation(s)
- Sarah Moraïs
- National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
- The Goldman Sonnenfeldt School of Sustainability and Climate Change, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Sarah Winkler
- National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
- The Goldman Sonnenfeldt School of Sustainability and Climate Change, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Alvah Zorea
- National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
- The Goldman Sonnenfeldt School of Sustainability and Climate Change, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Liron Levin
- Bioinformatics Core Facility, llse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Falk S. P. Nagies
- Department of Biology, Institute for Molecular Evolution, Heinrich-Heine-Universität Düsseldorf, D-40225, Düsseldorf, Germany
| | - Nils Kapust
- Department of Biology, Institute for Molecular Evolution, Heinrich-Heine-Universität Düsseldorf, D-40225, Düsseldorf, Germany
| | - Eva Lamed
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 7610001 Israel
| | - Avital Artan-Furman
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 7610001 Israel
| | - David N. Bolam
- Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Madhav P. Yadav
- US Department of Agriculture, Agricultural Research Service, Eastern Regional Research Center, 600 East Mermaid Lane, Wyndmoor, PA 19038, USA
| | - Edward A. Bayer
- National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 7610001 Israel
| | - William F. Martin
- Department of Biology, Institute for Molecular Evolution, Heinrich-Heine-Universität Düsseldorf, D-40225, Düsseldorf, Germany
| | - Itzhak Mizrahi
- National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
- The Goldman Sonnenfeldt School of Sustainability and Climate Change, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
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Ahmad HI, Mahmood S, Hassan M, Sajid M, Ahmed I, Shokrollahi B, Shahzad AH, Abbas S, Raza S, Khan K, Muhammad SA, Fouad D, Ataya FS, Li Z. Genomic insights into Yak (Bos grunniens) adaptations for nutrient assimilation in high-altitudes. Sci Rep 2024; 14:5650. [PMID: 38453987 PMCID: PMC10920680 DOI: 10.1038/s41598-024-55712-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 02/27/2024] [Indexed: 03/09/2024] Open
Abstract
High-altitude environments present formidable challenges for survival and reproduction, with organisms facing limited oxygen availability and scarce nutrient resources. The yak (Bos grunniens), indigenous to the Tibetan Plateau, has notably adapted to these extreme conditions. This study delves into the genomic basis of the yak's adaptation, focusing on the positive selection acting on genes involved in nutrient assimilation pathways. Employing techniques in comparative genomics and molecular evolutionary analyses, we selected genes in the yak that show signs of positive selection associated with nutrient metabolism, absorption, and transport. Our findings reveal specific genetic adaptations related to nutrient metabolism in harsh climatic conditions. Notably, genes involved in energy metabolism, oxygen transport, and thermoregulation exhibited signs of positive selection, suggesting their crucial role in the yak's successful colonization of high-altitude regions. The study also sheds light on the yak's immune system adaptations, emphasizing genes involved in response to various stresses prevalent at elevated altitudes. Insights into the yak's genomic makeup provide valuable information for understanding the broader implications of high-altitude adaptations in mammalian evolution. They may contribute to efforts in enhancing livestock resilience to environmental challenges.
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Affiliation(s)
- Hafiz Ishfaq Ahmad
- Department of Animal Breeding and Genetics, Faculty of Veterinary and Animal Sciences, The Islamia University of Bahawalpur, Bahawalpur, Pakistan.
