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Huang Y, Hu H, Zhang T, Wang W, Liu W, Tang H. Meta-omics assisted microbial gene and strain resources mining in contaminant environment. Eng Life Sci 2024; 24:2300207. [PMID: 38708415 PMCID: PMC11065330 DOI: 10.1002/elsc.202300207] [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: 05/04/2023] [Revised: 07/11/2023] [Accepted: 07/11/2023] [Indexed: 05/07/2024] Open
Abstract
Human activities have led to the release of various environmental pollutants, triggering ecological challenges. In situ, microbial communities in these contaminated environments are usually assumed to possess the potential capacity of pollutant degradation. However, the majority of genes and microorganisms in these environments remain uncharacterized and uncultured. The advent of meta-omics provided culture-independent solutions for exploring the functional genes and microorganisms within complex microbial communities. In this review, we highlight the applications and methodologies of meta-omics in uncovering of genes and microbes from contaminated environments. These findings may assist in future bioremediation research.
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Affiliation(s)
- Yiqun Huang
- State Key Laboratory of Microbial Metabolismand School of Life Sciences & BiotechnologyShanghai Jiao Tong UniversityShanghaiPeople's Republic of China
| | - Haiyang Hu
- State Key Laboratory of Microbial Metabolismand School of Life Sciences & BiotechnologyShanghai Jiao Tong UniversityShanghaiPeople's Republic of China
| | - Tingting Zhang
- China Tobacco Henan Industrial Co. Ltd.ZhengzhouPeople's Republic of China
| | - Weiwei Wang
- State Key Laboratory of Microbial Metabolismand School of Life Sciences & BiotechnologyShanghai Jiao Tong UniversityShanghaiPeople's Republic of China
| | - Wenzhao Liu
- China Tobacco Henan Industrial Co. Ltd.ZhengzhouPeople's Republic of China
| | - Hongzhi Tang
- State Key Laboratory of Microbial Metabolismand School of Life Sciences & BiotechnologyShanghai Jiao Tong UniversityShanghaiPeople's Republic of China
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Romanzin A, Braidot M, Beraldo P, Spanghero M. Rumen fermentation parameters and papillae development in Simmental growing bulls with divergent residual feed intake. Animal 2024; 18:101149. [PMID: 38663151 DOI: 10.1016/j.animal.2024.101149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 03/22/2024] [Accepted: 03/25/2024] [Indexed: 05/18/2024] Open
Abstract
Residual feed intake (RFI), a widespread index used to measure animal feed efficiency, is influenced by various individual biological factors related to inter-animal variation that need to be assessed. Herein, 30 Simmental bulls, raised under the same farm conditions, were divided on the basis of RFI values into a high efficient group (HE, RFI = - 1.18 ± 0.33 kg DM/d, n = 15) and a low efficient group (LE, RFI = 0.92 ± 0.35 kg DM/d, n = 15). Subsequently, bulls were slaughtered at an average BW of 734 ± 39.4 kg. Their ruminal fermentation traits were analysed immediately after slaughtering and after 24 h of in vitro incubation. Furthermore, ruminal micro-biota composition and ruminal papillae morphology were examined. The LE group exhibited a higher propionate concentration as a percentage of total volatile fatty acids (17.3 vs 16.1%, P = 0.04) in the rumen fluid collected during slaughtering, which was also confirmed after in vitro fermentation (16.6 vs 15.4% respectively for LE and HE, P = 0.01). This phenomenon resulted in a significant alteration in the acetate-to-propionate ratio (A:P) with higher values for the HE group, both after slaughter (4.01 vs 3.66, P = 0.02) and after in vitro incubation (3.78 vs 3.66, P = 0.02). Methane production was similar in both groups either as absolute production (227 vs 218 mL for HE and LE, respectively) or expressed as a percentage of total gas (approximately 22%). Even if significant differences (P < 0.20) in the relative abundance of some bacterial genera were observed for the two RFI groups, no significant variations were observed in the alpha (Shannon index) and beta (Bray-Curtis index) diversity. Considering the papillae morphology, the LE subjects have shown higher length values (6.26 vs 4.90 mm, P < 0.01) while HE subjects have demonstrated higher papillae density (46.4 vs 40.5 n/cm2, P = 0.02). Histo-morphometric analysis did not reveal appreciable modifications in the total papilla thickness, boundaries or surface between the experimental groups. In conclusion, our results contribute to efforts to analyse the factors affecting feed efficiency at the ruminal level. Propionate production, papillae morphology and a few bacterial genera certainly play a role in this regard, although not a decisive one.
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Affiliation(s)
- A Romanzin
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Via Sondrio, 2/A, 33100 Udine, Italy
| | - M Braidot
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Via Sondrio, 2/A, 33100 Udine, Italy.
| | - P Beraldo
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Via Sondrio, 2/A, 33100 Udine, Italy
| | - M Spanghero
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Via Sondrio, 2/A, 33100 Udine, Italy
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Zhong Z, Sun P, Zhang Y, Li L, Han D, Pan X, Zhang R. Differential responses of rumen and fecal fermentation and microbiota of Liaoning cashmere goats after 2-hydroxy-4-(methylthio) butanoic acid isopropyl ester supplementation. Sci Rep 2024; 14:8505. [PMID: 38605045 PMCID: PMC11009298 DOI: 10.1038/s41598-024-58581-y] [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: 12/19/2023] [Accepted: 04/01/2024] [Indexed: 04/13/2024] Open
Abstract
The 2-hydroxy-4-(methylthio) butanoic acid isopropyl ester (HMBi), a rumen protective methionine, has been extensively studied in dairy cows and beef cattle and has been shown to regulate gastrointestinal microbiota and improve production performance. However, knowledge of the application of HMBi on cashmere goats and the simultaneous study of rumen and hindgut microbiota is still limited. In this study, HMBi supplementation increased the concentration of total serum protein, the production of microbial protein in the rumen and feces, as well as butyrate production in the feces. The results of PCoA and PERMANOVA showed no significant difference between the rumen microbiota, but there was a dramatic difference between the fecal microbiota of the two groups of Cashmere goats after the HMBi supplementation. Specifically, in the rumen, HMBi significantly increased the relative abundance of some fiber-degrading bacteria (such as Fibrobacter) compared with the CON group. In the feces, as well as a similar effect as in the rumen (increasing the relative abundance of some fiber-degrading bacteria, such as Lachnospiraceae FCS020 group and ASV32), HMBi diets also increased the proliferation of butyrate-producing bacteria (including Oscillospiraceae UCG-005 and Christensenellaceae R-7 group). Overall, these results demonstrated that HMBi could regulate the rumen and fecal microbial composition of Liaoning cashmere goats and benefit the host.
