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Dai R, Ma X, Dingkao R, Huang C, La Y, Li X, Ma X, Wu X, Chu M, Guo X, Pei J, Yan P, Liang C. Effects of dietary crude protein levels in the concentrate supplement after grazing on rumen microbiota and metabolites by using metagenomics and metabolomics in Jersey-yak. Front Microbiol 2023; 14:1124917. [PMID: 37200912 PMCID: PMC10185794 DOI: 10.3389/fmicb.2023.1124917] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 04/13/2023] [Indexed: 05/20/2023] Open
Abstract
Introduction The crude protein level in the diet will affect the fermentation parameters, microflora, and metabolites in the rumen of ruminants. It is of great significance to study the effect of crude protein levels in supplementary diet on microbial community and metabolites for improving animal growth performance. At present, the effects of crude protein level in supplementary diet on rumen fermentation parameters, microbial community, and metabolites of Jersey-Yak (JY) are still unclear. Methods The purpose of this experiment was to study the appropriate crude protein level in the diet of JY. The rumen fermentation indexes (volatile fatty acids and pH) were determined by supplementary diets with crude protein levels of 15.16 and 17.90%, respectively, and the microbial community and metabolites of JYs were analyzed by non-target metabonomics and metagenome sequencing technology, and the changes of rumen fermentation parameters, microbial flora, and metabolites in the three groups and their interactions were studied. Results and Discussion The crude protein level in the supplementary diet had significant effects on pH, valeric acid, and the ratio of acetic acid to propionic acid (p < 0.05). The protein level had no significant effect on the dominant microflora at the phylum level (p > 0.05), and all three groups were Bacteroides and Firmicutes. The results of metabolite analysis showed that the crude protein level of supplementary diet significantly affected the metabolic pathways such as Bile secretion and styrene degradation (p < 0.05), and there were different metabolites between the LP group and HP group, and these different metabolites were related to the dominant microbial to some extent. To sum up, in this experiment, the effects of crude protein level in supplementary diet on rumen microorganisms and metabolites of JY and their relationship were studied, which provided the theoretical basis for formulating a more scientific and reasonable supplementary diet in the future.
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Affiliation(s)
- Rongfeng Dai
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
| | - Xiaoming Ma
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
| | - Renqing Dingkao
- Animal Husbandry Station, Gannan Tibetan Autonomous Prefecture, Gannan, Gansu, China
| | - Chun Huang
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
| | - Yongfu La
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
| | - Xinyi Li
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
| | - Xiaoyong Ma
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
| | - Xiaoyun Wu
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
| | - Min Chu
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
| | - Xian Guo
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
| | - Jie Pei
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
| | - Ping Yan
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
- Ping Yan,
| | - Chunnian Liang
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
- *Correspondence: Chunnian Liang,
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Peng X, Wilken SE, Lankiewicz TS, Gilmore SP, Brown JL, Henske JK, Swift CL, Salamov A, Barry K, Grigoriev IV, Theodorou MK, Valentine DL, O’Malley MA. Genomic and functional analyses of fungal and bacterial consortia that enable lignocellulose breakdown in goat gut microbiomes. Nat Microbiol 2021; 6:499-511. [PMID: 33526884 PMCID: PMC8007473 DOI: 10.1038/s41564-020-00861-0] [Citation(s) in RCA: 91] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 12/21/2020] [Indexed: 02/06/2023]
Abstract
The herbivore digestive tract is home to a complex community of anaerobic microbes that work together to break down lignocellulose. These microbiota are an untapped resource of strains, pathways and enzymes that could be applied to convert plant waste into sugar substrates for green biotechnology. We carried out more than 400 parallel enrichment experiments from goat faeces to determine how substrate and antibiotic selection influence membership, activity, stability and chemical productivity of herbivore gut communities. We assembled 719 high-quality metagenome-assembled genomes (MAGs) that are unique at the species level. More than 90% of these MAGs are from previously unidentified herbivore gut microorganisms. Microbial consortia dominated by anaerobic fungi outperformed bacterially dominated consortia in terms of both methane production and extent of cellulose degradation, which indicates that fungi have an important role in methane release. Metabolic pathway reconstructions from MAGs of 737 bacteria, archaea and fungi suggest that cross-domain partnerships between fungi and methanogens enabled production of acetate, formate and methane, whereas bacterially dominated consortia mainly produced short-chain fatty acids, including propionate and butyrate. Analyses of carbohydrate-active enzyme domains present in each anaerobic consortium suggest that anaerobic bacteria and fungi employ mostly complementary hydrolytic strategies. The division of labour among herbivore anaerobes to degrade plant biomass could be harnessed for industrial bioprocessing.