| | - Sammina Mahmood
- Department of Botany, Division of Science and Technology, University of Education, Lahore, Pakistan
| | - Mubashar Hassan
- Department of Clinical Sciences, College of Veterinary and Animal Sciences (Sub campus UVAS, Lahore), Jhang, 35200, Pakistan
| | - Muhammad Sajid
- Department of Pathobiology, College of Veterinary and Animal Sciences (Sub campus UVAS, Lahore), Jhang, 35200, Pakistan
| | - Irfan Ahmed
- Department of Animal Nutrition, Faculty of Veterinary and Animal Sciences, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Borhan Shokrollahi
- Hanwoo Research Institute, National Institute of Animal Science, Pyeongchang, 25340, Korea
| | - Abid Hussain Shahzad
- Department of Clinical Sciences, College of Veterinary and Animal Sciences (Sub campus UVAS, Lahore), Jhang, 35200, Pakistan
| | - Shaista Abbas
- Department of Physiology and Biochemistry, College of Veterinary and Animal Sciences, Jhang, 35200, Pakistan
| | - Sanan Raza
- Department of Clinical Sciences, College of Veterinary and Animal Sciences (Sub campus UVAS, Lahore), Jhang, 35200, Pakistan
| | - Komal Khan
- Department of Basic Sciences, Anatomy Section, College of Veterinary and Animal Sciences, Jhang, 35200, Pakistan
| | - Sayyed Aun Muhammad
- Department of Clinical Sciences, College of Veterinary and Animal Sciences (Sub campus UVAS, Lahore), Jhang, 35200, Pakistan
| | - Dalia Fouad
- Department of Zoology, College of Science, King Saud University, PO Box 22452, Riyadh, 11495, Saudi Arabia
| | - Farid S Ataya
- Department of Biochemistry, College of Science, King Saud University, PO Box 2455, 11495, Riyadh, Saudi Arabia
| | - Zhengtian Li
- Qujing Normal University, College of Biological Resource and Food Engineering, 655011, Yunnan, China.
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3
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Li B, Jia G, Wen D, Zhao X, Zhang J, Xu Q, Zhao X, Jiang N, Liu Z, Wang Y. Rumen microbiota of indigenous and introduced ruminants and their adaptation to the Qinghai-Tibetan plateau. Front Microbiol 2022; 13:1027138. [PMID: 36299720 PMCID: PMC9589358 DOI: 10.3389/fmicb.2022.1027138] [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: 08/24/2022] [Accepted: 09/20/2022] [Indexed: 12/03/2022] Open
Abstract
The grassland in the Qinghai-Tibetan plateau provide habitat for many indigenous and introduced ruminants which perform important ecological functions that impact the whole Qinghai-Tibetan plateau ecosystem. These indigenous Tibetan ruminants have evolved several adaptive traits to withstand the severe environmental conditions, especially cold, low oxygen partial pressure, high altitude, strong UV radiation, and poor forage availability on the alpine rangelands. Despite the challenges to husbandry associated with the need for enhanced adaptation, several domesticated ruminants have also been successfully introduced to the alpine pasture regions to survive in the harsh environment. For ruminants, these challenging conditions affect not only the host, but also their commensal microbiota, especially the diversity and composition of the rumen microbiota; multiple studies have described tripartite interactions among host-environment-rumen microbiota. Thus, there are significant benefits to understanding the role of rumen microbiota in the indigenous and introduced ruminants of the Qinghai-Tibetan plateau, which has co-evolved with the host to ensure the availability of specific metabolic functions required for host survival, health, growth, and development. In this report, we systemically reviewed the dynamics of rumen microbiota in both indigenous and introduced ruminants (including gut microbiota of wild ruminants) as well as their structure, functions, and interactions with changing environmental conditions, especially low food availability, that enable survival at high altitudes. We summarized that three predominant driving factors including increased VFA production, enhanced fiber degradation, and lower methane production as indicators of higher efficiency energy harvest and nutrient utilization by microbiota that can sustain the host during nutrient deficit. These cumulative studies suggested alteration of rumen microbiota structure and functional taxa with genes that encode cellulolytic enzymes to potentially enhance nutrient and energy harvesting in response to low quality and quantity forage and cold environment. Future progress toward understanding ruminant adaptation to high altitudes will require the integration of phenotypic data with multi-omics analyses to identify host-microbiota co-evolutionary adaptations enabling survival on the Qinghai-Tibetan plateau.