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Affiliation(s)
- Zhiqiang Zhong
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China
| | - Peiyuan Sun
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China
| | - Yuning Zhang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China
| | - Lingyun Li
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China
| | - Di Han
- Liaoning Province Modern Agricultural Production Base and Construction Engineering Center, Shenyang, 110032, China
| | - Xiaoguang Pan
- School of Artificial Intelligence and Software, Liaoning Petrochemical University, Fushun, 113001, China
| | - Ruiyang Zhang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China.
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangzhou, China.
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Liu S, Zheng N, Wang J, Zhao S. Relationships among bacterial cell size, diversity, and taxonomy in rumen. Front Microbiol 2024; 15:1376994. [PMID: 38628864 PMCID: PMC11018980 DOI: 10.3389/fmicb.2024.1376994] [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: 01/26/2024] [Accepted: 03/07/2024] [Indexed: 04/19/2024] Open
Abstract
Introduction The rumen microbial community plays a crucial role in the digestion and metabolic processes of ruminants. Although sequencing-based studies have helped reveal the diversity and functions of bacteria in the rumen, their physiological and biochemical characteristics, as well as their dynamic regulation along the digestion process in the rumen, remain poorly understood. Addressing these gaps requires pure culture studies to demystify the intricate mechanisms at play. Bacteria exhibit morphological differentiation associated with different species. Based on the difference in size or shape of microorganisms, size fractionation by filters with various pore sizes can be used to separate them. Methods In this study, we used polyvinylidene difluoride filters with pore sizes of 300, 120, 80, 40, 20, 8, 6, 2.1, and 0.6 μm. Bacterial suspensions were successively passed through these filters for the analysis of microbial population distribution using 16S rRNA gene sequences. Results We found that bacteria from the different pore sizes were clustered into four branches (> 120 μm, 40-120 μm, 6-20 μm, 20-40 μm, and < 0.6 μm), indicating that size fractionation had effects on enriching specific groups but could not effectively separate dominant groups by cell size alone. The species of unclassified Flavobacterium, unclassified Chryseobacterium, unclassified Delftia, Methylotenera mobilis, unclassified Caulobacteraceae, unclassified Oligella, unclassified Sphingomonas, unclassified Stenotrophomonas, unclassified Shuttleworthia, unclassified Sutterella, unclassified Alphaproteobacteria, and unclassified SR1 can be efficiently enriched or separated by size fractionation. Discussion In this study, we investigated the diversity of sorted bacteria populations in the rumen for preliminary investigations of the relationship between the size and classification of rumen bacteria that have the potential to improve our ability to isolate and culture bacteria from the rumen in the future.
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Affiliation(s)
- Sijia Liu
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Nan Zheng
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jiaqi Wang
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shengguo Zhao
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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Kong F, Wang F, Zhang Y, Wang S, Wang W, Li S. Repeated inoculation with rumen fluid accelerates the rumen bacterial transition with no benefit on production performance in postpartum Holstein dairy cows. J Anim Sci Biotechnol 2024; 15:17. [PMID: 38310317 PMCID: PMC10838461 DOI: 10.1186/s40104-023-00963-9] [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: 07/12/2023] [Accepted: 12/01/2023] [Indexed: 02/05/2024] Open
Abstract
BACKGROUND The dairy cow's postpartum period is characterized by dramatic physiological changes, therefore imposing severe challenges on the animal for maintaining health and milk output. The dynamics of the ruminal microbiota are also tremendous and may play a crucial role in lactation launch. We aim to investigate the potential benefits of early microbial intervention by fresh rumen microbiota transplantation (RMT) and sterile RMT in postpartum dairy cows. Twelve fistulated peak-lactation dairy cows were selected to be the donors for rumen fluid collection. Thirty postpartum cows were divided into 3 groups as the transplantation receptors respectively receiving 10 L fresh rumen fluid (FR), 10 L sterile rumen fluid (SR), or 10 L saline (CON) during 3 d after calving. RESULTS Production performance, plasma indices, plasma lipidome, ruminal microbiome, and liver transcriptome were recorded. After fresh and sterile RMT, we found that the molar proportion of propionic acid was increased on d 7 in the FR and SR groups and the bacterial composition was also significantly changed when compared with the CON group. A similarity analysis showed that the similarities between the CON group and FR or SR group on d 7 were 48.40% or 47.85%, whereas the similarities between microbiota on d 7 and 21 in the FR and SR groups were 68.34% or 66.85%. Dry matter intake and feed efficiency were not affected by treatments. Plasma β-hydroxybutyrate concentration in the FR group was decreased and significantly different lipids mainly included phosphatidylcholine and lysophosphatidylcholine containing polyunsaturated fatty acids. Hepatic transcriptomics analysis indicated acute-phase response pathways were upregulated in the SR group. CONCLUSIONS Our study suggests that RMT can shorten the transition process of the ruminal microbiota of postpartum dairy cows with no benefit on dry matter intake or feed efficiency. Inoculation with rumen fluid may not be a useful approach to promote the recovery of postpartum dairy cows.
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Affiliation(s)
- Fanlin Kong
- Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, State Key Laboratory of Animal Nutrition, Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, PR China
| | - Feiran Wang
- Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, State Key Laboratory of Animal Nutrition, Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, PR China
| | - Yijia Zhang
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, PR China
| | - Shuo Wang
- Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, State Key Laboratory of Animal Nutrition, Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, PR China
| | - Wei Wang
- Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, State Key Laboratory of Animal Nutrition, Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, PR China.
| | - Shengli Li
- Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, State Key Laboratory of Animal Nutrition, Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, PR China.
