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Khairunisa BH, Heryakusuma C, Ike K, Mukhopadhyay B, Susanti D. Evolving understanding of rumen methanogen ecophysiology. Front Microbiol 2023; 14:1296008. [PMID: 38029083 PMCID: PMC10658910 DOI: 10.3389/fmicb.2023.1296008] [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: 09/17/2023] [Accepted: 10/12/2023] [Indexed: 12/01/2023] Open
Abstract
Production of methane by methanogenic archaea, or methanogens, in the rumen of ruminants is a thermodynamic necessity for microbial conversion of feed to volatile fatty acids, which are essential nutrients for the animals. On the other hand, methane is a greenhouse gas and its production causes energy loss for the animal. Accordingly, there are ongoing efforts toward developing effective strategies for mitigating methane emissions from ruminant livestock that require a detailed understanding of the diversity and ecophysiology of rumen methanogens. Rumen methanogens evolved from free-living autotrophic ancestors through genome streamlining involving gene loss and acquisition. The process yielded an oligotrophic lifestyle, and metabolically efficient and ecologically adapted descendants. This specialization poses serious challenges to the efforts of obtaining axenic cultures of rumen methanogens, and consequently, the information on their physiological properties remains in most part inferred from those of their non-rumen representatives. This review presents the current knowledge of rumen methanogens and their metabolic contributions to enteric methane production. It also identifies the respective critical gaps that need to be filled for aiding the efforts to mitigate methane emission from livestock operations and at the same time increasing the productivity in this critical agriculture sector.
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Affiliation(s)
| | - Christian Heryakusuma
- Genetics, Bioinformatics, and Computational Biology, Virginia Tech, Blacksburg, VA, United States
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, United States
| | - Kelechi Ike
- Department of Biology, North Carolina Agricultural and Technical State University, Greensboro, NC, United States
| | - Biswarup Mukhopadhyay
- Genetics, Bioinformatics, and Computational Biology, Virginia Tech, Blacksburg, VA, United States
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, United States
- Virginia Tech Carilion School of Medicine, Virginia Tech, Blacksburg, VA, United States
| | - Dwi Susanti
- Microbial Discovery Research, BiomEdit, Greenfield, IN, United States
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Effect of Tea Saponins on Rumen Microbiota and Rumen Function in Qinchuan Beef Cattle. Microorganisms 2023; 11:microorganisms11020374. [PMID: 36838339 PMCID: PMC9963011 DOI: 10.3390/microorganisms11020374] [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: 12/05/2022] [Revised: 01/20/2023] [Accepted: 01/28/2023] [Indexed: 02/05/2023] Open
Abstract
Antibiotics can promote livestock growth but have side effects, so the search for safe and effective alternatives to antibiotics is urgent. This study aimed to evaluate the effect of supplementing cattle feed with tea saponins on ruminal bacteria and fungi. Sixteen Qinchuan beef cattle with a live body weight of 250 ± 10 kg were divided into four groups (four animals in each group) using a completely randomized experimental design. Four different levels of tea saponins were provided to the Qinchuan cattle as treatments, including 0 g/cattle per day control, CON), 10 g/cattle per day (low-level, LT), 20 g/cattle per day (medium-level, MT) and 30 g/cattle per day (high-level, HT). The pre-feeding period was 10 days and the official period was 80 days in this experiment. After 90 days of feeding, the rumen fluid from sixteen Qinchuan beef cattle was collected using an oral stomach tube for evaluating changes in ruminal microbiota and rumen fermentation parameters. Results indicate that the total VFAs and proportions of propionate in the LT group was significantly higher than that in the CON and HT groups (p < 0.05). For ruminal bacteria, results indicate that the Chao1 index of the MT group was significantly lower than the CON and HT groups (p < 0.05). The phyla Bacteroidetes and Firmicutes were found to be the most abundant in all treatment groups, with the LT group having significantly increased relative abundances of Proteobacteria, Actinobacteria and Ascomycota at the phylum level (p < 0.05). The relative abundance of Bacteroides was found to be relatively lower in the LT, MT and HT treatment groups compared with the CON treatment group at the genus level (p < 0.05). For ruminal fungi, the LT treatment group was found to have higher relative abundances of Saccharomyces and Aspergillus, and lower relative abundances of Succiniclasticum and Bacteroides at the at the phylum level (p < 0.05). Compared with the CON treatment group, a significant increase in the relative abundance of Saccharomyces and Aspergillus were observed in the LT treatment group at the genus level (p < 0.05). PICRUSt analyses identified pathways associated with Xenobiotic biodegradation and metabolism and glycolysisIII to be significantly enriched in the LT and HT treatment groups (p < 0.05). These findings could provide insights on how tea saponins may influence ruminal bacteria and fungi, providing a theoretical basis for replacing antibiotics with tea saponins for promoting growth in cattle.