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Affiliation(s)
- Xuefeng Peng
- grid.133342.40000 0004 1936 9676Department of Chemical Engineering, University of California, Santa Barbara, CA USA ,grid.133342.40000 0004 1936 9676Marine Science Institute, University of California, Santa Barbara, CA USA
| | - St. Elmo Wilken
- grid.133342.40000 0004 1936 9676Department of Chemical Engineering, University of California, Santa Barbara, CA USA
| | - Thomas S. Lankiewicz
- grid.133342.40000 0004 1936 9676Department of Chemical Engineering, University of California, Santa Barbara, CA USA ,grid.184769.50000 0001 2231 4551Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Sean P. Gilmore
- grid.133342.40000 0004 1936 9676Department of Chemical Engineering, University of California, Santa Barbara, CA USA
| | - Jennifer L. Brown
- grid.133342.40000 0004 1936 9676Department of Chemical Engineering, University of California, Santa Barbara, CA USA
| | - John K. Henske
- grid.133342.40000 0004 1936 9676Department of Chemical Engineering, University of California, Santa Barbara, CA USA
| | - Candice L. Swift
- grid.133342.40000 0004 1936 9676Department of Chemical Engineering, University of California, Santa Barbara, CA USA
| | - Asaf Salamov
- grid.184769.50000 0001 2231 4551Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Kerrie Barry
- grid.184769.50000 0001 2231 4551Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Igor V. Grigoriev
- grid.184769.50000 0001 2231 4551Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Michael K. Theodorou
- grid.417899.a0000 0001 2167 3798Department of Animal Production, Welfare and Veterinary Sciences, Harper Adams University, Newport, UK
| | - David L. Valentine
- grid.133342.40000 0004 1936 9676Department of Earth Science, University of California, Santa Barbara, CA USA
| | - Michelle A. O’Malley
- grid.133342.40000 0004 1936 9676Department of Chemical Engineering, University of California, Santa Barbara, CA USA ,grid.184769.50000 0001 2231 4551Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA USA
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Beloqui A, Nechitaylo TY, López-Cortés N, Ghazi A, Guazzaroni ME, Polaina J, Strittmatter AW, Reva O, Waliczek A, Yakimov MM, Golyshina OV, Ferrer M, Golyshin PN. Diversity of glycosyl hydrolases from cellulose-depleting communities enriched from casts of two earthworm species. Appl Environ Microbiol 2010; 76:5934-46. [PMID: 20622123 PMCID: PMC2935051 DOI: 10.1128/aem.00902-10] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2010] [Accepted: 07/01/2010] [Indexed: 11/20/2022] Open
Abstract
The guts and casts of earthworms contain microbial assemblages that process large amounts of organic polymeric substrates from plant litter and soil; however, the enzymatic potential of these microbial communities remains largely unexplored. In the present work, we retrieved carbohydrate-modifying enzymes through the activity screening of metagenomic fosmid libraries from cellulose-depleting microbial communities established with the fresh casts of two earthworm species, Aporrectodea caliginosa and Lumbricus terrestris, as inocula. Eight glycosyl hydrolases (GHs) from the A. caliginosa-derived community were multidomain endo-beta-glucanases, beta-glucosidases, beta-cellobiohydrolases, beta-galactosidase, and beta-xylosidases of known GH families. In contrast, two GHs derived from the L. terrestris microbiome had no similarity to any known GHs and represented two novel families of beta-galactosidases/alpha-arabinopyranosidases. Members of these families were annotated in public databases as conserved hypothetical proteins, with one being structurally related to isomerases/dehydratases. This study provides insight into their biochemistry, domain structures, and active-site architecture. The two communities were similar in bacterial composition but significantly different with regard to their eukaryotic inhabitants. Further sequence analysis of fosmids and plasmids bearing the GH-encoding genes, along with oligonucleotide usage pattern analysis, suggested that those apparently originated from Gammaproteobacteria (pseudomonads and Cellvibrio-like organisms), Betaproteobacteria (Comamonadaceae), and Alphaproteobacteria (Rhizobiales).