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Liu M, Wang T, Wang L, Xiao H, Li J, Duan C, Gao L, Liu Y, Yan H, Zhang Y, Ji S. Core microbiota for nutrient digestion remained and ammonia utilization increased after continuous batch culture of rumen microbiota in vitro. Front Microbiol 2024; 15:1331977. [PMID: 38328430 PMCID: PMC10848171 DOI: 10.3389/fmicb.2024.1331977] [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: 11/02/2023] [Accepted: 01/02/2024] [Indexed: 02/09/2024] Open
Abstract
Introduction This study aimed to investigate the digestive function, urea utilization ability, and bacterial composition changes in rumen microbiota under high urea (5% urea in diet) over 23 days of continuous batch culture in vitro. Methods The gas production, dry matter digestibility, and bacterial counts were determined for the continuously batch-cultured rumen fluid (CRF). The changes in fermentation parameters, NH3-N utilization efficiency, and microbial taxa were analyzed in CRF and were compared with that of fresh rumen fluid (RF), frozen rumen fluid (FRF, frozen rumen fluid at -80°C for 1 month), and the mixed rumen fluid (MRF, 3/4 RF mixed with 1/4 CRF) with in vitro rumen fermentation. Results The results showed that the dry matter digestibility remained stable while both the microbial counts and diversity significantly decreased over the 23 days of continuous batch culture. However, the NH3-N utilization efficiency of the CRF group was significantly higher than that of RF, FRF, and MRF groups (p < 0.05), while five core genera including Succinivibrio, Prevotella, Streptococcus, F082, and Megasphaera were retained after 23 days of continuous batch culture. The NH3-N utilization efficiency was effectively improved after continuous batch culture in vitro, and Streptococcus, Succinivibrio, Clostridium_sensu_stricto_1, p.251.o5, Oxalobacter, Bacteroidales_UCG.001, and p.1088.a5_gut_group were identified to explain 75.72% of the variation in NH3-N utilization efficiency with the RandomForest model. Conclusion Thus, core bacterial composition and function retained under high urea (5% urea in diet) over 23 days of continuous batch culture in vitro, and bacterial biomarkers for ammonia utilization were illustrated in this study. These findings might provide potential applications in improving the efficiency and safety of non-protein nitrogen utilization in ruminants.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Hui Yan
- College of Animal Science and Technology, Hebei Agricultural University, Baoding, China
| | - Yingjie Zhang
- College of Animal Science and Technology, Hebei Agricultural University, Baoding, China
| | - Shoukun Ji
- College of Animal Science and Technology, Hebei Agricultural University, Baoding, China
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Jia Y, Shi Y, Qiao H. Bacterial community and diversity in the rumen of 11 Mongolian cattle as revealed by 16S rRNA amplicon sequencing. Sci Rep 2024; 14:1546. [PMID: 38233488 PMCID: PMC10794206 DOI: 10.1038/s41598-024-51828-8] [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: 05/26/2023] [Accepted: 01/09/2024] [Indexed: 01/19/2024] Open
Abstract
Through microorganism in the rumen of ruminant, plant fiber can be converted to edible food such as meat and milk. Ruminants had a rich and complex microbial community within the rumen, and the bacteria comprised the dominant proportion of the ruminal microbes. High-throughput sequencing offered a viable solution for the study of rumen microbes. In this study, rumen fluid samples were taken from 11 cattle from Inner Mongolian, the DNA of 11 rumen fluid samples were extracted and bacterial amplicons of the V4 regions of 16S rRNA were subjected to Illumina sequencing. More than 90,000 raw reads and 60,000 effect Tags per sample were obtained. 28,122 operational taxonomic units (OTUs) were observed from 11 samples, in average 2557 ± 361 OTUs for each sample. Bacteroidetes (44.41 ± 7.31%), Firmicutes (29.07 ± 3.78%), and Proteobacteria (7.18 ± 5.63%) were the dominant phyla among the bacteria of rumen, accounting for 82%. At the genus level, the highest relative abundance was Prevotella. Their functions were predicted using the Kyoto Encyclopedia of Genes and Genomes (KEGG). The results showed that they included metabolism, genetic information processing, environmental information processing and cellular processes. It explored the bacterial community diversity and composition of the rumen of Mongolian cattle. On the whole, our research showed that there was a high diversity as well as rich bacterial flora function of rumen bacteria in Mongolian cattle. Meanwhile, these findings provided information for further studies on the relationship between the community, diversity, functions of rumen bacteria and the nutritional physiological functions of the host.
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Affiliation(s)
- Yijiu Jia
- College of Chemical Engineering, Inner Mongolia University of Technology, No. 49 Aimin Street, Xincheng District, Hohhot, 010051, China
| | - Yali Shi
- College of Chemical Engineering, Inner Mongolia University of Technology, No. 49 Aimin Street, Xincheng District, Hohhot, 010051, China.
| | - Huiyan Qiao
- College of Chemical Engineering, Inner Mongolia University of Technology, No. 49 Aimin Street, Xincheng District, Hohhot, 010051, China
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Vadroňová M, Šťovíček A, Jochová K, Výborná A, Tyrolová Y, Tichá D, Homolka P, Joch M. Combined effects of nitrate and medium-chain fatty acids on methane production, rumen fermentation, and rumen bacterial populations in vitro. Sci Rep 2023; 13:21961. [PMID: 38081855 PMCID: PMC10713576 DOI: 10.1038/s41598-023-49138-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 12/05/2023] [Indexed: 12/18/2023] Open
Abstract
This study investigated the combined effects of nitrate (NT) and medium-chain fatty acids (MCFA), including C8, C10, C12, and C14, on methane (CH4) production, rumen fermentation characteristics, and rumen bacteria using a 24 h batch incubation technique. Four types of treatments were used: control (no nitrate, no MCFA), NT (nitrate at 3.65 mM), NT + MCFA (nitrate at 3.65 mM + one of the four MCFA at 500 mg/L), and NT + MCFA/MCFA (nitrate at 3.65 mM + a binary combination of MCFA at 250 and 250 mg/L). All treatments decreased (P < 0.001) methanogenesis (mL/g dry matter incubated) compared with the control, but their efficiency was dependent on the MCFA type. The most efficient CH4 inhibitor was the NT + C10 treatment (- 40%). The combinations containing C10 and C12 had the greatest effect on bacterial alpha and beta diversity and relative microbial abundance (P < 0.001). Next-generation sequencing showed that the family Succinivibrionaceae was favored in treatments with the greatest CH4 inhibition at the expense of Prevotella and Ruminococcaceae. Furthermore, the relative abundance of Archaea decreased (P < 0.05) in the NT + C10 and NT + C10/C12 treatments. These results confirm that the combination of NT with MCFA (C10 and C12 in particular) may effectively reduce CH4 production.