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Affiliation(s)
- Bin Li
- Institute of Animal Husbandry and Veterinary, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
- Agricultural College, Ningxia University, Yinchuan, China
| | - Gaobin Jia
- Institute of Animal Husbandry and Veterinary, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
- Colleges of Life Science and Technology, Dalian University, Dalian Economic Technological Development Zone, Dalian, China
| | - Dongxu Wen
- Institute of Animal Husbandry and Veterinary, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Xiuxin Zhao
- Agricultural College, Ningxia University, Yinchuan, China
| | - Junxing Zhang
- Agricultural College, Ningxia University, Yinchuan, China
| | - Qing Xu
- Institute of Life Sciences and Bio-Engineering, Beijing Jiaotong University, Beijing, China
| | - Xialing Zhao
- Institute of Animal Husbandry and Veterinary, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Nan Jiang
- Colleges of Life Science and Technology, Dalian University, Dalian Economic Technological Development Zone, Dalian, China
| | - Zhenjiang Liu
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, China
| | - Yachun Wang
- Agricultural College, Ningxia University, Yinchuan, China
- Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
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Liu H, Han X, Zhao N, Hu L, Wang X, Luo C, Chen Y, Zhao X, Xu S. The Gut Microbiota Determines the High-Altitude Adaptability of Tibetan Wild Asses (Equus kiang) in Qinghai-Tibet Plateau. Front Microbiol 2022; 13:949002. [PMID: 35923394 PMCID: PMC9342865 DOI: 10.3389/fmicb.2022.949002] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 06/17/2022] [Indexed: 12/14/2022] Open
Abstract
It was acknowledged long ago that microorganisms have played critical roles in animal evolution. Tibetan wild asses (TWA, Equus kiang) are the only wild perissodactyls on the Qinghai-Tibet Plateau (QTP) and the first national protected animals; however, knowledge about the relationships between their gut microbiota and the host's adaptability remains poorly understood. Herein, 16S rRNA and meta-genomic sequencing approaches were employed to investigate the gut microbiota–host associations in TWA and were compared against those of the co-resident livestock of yak (Bos grunnies) and Tibetan sheep (Ovis aries). Results revealed that the gut microbiota of yak and Tibetan sheep underwent convergent evolution. By contrast, the intestinal microflora of TWA diverged in a direction enabling the host to subsist on sparse and low-quality forage. Meanwhile, high microbial diversity (Shannon and Chao1 indices), cellulolytic activity, and abundant indicator species such as Spirochaetes, Bacteroidetes, Prevotella_1, and Treponema_2 supported forage digestion and short-chain fatty acid production in the gut of TWA. Meanwhile, the enterotype identification analysis showed that TWA shifted their enterotype in response to low-quality forage for a better utilization of forage nitrogen and short-chain fatty acid production. Metagenomic analysis revealed that plant biomass degrading microbial consortia, genes, and enzymes like the cellulolytic strains (Prevotella ruminicola, Ruminococcus flavefaciens, Ruminococcus albus, Butyrivibrio fibrisolvens, and Ruminobacter amylophilus), as well as carbohydrate metabolism genes (GH43, GH3, GH31, GH5, and GH10) and enzymes (β-glucosidase, xylanase, and β-xylosidase, etc.) had a significantly higher enrichment in TWA. Our results indicate that gut microbiota can improve the adaptability of TWA through plant biomass degradation and energy maintenance by the functions of gut microbiota in the face of nutritional deficiencies and also provide a strong rationale for understanding the roles of gut microbiota in the adaptation of QTP wildlife when facing harsh feeding environments.