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Affiliation(s)
- Ana Beloqui
- CSIC, Institute of Catalysis, 28049 Madrid, Spain, HZI-Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany, CSIC, Instituto de Agroquímica y Tecnología de Alimentos, 46980 Valencia, Spain, Eurofins MWG Operon, 85560 Ebersberg, Germany, Department of Biochemistry, University of Pretoria, 0002 Pretoria, South Africa, Istituto per l'Ambiente Marino Costiero, CNR, Messina 98122, Italy, School of Biological Sciences, Bangor University, Gwynedd LL57 2UW, United Kingdom, Centre for Integrated Research in the Rural Environment (CRRE), Aberystwyth University-Bangor University Partnership, Aberystwyth, Ceredigion SY23 3BF, United Kingdom
| | - Taras Y. Nechitaylo
- CSIC, Institute of Catalysis, 28049 Madrid, Spain, HZI-Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany, CSIC, Instituto de Agroquímica y Tecnología de Alimentos, 46980 Valencia, Spain, Eurofins MWG Operon, 85560 Ebersberg, Germany, Department of Biochemistry, University of Pretoria, 0002 Pretoria, South Africa, Istituto per l'Ambiente Marino Costiero, CNR, Messina 98122, Italy, School of Biological Sciences, Bangor University, Gwynedd LL57 2UW, United Kingdom, Centre for Integrated Research in the Rural Environment (CRRE), Aberystwyth University-Bangor University Partnership, Aberystwyth, Ceredigion SY23 3BF, United Kingdom
| | - Nieves López-Cortés
- CSIC, Institute of Catalysis, 28049 Madrid, Spain, HZI-Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany, CSIC, Instituto de Agroquímica y Tecnología de Alimentos, 46980 Valencia, Spain, Eurofins MWG Operon, 85560 Ebersberg, Germany, Department of Biochemistry, University of Pretoria, 0002 Pretoria, South Africa, Istituto per l'Ambiente Marino Costiero, CNR, Messina 98122, Italy, School of Biological Sciences, Bangor University, Gwynedd LL57 2UW, United Kingdom, Centre for Integrated Research in the Rural Environment (CRRE), Aberystwyth University-Bangor University Partnership, Aberystwyth, Ceredigion SY23 3BF, United Kingdom
| | - Azam Ghazi
- CSIC, Institute of Catalysis, 28049 Madrid, Spain, HZI-Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany, CSIC, Instituto de Agroquímica y Tecnología de Alimentos, 46980 Valencia, Spain, Eurofins MWG Operon, 85560 Ebersberg, Germany, Department of Biochemistry, University of Pretoria, 0002 Pretoria, South Africa, Istituto per l'Ambiente Marino Costiero, CNR, Messina 98122, Italy, School of Biological Sciences, Bangor University, Gwynedd LL57 2UW, United Kingdom, Centre for Integrated Research in the Rural Environment (CRRE), Aberystwyth University-Bangor University Partnership, Aberystwyth, Ceredigion SY23 3BF, United Kingdom
| | - María-Eugenia Guazzaroni
- CSIC, Institute of Catalysis, 28049 Madrid, Spain, HZI-Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany, CSIC, Instituto de Agroquímica y Tecnología de Alimentos, 46980 Valencia, Spain, Eurofins MWG Operon, 85560 Ebersberg, Germany, Department of Biochemistry, University of Pretoria, 0002 Pretoria, South Africa, Istituto per l'Ambiente Marino Costiero, CNR, Messina 98122, Italy, School of Biological Sciences, Bangor University, Gwynedd LL57 2UW, United Kingdom, Centre for Integrated Research in the Rural Environment (CRRE), Aberystwyth University-Bangor University Partnership, Aberystwyth, Ceredigion SY23 3BF, United Kingdom
| | - Julio Polaina
- CSIC, Institute of Catalysis, 28049 Madrid, Spain, HZI-Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany, CSIC, Instituto de Agroquímica y Tecnología de Alimentos, 46980 Valencia, Spain, Eurofins MWG Operon, 85560 Ebersberg, Germany, Department of Biochemistry, University of Pretoria, 0002 Pretoria, South Africa, Istituto per l'Ambiente Marino Costiero, CNR, Messina 98122, Italy, School of Biological Sciences, Bangor University, Gwynedd LL57 2UW, United Kingdom, Centre for Integrated Research in the Rural Environment (CRRE), Aberystwyth University-Bangor University Partnership, Aberystwyth, Ceredigion SY23 3BF, United Kingdom
| | - Axel W. Strittmatter