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Affiliation(s)
- Mariana Vadroňová
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, Kamýcká 129, 165 00, Prague, Czech Republic
- Department of Nutrition and Feeding of Farm Animals, Institute of Animal Science, Přátelství 815, 104 00, Prague, Czech Republic
| | - Adam Šťovíček
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, Kamýcká 129, 165 00, Prague, Czech Republic
| | - Kateřina Jochová
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, Kamýcká 129, 165 00, Prague, Czech Republic
- Department of Nutrition and Feeding of Farm Animals, Institute of Animal Science, Přátelství 815, 104 00, Prague, Czech Republic
| | - Alena Výborná
- Department of Nutrition and Feeding of Farm Animals, Institute of Animal Science, Přátelství 815, 104 00, Prague, Czech Republic
| | - Yvona Tyrolová
- Department of Nutrition and Feeding of Farm Animals, Institute of Animal Science, Přátelství 815, 104 00, Prague, Czech Republic
| | - Denisa Tichá
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, Kamýcká 129, 165 00, Prague, Czech Republic
- Department of Nutrition and Feeding of Farm Animals, Institute of Animal Science, Přátelství 815, 104 00, Prague, Czech Republic
| | - Petr Homolka
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, Kamýcká 129, 165 00, Prague, Czech Republic
- Department of Nutrition and Feeding of Farm Animals, Institute of Animal Science, Přátelství 815, 104 00, Prague, Czech Republic
| | - Miroslav Joch
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, Kamýcká 129, 165 00, Prague, Czech Republic.
- Department of Nutrition and Feeding of Farm Animals, Institute of Animal Science, Přátelství 815, 104 00, Prague, Czech Republic.
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Aryee G, Luecke SM, Dahlen CR, Swanson KC, Amat S. Holistic View and Novel Perspective on Ruminal and Extra-Gastrointestinal Methanogens in Cattle. Microorganisms 2023; 11:2746. [PMID: 38004757 PMCID: PMC10673468 DOI: 10.3390/microorganisms11112746] [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: 10/23/2023] [Revised: 11/08/2023] [Accepted: 11/09/2023] [Indexed: 11/26/2023] Open
Abstract
Despite the extensive research conducted on ruminal methanogens and anti-methanogenic intervention strategies over the last 50 years, most of the currently researched enteric methane (CH4) abatement approaches have shown limited efficacy. This is largely because of the complex nature of animal production and the ruminal environment, host genetic variability of CH4 production, and an incomplete understanding of the role of the ruminal microbiome in enteric CH4 emissions. Recent sequencing-based studies suggest the presence of methanogenic archaea in extra-gastrointestinal tract tissues, including respiratory and reproductive tracts of cattle. While these sequencing data require further verification via culture-dependent methods, the consistent identification of methanogens with relatively greater frequency in the airway and urogenital tract of cattle, as well as increasing appreciation of the microbiome-gut-organ axis together highlight the potential interactions between ruminal and extra-gastrointestinal methanogenic communities. Thus, a traditional singular focus on ruminal methanogens may not be sufficient, and a holistic approach which takes into consideration of the transfer of methanogens between ruminal, extra-gastrointestinal, and environmental microbial communities is of necessity to develop more efficient and long-term ruminal CH4 mitigation strategies. In the present review, we provide a holistic survey of the methanogenic archaea present in different anatomical sites of cattle and discuss potential seeding sources of the ruminal methanogens.
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Affiliation(s)
- Godson Aryee
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND 58108, USA; (G.A.); (S.M.L.)
| | - Sarah M. Luecke
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND 58108, USA; (G.A.); (S.M.L.)
| | - Carl R. Dahlen
- Department of Animal Sciences, and Center for Nutrition and Pregnancy, North Dakota State University, Fargo, ND 58102, USA; (C.R.D.); (K.C.S.)
| | - Kendall C. Swanson
- Department of Animal Sciences, and Center for Nutrition and Pregnancy, North Dakota State University, Fargo, ND 58102, USA; (C.R.D.); (K.C.S.)
| | - Samat Amat
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND 58108, USA; (G.A.); (S.M.L.)
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Li Z, Wang M, Usman S, Khan A, Zhang Y, Li F, Bai J, Chen M, Zhang Y, Guo X. Effects of nisin on bacterial community and fermentation profiles, in vitro rumen fermentation, microbiota, and methane emission of alfalfa silage. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2023; 103:6706-6718. [PMID: 37276023 DOI: 10.1002/jsfa.12765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 05/11/2023] [Accepted: 06/05/2023] [Indexed: 06/07/2023]
Abstract
BACKGROUND Alfalfa (Medicago sativa L.) has been used widely in preparing silage. However, forage legumes are prone to contamination by spoilage bacteria during fermentation. Nisin has broad-spectrum antibacterial properties and has been applied as an inhibitor of rumen methane emissions. However, little research has been carried out on the application of nisin in silage. This study therefore aimed to investigate the impacts of different nisin concentrations on the bacterial community and fermentation dynamics, in vitro ruminal fermentation characteristics, microbiota, and methane emissions of alfalfa silage. RESULTS The detection limits of organic acid in nisin-treated silages were not reached in 0.09 g kg-1 nisin (0.09 level) from days 1 to 7 of ensiling. With increasing nisin concentrations, the silage dry matter increased linearly (P < 0.05), and dry matter loss decreased linearly (P < 0.05). Moreover, both the 0.06 g kg-1 nisin (0.06 level) and 0.09 level treatments increased the relative abundance of Pediococcus acidilactici during ensiling. Concurrently, as the nisin concentrations increased, ruminal methane production decreased linearly (P < 0.05), while the relative abundances of ruminal Succinivibrio, Fibrobacter succinogenes and Ruminobacter amylophilus increased linearly (P < 0.05). The populations of ruminal total bacteria, methanogens, protozoa, and fungi decreased linearly with increasing nisin concentrations (P < 0.05). CONCLUSION The addition of nisin delayed the fermentation process, preserved more nutrients in alfalfa silage, and promoted fermentation dominated by P. acidilactici in the late phase of ensiling. Moreover, nisin reduced in vitro rumen methane emissions without adverse effects on dry matter digestibility. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Ziqian Li