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Wei Y, Yang H, Wang Z, Zhao J, Qi H, Wang C, Zhang J, Yang T. Roughage biodegradation by natural co-cultures of rumen fungi and methanogens from Qinghai yaks. AMB Express 2022; 12:123. [PMID: 36121525 PMCID: PMC9485394 DOI: 10.1186/s13568-022-01462-2] [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: 01/12/2022] [Accepted: 09/10/2022] [Indexed: 11/10/2022] Open
Abstract
Anaerobic fungus–methanogen co-cultures from rumen liquids and faeces can degrade lignocellulose efficiently. In this study, 31 fungus–methanogen co-cultures were first obtained from the rumen of yaks grazing in Qinghai Province, China, using the Hungate roll-tube technique. The fungi were identified according to morphological characteristics and internal transcribed spacer (ITS) sequences. The methanogens associated with each fungus were identified by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) and 16S rRNA gene sequencing. They were five co-culture types: Neocallimastix frontalis + Methanobrevibacter ruminantium, Neocallimastix frontalis + Methanobrevibacter gottschalkii, Orpinomyces joyonii + Methanobrevibacter ruminantium, Caecomyces communis + Methanobrevibacter ruminantium, and Caecomyces communis + Methanobrevibacter millerae. Among the 31 co-cultures, during the 5-day incubation, the N. frontalis + M. gottschalkii co-culture YakQH5 degraded 59.0%–68.1% of the dry matter (DM) and 49.5%–59.7% of the neutral detergent fiber (NDF) of wheat straw, corn stalk, rice straw, oat straw and sorghum straw to produce CH4 (3.0–4.6 mmol/g DM) and acetate (7.3–8.6 mmol/g DM) as end-products. Ferulic acid (FA) released at 4.8 mg/g DM on corn stalk and p-coumaric acid (PCA) released at 11.7 mg/g DM on sorghum straw showed the highest values, with the following peak values of enzyme activities: xylanase at 12,910 mU/mL on wheat straw, ferulic acid esterase (FAE) at 10.5 mU/mL on corn stalk, and p-coumaric acid esterase (CAE) at 20.5 mU/mL on sorghum straw. The N. frontalis + M. gottschalkii co-culture YakQH5 from Qinghai yaks represents a new efficient combination for lignocellulose biodegradation, performing better than previously reported fungus–methanogen co-cultures from the digestive tract of ruminants.
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Affiliation(s)
- Yaqin Wei
- Key Laboratory of Microbial Resources Exploitation and Application of Gansu Province, Institute of Biology, Gansu Academy of Sciences, Lanzhou, 730000, People's Republic of China. .,Center for Anaerobic Microbes, Institute of Biology, Gansu Academy of Sciences, No. 197 Dingxi South Road, Lanzhou, 730000, Gansu, People's Republic of China.
| | - Hui Yang
- Key Laboratory of Microbial Resources Exploitation and Application of Gansu Province, Institute of Biology, Gansu Academy of Sciences, Lanzhou, 730000, People's Republic of China.,Center for Anaerobic Microbes, Institute of Biology, Gansu Academy of Sciences, No. 197 Dingxi South Road, Lanzhou, 730000, Gansu, People's Republic of China
| | - Zhiye Wang
- Key Laboratory of Microbial Resources Exploitation and Application of Gansu Province, Institute of Biology, Gansu Academy of Sciences, Lanzhou, 730000, People's Republic of China.,Center for Anaerobic Microbes, Institute of Biology, Gansu Academy of Sciences, No. 197 Dingxi South Road, Lanzhou, 730000, Gansu, People's Republic of China
| | - Jiang Zhao
- Key Laboratory of Microbial Resources Exploitation and Application of Gansu Province, Institute of Biology, Gansu Academy of Sciences, Lanzhou, 730000, People's Republic of China.,Center for Anaerobic Microbes, Institute of Biology, Gansu Academy of Sciences, No. 197 Dingxi South Road, Lanzhou, 730000, Gansu, People's Republic of China
| | - Hongshan Qi
- Key Laboratory of Microbial Resources Exploitation and Application of Gansu Province, Institute of Biology, Gansu Academy of Sciences, Lanzhou, 730000, People's Republic of China.,Center for Anaerobic Microbes, Institute of Biology, Gansu Academy of Sciences, No. 197 Dingxi South Road, Lanzhou, 730000, Gansu, People's Republic of China
| | - Chuan Wang
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, 730000, People's Republic of China
| | - Jingrong Zhang
- Key Laboratory of Microbial Resources Exploitation and Application of Gansu Province, Institute of Biology, Gansu Academy of Sciences, Lanzhou, 730000, People's Republic of China.,Center for Anaerobic Microbes, Institute of Biology, Gansu Academy of Sciences, No. 197 Dingxi South Road, Lanzhou, 730000, Gansu, People's Republic of China
| | - Tao Yang
- Key Laboratory of Microbial Resources Exploitation and Application of Gansu Province, Institute of Biology, Gansu Academy of Sciences, Lanzhou, 730000, People's Republic of China.,Center for Anaerobic Microbes, Institute of Biology, Gansu Academy of Sciences, No. 197 Dingxi South Road, Lanzhou, 730000, Gansu, People's Republic of China
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