- CSIC, Institute of Catalysis, 28049 Madrid, Spain, HZI-Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany, CSIC, Instituto de Agroquímica y Tecnología de Alimentos, 46980 Valencia, Spain, Eurofins MWG Operon, 85560 Ebersberg, Germany, Department of Biochemistry, University of Pretoria, 0002 Pretoria, South Africa, Istituto per l'Ambiente Marino Costiero, CNR, Messina 98122, Italy, School of Biological Sciences, Bangor University, Gwynedd LL57 2UW, United Kingdom, Centre for Integrated Research in the Rural Environment (CRRE), Aberystwyth University-Bangor University Partnership, Aberystwyth, Ceredigion SY23 3BF, United Kingdom
| | - Oleg Reva
- CSIC, Institute of Catalysis, 28049 Madrid, Spain, HZI-Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany, CSIC, Instituto de Agroquímica y Tecnología de Alimentos, 46980 Valencia, Spain, Eurofins MWG Operon, 85560 Ebersberg, Germany, Department of Biochemistry, University of Pretoria, 0002 Pretoria, South Africa, Istituto per l'Ambiente Marino Costiero, CNR, Messina 98122, Italy, School of Biological Sciences, Bangor University, Gwynedd LL57 2UW, United Kingdom, Centre for Integrated Research in the Rural Environment (CRRE), Aberystwyth University-Bangor University Partnership, Aberystwyth, Ceredigion SY23 3BF, United Kingdom
| | - Agnes Waliczek
- CSIC, Institute of Catalysis, 28049 Madrid, Spain, HZI-Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany, CSIC, Instituto de Agroquímica y Tecnología de Alimentos, 46980 Valencia, Spain, Eurofins MWG Operon, 85560 Ebersberg, Germany, Department of Biochemistry, University of Pretoria, 0002 Pretoria, South Africa, Istituto per l'Ambiente Marino Costiero, CNR, Messina 98122, Italy, School of Biological Sciences, Bangor University, Gwynedd LL57 2UW, United Kingdom, Centre for Integrated Research in the Rural Environment (CRRE), Aberystwyth University-Bangor University Partnership, Aberystwyth, Ceredigion SY23 3BF, United Kingdom
| | - Michail M. Yakimov
- CSIC, Institute of Catalysis, 28049 Madrid, Spain, HZI-Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany, CSIC, Instituto de Agroquímica y Tecnología de Alimentos, 46980 Valencia, Spain, Eurofins MWG Operon, 85560 Ebersberg, Germany, Department of Biochemistry, University of Pretoria, 0002 Pretoria, South Africa, Istituto per l'Ambiente Marino Costiero, CNR, Messina 98122, Italy, School of Biological Sciences, Bangor University, Gwynedd LL57 2UW, United Kingdom, Centre for Integrated Research in the Rural Environment (CRRE), Aberystwyth University-Bangor University Partnership, Aberystwyth, Ceredigion SY23 3BF, United Kingdom
| | - Olga V. Golyshina
- CSIC, Institute of Catalysis, 28049 Madrid, Spain, HZI-Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany, CSIC, Instituto de Agroquímica y Tecnología de Alimentos, 46980 Valencia, Spain, Eurofins MWG Operon, 85560 Ebersberg, Germany, Department of Biochemistry, University of Pretoria, 0002 Pretoria, South Africa, Istituto per l'Ambiente Marino Costiero, CNR, Messina 98122, Italy, School of Biological Sciences, Bangor University, Gwynedd LL57 2UW, United Kingdom, Centre for Integrated Research in the Rural Environment (CRRE), Aberystwyth University-Bangor University Partnership, Aberystwyth, Ceredigion SY23 3BF, United Kingdom
| | - Manuel Ferrer
- CSIC, Institute of Catalysis, 28049 Madrid, Spain, HZI-Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany, CSIC, Instituto de Agroquímica y Tecnología de Alimentos, 46980 Valencia, Spain, Eurofins MWG Operon, 85560 Ebersberg, Germany, Department of Biochemistry, University of Pretoria, 0002 Pretoria, South Africa, Istituto per l'Ambiente Marino Costiero, CNR, Messina 98122, Italy, School of Biological Sciences, Bangor University, Gwynedd LL57 2UW, United Kingdom, Centre for Integrated Research in the Rural Environment (CRRE), Aberystwyth University-Bangor University Partnership, Aberystwyth, Ceredigion SY23 3BF, United Kingdom
| | - Peter N. Golyshin
- CSIC, Institute of Catalysis, 28049 Madrid, Spain, HZI-Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany, CSIC, Instituto de Agroquímica y Tecnología de Alimentos, 46980 Valencia, Spain, Eurofins MWG Operon, 85560 Ebersberg, Germany, Department of Biochemistry, University of Pretoria, 0002 Pretoria, South Africa, Istituto per l'Ambiente Marino Costiero, CNR, Messina 98122, Italy, School of Biological Sciences, Bangor University, Gwynedd LL57 2UW, United Kingdom, Centre for Integrated Research in the Rural Environment (CRRE), Aberystwyth University-Bangor University Partnership, Aberystwyth, Ceredigion SY23 3BF, United Kingdom
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