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Affiliation(s)
- Hongjin Liu
- Northwest Institute of Plateau Biology and Institute of Sanjiangyuan National Park, Chinese Academy of Sciences, Xining, China
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Chinese Academy of Sciences, Xining, China
| | - Xueping Han
- Technology Extension Service of Animal Husbandry of Qinghai, Xining, China
| | - Na Zhao
- Northwest Institute of Plateau Biology and Institute of Sanjiangyuan National Park, Chinese Academy of Sciences, Xining, China
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Chinese Academy of Sciences, Xining, China
| | - Linyong Hu
- Northwest Institute of Plateau Biology and Institute of Sanjiangyuan National Park, Chinese Academy of Sciences, Xining, China
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Chinese Academy of Sciences, Xining, China
| | - Xungang Wang
- Northwest Institute of Plateau Biology and Institute of Sanjiangyuan National Park, Chinese Academy of Sciences, Xining, China
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Chinese Academy of Sciences, Xining, China
| | - Chongliang Luo
- Northwest Institute of Plateau Biology and Institute of Sanjiangyuan National Park, Chinese Academy of Sciences, Xining, China
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Chinese Academy of Sciences, Xining, China
| | - Yongwei Chen
- Technology Extension Service of Animal Husbandry of Qinghai, Xining, China
| | - Xinquan Zhao
- Northwest Institute of Plateau Biology and Institute of Sanjiangyuan National Park, Chinese Academy of Sciences, Xining, China
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Chinese Academy of Sciences, Xining, China
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
- Xinquan Zhao
| | - Shixiao Xu
- Northwest Institute of Plateau Biology and Institute of Sanjiangyuan National Park, Chinese Academy of Sciences, Xining, China
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Chinese Academy of Sciences, Xining, China
- *Correspondence: Shixiao Xu
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Qin W, Li S, Wu N, Wen Z, Xie J, Ma H, Zhang S. Main Factors Influencing the Gut Microbiota of Datong Yaks in Mixed Group. Animals (Basel) 2022; 12:ani12141777. [PMID: 35883324 PMCID: PMC9312300 DOI: 10.3390/ani12141777] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 06/28/2022] [Accepted: 07/05/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary This study examined the differences and similarities in gut microbial diversity and ecological assembly processes of Datong yaks, including domestic males and females and wild males, which were fed together on the Qinghai-Tibet Plateau in a mixed group. The results revealed that mixed grouping could influence the gut microbiota of these three groups of yaks and improve the gut microbial diversity of domestic females. The findings of this study can help to understand the effects of mixed grouping on the gut microbiota of livestock on the Qinghai-Tibet Plateau and improve the production of Datong yaks. Abstract The Datong yak (Bos grunniens) is the first artificial breed of yaks in the world and has played an important role in the improvement of domestic yak quality on the Qinghai-Tibet Plateau. The Datong yak breeding farm in the Qinghai province of China is the main place for the breeding and feeding of Datong yaks. It hosts domestic Datong yaks and wild male yaks, mainly in mixed groups. Different managements have different effects on livestock. The gut microbiota is closely related to the health and immunity of Datong yaks, and mixed grouping can affect the composition and diversity of the gut microbiota of Datong yaks. To reveal the effects of mixed grouping on the gut microbiota of Datong yaks and wild yaks and identify the main dominant factors, we compared the gut microbial diversities of domestic males and females and wild males based on 16S rRNA V3–V4 regions using fresh fecal samples. The data showed significant differences in the gut microbial diversity of these three groups, and the α-diversity was the highest in wild males. Different factors influence the gut microbiota, and the main influencing factors were different in different groups, including sex differences, host genetics, and physical interactions. We also compared ecological assembly processes in the three groups. The results showed that mixed grouping contributed to the improvement of gut microbial diversity in domestic females. Our study provides effective and feasible suggestions for the feeding and management of the Datong yaks.