- State Key Laboratory of Grassland Agro-ecosystems, School of Life Sciences, Lanzhou University, Lanzhou, P.R. China
| | - Musen Wang
- State Key Laboratory of Grassland Agro-ecosystems, School of Life Sciences, Lanzhou University, Lanzhou, P.R. China
- State Key Laboratory of Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, P. R. China
- College of Animal Science and Technology, Hainan University, Haikou, P.R. China
| | - Samaila Usman
- State Key Laboratory of Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, P. R. China
| | - Ashiq Khan
- State Key Laboratory of Grassland Agro-ecosystems, School of Life Sciences, Lanzhou University, Lanzhou, P.R. China
| | - Yixin Zhang
- State Key Laboratory of Grassland Agro-ecosystems, School of Life Sciences, Lanzhou University, Lanzhou, P.R. China
| | - Fuhou Li
- State Key Laboratory of Grassland Agro-ecosystems, School of Life Sciences, Lanzhou University, Lanzhou, P.R. China
- State Key Laboratory of Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, P. R. China
| | - Jie Bai
- State Key Laboratory of Grassland Agro-ecosystems, School of Life Sciences, Lanzhou University, Lanzhou, P.R. China
- State Key Laboratory of Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, P. R. China
| | - Mengyan Chen
- State Key Laboratory of Grassland Agro-ecosystems, School of Life Sciences, Lanzhou University, Lanzhou, P.R. China
| | - Ying Zhang
- State Key Laboratory of Grassland Agro-ecosystems, School of Life Sciences, Lanzhou University, Lanzhou, P.R. China
| | - Xusheng Guo
- State Key Laboratory of Grassland Agro-ecosystems, School of Life Sciences, Lanzhou University, Lanzhou, P.R. China
- State Key Laboratory of Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, P. R. China
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11
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Wang D, Chen L, Tang G, Yu J, Chen J, Li Z, Cao Y, Lei X, Deng L, Wu S, Guan LL, Yao J. Multi-omics revealed the long-term effect of ruminal keystone bacteria and the microbial metabolome on lactation performance in adult dairy goats. MICROBIOME 2023; 11:215. [PMID: 37773207 PMCID: PMC10540338 DOI: 10.1186/s40168-023-01652-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 08/23/2023] [Indexed: 10/01/2023]
Abstract
BACKGROUND The increased growth rate of young animals can lead to higher lactation performance in adult goats; however, the effects of the ruminal microbiome on the growth of young goats, and the contribution of the early-life rumen microbiome to lifelong growth and lactation performance in goats has not yet been well defined. Hence, this study assessed the rumen microbiome in young goats with different average daily gains (ADG) and evaluated its contribution to growth and lactation performance during the first lactation period. RESULTS Based on monitoring of a cohort of 99 goats from youth to first lactation, the 15 highest ADG (HADG) goats and 15 lowest ADG (LADG) goats were subjected to rumen fluid microbiome and metabolome profiling. The comparison of the rumen metagenome of HADG and LADG goats revealed that ruminal carbohydrate metabolism and amino acid metabolism function were enhanced in HADG goats, suggesting that the rumen fluid microbiome of HADG goats has higher feed fermentation ability. Co-occurrence network and correlation analysis revealed that Streptococcus, Candidatus Saccharimonans, and Succinivibrionaceae UCG-001 were significantly positively correlated with young goats' growth rates and some HADG-enriched carbohydrate and protein metabolites, such as propionate, butyrate, maltoriose, and amino acids, while several genera and species of Prevotella and Methanogens exhibited a negative relationship with young goats' growth rates and correlated with LADG-enriched metabolites, such as rumen acetate as well as methane. Additionally, some functional keystone bacterial taxa, such as Prevotella, in the rumen of young goats were significantly correlated with the same taxa in the rumen of adult lactation goats. Prevotella also enriched the rumen of LADG lactating goats and had a negative effect on rumen fermentation efficiency in lactating goats. Additional analysis using random forest machine learning showed that rumen fluid microbiota and their metabolites of young goats, such as Prevotellaceae UCG-003, acetate to propionate ratio could be potential microbial markers that can potentially classify high or low ADG goats with an accuracy of prediction of > 81.3%. Similarly, the abundance of Streptococcus in the rumen of young goats could be predictive of milk yield in adult goats with high accuracy (area under the curve 91.7%). CONCLUSIONS This study identified the keystone bacterial taxa that influence carbohydrate and amino acid metabolic functions and shape the rumen fluid microbiota in the rumen of adult animals. Keystone bacteria and their effects on rumen fluid microbiota and metabolome composition during early life can lead to higher lactation performance in adult ruminants. These findings suggest that the rumen microbiome together with their metabolites in young ruminants have long-term effect on feed efficiency and animal performance. The fundamental knowledge may allow us to develop advanced methods to manipulate the rumen microbiome and improve production efficiency of ruminants. Video Abstract.
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Affiliation(s)
- Dangdang Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Luyu Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Guangfu Tang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Junjian Yu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Jie Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Zongjun Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Yangchun Cao
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Xinjian Lei
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Lu Deng
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Shengru Wu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China.
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China.
| | - Le Luo Guan
- Department of Agricultural, Food and Nutritional Science, University of Alberta, 116 St. and 85 Ave, Edmonton, AB, Canada.
| | - Junhu Yao
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China.
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China.