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Affiliation(s)
- Wen Qin
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China;
| | - Shuang Li
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810001, China;
| | - Nan Wu
- College of Ecological and Environmental Engineering, Qinghai University, Xining 810016, China; (N.W.); (Z.W.)
| | - Zhouxuan Wen
- College of Ecological and Environmental Engineering, Qinghai University, Xining 810016, China; (N.W.); (Z.W.)
| | - Jiuxiang Xie
- College of Agriculture and Animal Husbandry, Qinghai University, Xining 810016, China;
| | - Hongyi Ma
- Forestry and Grassland Comprehensive Service Center of Yushu Prefecture, Yushu 815000, China;
| | - Shoudong Zhang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Coastal Ecosystems Research Station of the Yangtze River Estuary, School of Life Sciences, Fudan University, Shanghai 200433, China
- Global Flyway Ecology, Conservation Ecology Group, Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, 9700 CC Groningen, The Netherlands
- Correspondence:
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Su Y, Su J, Li F, Tian X, Liu Z, Ding G, Bai J, Li Z, Ma Z, Peppelenbosch MP. Yak Gut Microbiota: A Systematic Review and Meta-Analysis. Front Vet Sci 2022; 9:889594. [PMID: 35836500 PMCID: PMC9274166 DOI: 10.3389/fvets.2022.889594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 05/30/2022] [Indexed: 11/30/2022] Open
Abstract
The yak (Bos grunniens) is closely related to common cows (Bos taurus), but is clearly a distinct species. Yaks are of substantial importance to food and leather production in certain high-altitude regions of Asia. The animal is increasing elsewhere as well, mainly because of the perceived health benefits of its milk. Like all ruminants, the animal harbors a complex community of microbial cells in its gut, crucial for its physiology. Despite yaks being important domestic animals, the composition of its gut microbiota and how the composition is guided by its specific high-altitude environment remains largely uncategorized. Hence, online databases (Embase, Medline ALL, Web of Science Core Collection, Cochrane Central Register of Controlled Trials, and Google Scholar) were searched for articles on yak intestinal microbiota. The pooled taxonomic abundance was compared between regions, sexes, different age groups, and feeding patterns. The gut microbiota distribution across different yak intestinal segments was established through pooled average taxonomic abundance. A total of 34 studies met the inclusion criteria and yielded information on 982 unique yak gut microbiota samples. An analysis of overall pooled microbiota revealed a segmented microbial community composition of the yak gut. Yak rumen microbiota was significantly influenced by difference in region, sex, and feeding patterns, the latter factor being dominant in this respect. Yak microbiome is shaped by the feeding strategy and provides an obvious avenue for improving health and productivity of the animal. More generally, the current segmental description of physiological gut microbiome provides insight into how the microbiology of this animal has adapted itself to help comping yaks with its high-altitude habitat.
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Affiliation(s)
- Yuxin Su
- China-Malaysia National Joint Laboratory, Biomedical Research Center of Northwest Minzu University, Lanzhou, China
| | - Junhong Su
- Department of Gastroenterology and Hepatology, Erasmus MC – University Medical Center, Rotterdam, Netherlands
| | - Fanglin Li
- China-Malaysia National Joint Laboratory, Biomedical Research Center of Northwest Minzu University, Lanzhou, China
| | - Xiaojing Tian
- China-Malaysia National Joint Laboratory, Biomedical Research Center of Northwest Minzu University, Lanzhou, China
- Ganan Research Institute of Yak Milk, Hezuo, China
| | - Zewen Liu
- China-Malaysia National Joint Laboratory, Biomedical Research Center of Northwest Minzu University, Lanzhou, China
| | - Gongtao Ding
- China-Malaysia National Joint Laboratory, Biomedical Research Center of Northwest Minzu University, Lanzhou, China
| | - Jialin Bai
- China-Malaysia National Joint Laboratory, Biomedical Research Center of Northwest Minzu University, Lanzhou, China
| | - Zhuo Li