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12
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Stepanchenko N, Stefenoni H, Hennessy M, Nagaraju I, Wasson DE, Cueva SF, Räisänen SE, Dechow CD, Pitta DW, Hristov AN. Microbial composition, rumen fermentation parameters, enteric methane emissions, and lactational performance of phenotypically high and low methane-emitting dairy cows. J Dairy Sci 2023; 106:6146-6170. [PMID: 37479584 DOI: 10.3168/jds.2022-23190] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 03/05/2023] [Indexed: 07/23/2023]
Abstract
This experiment was designed to investigate the relation of high and low methane-yield phenotypes with body weight (BW), dry matter intake (DMI), lactation performance, enteric CH4 emissions, and rumen fermentation parameters in lactating dairy cows. A total of 130 multi- and primiparous Holstein cows were screened for enteric CH4 emissions using the GreenFeed system (C-Lock Inc.). Out of these 130 cows, 5 were identified as phenotypically high (HM) and 5 as phenotypically low (LM) CH4 emitters. Cows in the LM group had lower daily enteric CH4 emissions than cows in the HM group (on average 346 vs. 439 g/d, respectively), lower CH4 yield (15.5 vs. 20.4 g of CH4/kg of DMI), and CH4 intensity (13.2 vs. 17.0 g of CH4/ kg of energy-corrected milk yield). Enteric emissions of CO2 and H2 did not differ between HM and LM cows. These 10 cows were blocked by parity, days in milk, and milk production, and were used in a 5-wk randomized complete block design experiment. Milk composition, production, and BW were also not different between LM and HM cows. The concentration of total volatile fatty acids in ruminal contents did not differ between CH4 phenotypes, but LM cows had a lower molar proportion of acetate (57 vs. 62.1%), a higher proportion of propionate (27.5 vs. 21.6%, respectively), and therefore a lower acetate-to-propionate ratio than HM cows. Consistently, the 16S cDNA analysis revealed the abundance of Succinivibrionaceae and unclassified Veillonellaceae to be higher in LM cows compared with HM cows, bacteria that were positively correlated with ruminal propionate concentration. Notably, Succinivibrionaceae trigger the formation of propionate via oxaloacetate pathway from phosphoenolpyruvate via Enzyme Commission: 4.1.1.49, which showed a trend to be higher in LM cows compared with HM cows. Additionally, LM cows possessed fewer transcripts of a gene encoding for methyl-CoM reductase enzyme compared with HM. In this study, low and high CH4-yield cows have similar production performance and milk composition, but total-tract apparent digestibility of organic matter and fiber fractions was lower in the former group of animals.
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Affiliation(s)
- N Stepanchenko
- Department of Animal Science, The Pennsylvania State University, University Park 16802
| | - H Stefenoni
- Department of Animal Science, The Pennsylvania State University, University Park 16802
| | - M Hennessy
- Department of Clinical Studies, School of Veterinary Medicine, University of Pennsylvania, New Bolton Center, Kennett Square 193482
| | - I Nagaraju
- Department of Clinical Studies, School of Veterinary Medicine, University of Pennsylvania, New Bolton Center, Kennett Square 193482
| | - D E Wasson
- Department of Animal Science, The Pennsylvania State University, University Park 16802
| | - S F Cueva
- Department of Animal Science, The Pennsylvania State University, University Park 16802
| | - S E Räisänen
- Department of Animal Science, The Pennsylvania State University, University Park 16802; Department of Agricultural Sciences, University of Helsinki, P.O. Box 28, FI-00014 University of Helsinki, Finland
| | - C D Dechow
- Department of Animal Science, The Pennsylvania State University, University Park 16802
| | - D W Pitta
- Department of Clinical Studies, School of Veterinary Medicine, University of Pennsylvania, New Bolton Center, Kennett Square 193482.
| | - A N Hristov
- Department of Animal Science, The Pennsylvania State University, University Park 16802.
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13
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Volmer JG, McRae H, Morrison M. The evolving role of methanogenic archaea in mammalian microbiomes. Front Microbiol 2023; 14:1268451. [PMID: 37727289 PMCID: PMC10506414 DOI: 10.3389/fmicb.2023.1268451] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 08/18/2023] [Indexed: 09/21/2023] Open
Abstract
Methanogenic archaea (methanogens) represent a diverse group of microorganisms that inhabit various environmental and host-associated microbiomes. These organisms play an essential role in global carbon cycling given their ability to produce methane, a potent greenhouse gas, as a by-product of their energy production. Recent advances in culture-independent and -dependent studies have highlighted an increased prevalence of methanogens in the host-associated microbiome of diverse animal species. Moreover, there is increasing evidence that methanogens, and/or the methane they produce, may play a substantial role in human health and disease. This review addresses the expanding host-range and the emerging view of host-specific adaptations in methanogen biology and ecology, and the implications for host health and disease.
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Affiliation(s)
- James G. Volmer
- Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, Woolloongabba, QLD, Australia
| | - Harley McRae
- Faculty of Medicine, University of Queensland Frazer Institute, Translational Research Institute, Woolloongabba, QLD, Australia
| | - Mark Morrison
- Faculty of Medicine, University of Queensland Frazer Institute, Translational Research Institute, Woolloongabba, QLD, Australia
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14
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Thorsteinsson M, Lund P, Weisbjerg MR, Noel SJ, Schönherz AA, Hellwing ALF, Hansen HH, Nielsen MO. Enteric methane emission of dairy cows supplemented with iodoform in a dose-response study. Sci Rep 2023; 13:12797. [PMID: 37550361 PMCID: PMC10406889 DOI: 10.1038/s41598-023-38149-y] [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: 01/09/2023] [Accepted: 07/04/2023] [Indexed: 08/09/2023] Open
Abstract
Enteric methane (CH4) emission is one of the major greenhouse gasses originating from cattle. Iodoform has in studies been found to be a potent mitigator of rumen CH4 formation in vitro. This study aimed to quantify potential of iodoform as an anti-methanogenic feed additive for dairy cows and investigate effects on feed intake, milk production, feed digestibility, rumen microbiome, and animal health indicators. The experiment was conducted as a 4 × 4 Latin square design using four lactating rumen, duodenal, and ileal cannulated Danish Holstein dairy cows. The treatments consisted of four different doses of iodoform (1) 0 mg/day, (2) 320 mg/day, (3) 640 mg/day, and (4) 800 mg/day. Iodoform was supplemented intra-ruminally twice daily. Each period consisted of 7-days of adaptation, 3-days of digesta and blood sampling, and 4-days of gas exchange measurements using respiration chambers. Milk yield and dry matter intake (DMI) were recorded daily. Rumen samples were collected for microbial analyses and investigated for fermentation parameters. Blood was sampled and analyzed for metabolic and health status indicators. Dry matter intake and milk production decreased linearly by maximum of 48% and 33%, respectively, with increasing dose. Methane yield (g CH4/kg DMI) decreased by maximum of 66%, while up to 125-fold increases were observed in hydrogen yield (g H2/kg DMI) with increasing dose of iodoform. Total tract digestibility of DM, OM, CP, C, NDF, and starch were unaffected by treatments, but large shifts, except for NDF, were observed for ruminal to small intestinal digestion of the nutrients. Some indicators of disturbed rumen microbial activity and fermentation dynamics were observed with increasing dose, but total number of ruminal bacteria was unaffected by treatment. Serum and plasma biomarkers did not indicate negative effects of iodoform on cow health. In conclusion, iodoform was a potent mitigator of CH4 emission. However, DMI and milk production were negatively affected and associated with indications of depressed ruminal fermentation. Future studies might reveal if depression of milk yield and feed intake can be avoided if iodoform is continuously administered by mixing it into a total mixed ration.