- China-Malaysia National Joint Laboratory, Biomedical Research Center of Northwest Minzu University, Lanzhou, China
- Zhuo Li
| | - Zhongren Ma
- China-Malaysia National Joint Laboratory, Biomedical Research Center of Northwest Minzu University, Lanzhou, China
- Ganan Research Institute of Yak Milk, Hezuo, China
- Zhongren Ma
| | - Maikel P. Peppelenbosch
- Department of Gastroenterology and Hepatology, Erasmus MC – University Medical Center, Rotterdam, Netherlands
- *Correspondence: Maikel P. Peppelenbosch
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Fu H, Zhang L, Fan C, Li W, Liu C, Zhang H, Cheng Q, Zhang Y. Sympatric Yaks and Plateau Pikas Promote Microbial Diversity and Similarity by the Mutual Utilization of Gut Microbiota. Microorganisms 2021; 9:microorganisms9091890. [PMID: 34576785 PMCID: PMC8467723 DOI: 10.3390/microorganisms9091890] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/31/2021] [Accepted: 09/01/2021] [Indexed: 01/17/2023] Open
Abstract
Interactions between species provide the basis for understanding coexisting mechanisms. The plateau pika (Ochotona curzoniae) and the yak (Bos grunniens) are considered competitors because they have shared habitats and consumed similar food on the Qinghai–Tibetan Plateau for more than 1 million years. Interestingly, the population density of plateau pikas increases with yak population expansion and subsequent overgrazing. To reveal the underlying mechanism, we sequenced the fecal microbial 16S rDNA from both sympatric and allopatric pikas and yaks. Our results indicated that sympatry increased both gut microbial diversity and similarity between pikas and yaks. The abundance of Firmicutes, Proteobacteria, Cyanobacteria, and Tenericutes decreased, while that of Verrucomicrobia increased in sympatric pikas. As for sympatric yaks, Firmicutes, Bacteroidetes, and Spirochaetes significantly increased, while Cyanobacteria, Euryarchaeota, and Verrucomicrobia significantly decreased. In sympatry, plateau pikas acquired 2692 OTUs from yaks, and yaks obtained 453 OTUs from pikas. The predominant horizontally transmitted bacteria were Firmicutes, Bacteroidetes, Verrucomicrobia, and Proteobacteria. These bacteria enhanced the enrichment of pathways related to prebiotics and immunity for pikas, such as heparin sulfate, heparin, chitin disaccharide, chondroitin-sulfate-ABC, and chondroitin-AC degradation pathways. In yaks, the horizontally transmitted bacteria enhanced pathways related to hepatoprotection, xenobiotic biodegradation, and detoxification. Our results suggest that horizontal transmission is a process of selection, and pikas and yaks tend to develop reciprocity through the horizontal transmission of gut microbiota.
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Affiliation(s)
- Haibo Fu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China; (H.F.); (L.Z.); (C.F.); (W.L.); (C.L.); (H.Z.); (Q.C.)
- Qinghai Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liangzhi Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China; (H.F.); (L.Z.); (C.F.); (W.L.); (C.L.); (H.Z.); (Q.C.)
- Qinghai Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
| | - Chao Fan
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China; (H.F.); (L.Z.); (C.F.); (W.L.); (C.L.); (H.Z.); (Q.C.)
- Qinghai Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenjing Li
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China; (H.F.); (L.Z.); (C.F.); (W.L.); (C.L.); (H.Z.); (Q.C.)
- Qinghai Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
| | - Chuanfa Liu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China; (H.F.); (L.Z.); (C.F.); (W.L.); (C.L.); (H.Z.); (Q.C.)
- Qinghai Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - He Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China; (H.F.); (L.Z.); (C.F.); (W.L.); (C.L.); (H.Z.); (Q.C.)
- Qinghai Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
| | - Qi Cheng
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China; (H.F.); (L.Z.); (C.F.); (W.L.); (C.L.); (H.Z.); (Q.C.)
- Qinghai Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanming Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China; (H.F.); (L.Z.); (C.F.); (W.L.); (C.L.); (H.Z.); (Q.C.)
- Qinghai Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
- Correspondence:
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