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Affiliation(s)
- Mirka Thorsteinsson
- Department of Animal and Veterinary Sciences, AU Viborg - Research Centre Foulum, Aarhus University, 8830, Tjele, Denmark.
- iCLIMATE - Interdisciplinary Centre for Climate Change, Aarhus University, 8830, Tjele, Denmark.
- CBIO - Centre for Circular Bioeconomy, Aarhus University, 8830, Tjele, Denmark.
| | - Peter Lund
- Department of Animal and Veterinary Sciences, AU Viborg - Research Centre Foulum, Aarhus University, 8830, Tjele, Denmark
- iCLIMATE - Interdisciplinary Centre for Climate Change, Aarhus University, 8830, Tjele, Denmark
- CBIO - Centre for Circular Bioeconomy, Aarhus University, 8830, Tjele, Denmark
| | - Martin Riis Weisbjerg
- Department of Animal and Veterinary Sciences, AU Viborg - Research Centre Foulum, Aarhus University, 8830, Tjele, Denmark
- iCLIMATE - Interdisciplinary Centre for Climate Change, Aarhus University, 8830, Tjele, Denmark
- CBIO - Centre for Circular Bioeconomy, Aarhus University, 8830, Tjele, Denmark
| | - Samantha Joan Noel
- Department of Animal and Veterinary Sciences, AU Viborg - Research Centre Foulum, Aarhus University, 8830, Tjele, Denmark
- iCLIMATE - Interdisciplinary Centre for Climate Change, Aarhus University, 8830, Tjele, Denmark
- CBIO - Centre for Circular Bioeconomy, Aarhus University, 8830, Tjele, Denmark
| | - Anna Amanda Schönherz
- Department of Animal and Veterinary Sciences, AU Viborg - Research Centre Foulum, Aarhus University, 8830, Tjele, Denmark
- iCLIMATE - Interdisciplinary Centre for Climate Change, Aarhus University, 8830, Tjele, Denmark
- CBIO - Centre for Circular Bioeconomy, Aarhus University, 8830, Tjele, Denmark
| | - Anne Louise Frydendahl Hellwing
- Department of Animal and Veterinary Sciences, AU Viborg - Research Centre Foulum, Aarhus University, 8830, Tjele, Denmark
- iCLIMATE - Interdisciplinary Centre for Climate Change, Aarhus University, 8830, Tjele, Denmark
- CBIO - Centre for Circular Bioeconomy, Aarhus University, 8830, Tjele, Denmark
| | - Hanne Helene Hansen
- Department of Veterinary and Animal Sciences, University of Copenhagen, 1870, Frederiksberg, Denmark
| | - Mette Olaf Nielsen
- Department of Animal and Veterinary Sciences, AU Viborg - Research Centre Foulum, Aarhus University, 8830, Tjele, Denmark
- iCLIMATE - Interdisciplinary Centre for Climate Change, Aarhus University, 8830, Tjele, Denmark
- CBIO - Centre for Circular Bioeconomy, Aarhus University, 8830, Tjele, Denmark
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15
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Wang Q, Cui Y, Indugu N, Loor JJ, Jiang Q, Yu Z, Baker L, Pitta D, Deng Z, Xu C. Integrated meta-omics analyses reveal a role of ruminal microorganisms in ketone body accumulation and ketosis in lactating dairy cows. J Dairy Sci 2023:S0022-0302(23)00327-2. [PMID: 37296048 DOI: 10.3168/jds.2022-22282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 12/13/2022] [Indexed: 06/12/2023]
Abstract
The extent to which a nutrition-related disorder such as ketosis alters the ruminal microbiota or whether microbiota composition is related to ketosis and potential associations with host metabolism is unknown. We aimed to evaluate variations occurring in the ruminal microbiota of ketotic and nonketotic cows in the early postpartum period, and how those changes may affect the risk of developing the disease. Data on milk yield, dry matter intake (DMI), body condition score, and blood β-hydroxybutyrate (BHB) concentrations at 21 d postpartum were used to select 27 cows, which were assigned (n = 9 per group) to a clinical ketotic (CK, 4.10 ± 0.72 mmol BHB/L, DMI 11.61 ± 0.49 kg/d, ruminal pH 7.55 ± 0.07), subclinical ketotic (SK, 1.36 ± 0.12 mmol BHB/L, DMI 15.24 ± 0.34 kg/d, ruminal pH 7.58 ± 0.08), or control (NK, 0.88 ± 0.14 mmol BHB/L, DMI 16.74 ± 0.67/d, ruminal pH 7.61 ± 0.03) group. Cows averaged 3.6 ± 0.5 lactations and a body condition score of 3.11 ± 0.34 at the time of sampling. After blood serum collection for metabolomics analysis (1H nuclear magnetic resonance spectra), 150 mL of ruminal digesta was collected from each cow using an esophageal tube, paired-end (2 × 300 bp) sequencing of isolated DNA from ruminal digesta was performed via Illumina MiSeq, and sequencing data were analyzed using QIIME2 (v 2020.6) to measure the ruminal microbiota composition and relative abundance. Spearman correlation coefficients were used to evaluate relationships between relative abundance of bacterial genera and concentrations of serum metabolites. There were more than 200 genera, with approximately 30 being significant between NK and CK cows. Succinivibrionaceae UCG 1 taxa decreased in CK compared with NK cows. Christensenellaceae (Spearman correlation coefficient = 0.6), Ruminococcaceae (Spearman correlation coefficient = 0.6), Lachnospiraceae (Spearman correlation coefficient = 0.5), and Prevotellaceae (Spearman correlation coefficient = 0.6) genera were more abundant in the CK group and were highly positively correlated with plasma BHB. Metagenomic analysis indicated a high abundance of predicted functions related to metabolism (37.7%), genetic information processing (33.4%), and Brite hierarchies (16.3%) in the CK group. The 2 most important metabolic pathways for butyrate and propionate production were enriched in CK cows, suggesting increased production of acetyl coenzyme A and butyrate and decreased production of propionate. Overall, the combined data suggested that microbial populations may be related to ketosis by affecting short-chain fatty acid metabolism and BHB accumulation even in cows with adequate feed intake in the early postpartum period.
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Affiliation(s)
- Qiuju Wang
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, No. 2 Xinyang Road, New Development District, Daqing, Heilongjiang, China 163319; Key Laboratory of Efficient Utilization of Feed Resources and Nutrition Manipulation in Cold Region of Heilongjiang Province, China 163319
| | - Yizhe Cui
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, No. 2 Xinyang Road, New Development District, Daqing, Heilongjiang, China 163319
| | - Nagaraju Indugu
- Department of Clinical Studies, School of Veterinary Medicine, New Bolton Center, University of Pennsylvania, Kennett Square 19348
| | - Juan J Loor
- Department of Animal Sciences and Division of Nutritional Sciences, University of Illinois, Urbana 61801
| | - Qianming Jiang
- Department of Animal Sciences and Division of Nutritional Sciences, University of Illinois, Urbana 61801
| | - Zhongtang Yu
- Department of Animal Sciences, The Ohio State University, Columbus 43210
| | - Linda Baker
- Department of Clinical Studies, School of Veterinary Medicine, New Bolton Center, University of Pennsylvania, Kennett Square 19348
| | - Dipti Pitta
- Department of Clinical Studies, School of Veterinary Medicine, New Bolton Center, University of Pennsylvania, Kennett Square 19348
| | - Zhaoju Deng
- College of Veterinary Medicine, China Agricultural University, Beijing, China 100083
| | - Chuang Xu
- College of Veterinary Medicine, China Agricultural University, Beijing, China 100083.
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16
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Lin X, Ju L, Cheng Q, Jiang Y, Hou Q, Hu Z, Wang Y, Wang Z. Comparison of growth performance and rumen metabolic pathways in sheep and goats under the same feeding pattern. Front Vet Sci 2023; 10:1013252. [PMID: 36846256 PMCID: PMC9948245 DOI: 10.3389/fvets.2023.1013252] [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: 08/06/2022] [Accepted: 01/16/2023] [Indexed: 02/11/2023] Open
Abstract
Diet and species are important factors affecting the rumen microbiota, with roughage stimulating rumen development and concentrate feeds being broken down by the decomposition of Ruminal flora to provide the organism with a large amount of energy. This study aimed to explore the effects of host and dietary factors on rumen flora composition and diversity, as well as on host metabolism. The study reports the research conducted on 5-month-old male Small-tail Han sheep and 5-month-old male Boer goat, each with an average weight of 33.87 ± 1.70 kg. Five animals of each species were divided into two groups, namely, the S group (Small-tail Han sheep) and the B group (Boer goat). The experiment was carried out in two various periods, namely, X and Y for groups S and B, respectively. The rations were fed with concentrate-to-roughage ratios of 3:7 and 5:5, respectively. Growth performance was measured by the weight increase index. The results showed that, under the same raising conditions, the ratio between body weight increases and the amount of feed was lower in the S group than in the B group, but the differences were not significant. According to the analysis of the apparent digestibility ratio of nutrition ingredients, the XS group had a significantly higher apparent digestibility ratio for acid detergent fiber than the XB group (p < 0.05). Even though the analysis of rumen fermentation parameters showed that the rumen pH has no significant differences between the XS and XB groups, it was significantly lower in the YS group than in the YB group. The XS group contained a significantly lower content of total volatile fatty acids than the XB group (p < 0.05). Analysis of the 16S rDNA sequencing results revealed that, compared to the B group, the S group was highly enriched with the following bacteria: Proteobacteria, γ-proteobacteria, Aeromonadales, and Succinivibrionaceae. Thus, the host species affected the abundance and diversity of rumen bacteria. Feed utilization efficiency of Small-tail Han sheep was higher than Boer goats, which might be specifically associated with Succinivibrionaceae. The results from this study show that animals belonging to the same family but different genera and species can differ in metabolic pathways even when they are provided with the same animal feed.
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Affiliation(s)
| | | | - Qianjin Cheng
- College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Taian, Shandong, China
| | - Yue Jiang
- College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Taian, Shandong, China
| | - Qiuling Hou
- College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Taian, Shandong, China
| | - Zhiyong Hu
- College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Taian, Shandong, China
| | - Yun Wang
- College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Taian, Shandong, China
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Kim M. - Invited Review - Assessment of the gastrointestinal microbiota using 16S ribosomal RNA gene amplicon sequencing in ruminant nutrition. Anim Biosci 2023; 36:364-373. [PMID: 36701925 PMCID: PMC9899581 DOI: 10.5713/ab.22.0382] [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: 10/04/2022] [Accepted: 01/19/2023] [Indexed: 01/25/2023] Open
Abstract
The gastrointestinal (GI) tract of ruminants contains diverse microbes that ferment various feeds ingested by animals to produce various fermentation products, such as volatile fatty acids. Fermentation products can affect animal performance, health, and well-being. Within the GI microbes, the ruminal microbes are highly diverse, greatly contribute to fermentation, and are the most important in ruminant nutrition. Although traditional cultivation methods provided knowledge of the metabolism of GI microbes, most of the GI microbes could not be cultured on standard culture media. By contrast, amplicon sequencing of 16S rRNA genes can be used to detect unculturable microbes. Using this approach, ruminant nutritionists and microbiologists have conducted a plethora of nutritional studies, many including dietary interventions, to improve fermentation efficiency and nutrient utilization, which has greatly expanded knowledge of the GI microbiota. This review addresses the GI content sampling method, 16S rRNA gene amplicon sequencing, and bioinformatics analysis and then discusses recent studies on the various factors, such as diet, breed, gender, animal performance, and heat stress, that influence the GI microbiota and thereby ruminant nutrition.
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Affiliation(s)
- Minseok Kim
- Division of Animal Science, Chonnam National University, Gwangju 61186,
Korea,Corresponding Author: Minseok Kim, Tel: +82-62-530-2128, Fax: +82-62-530-2129, E-mail:
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18
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Wang Z, Liang Y, Lu J, Wei Z, Bao Y, Yao X, Fan Y, Wang F, Wang D, Zhang Y. Dietary spirulina supplementation modifies rumen development, fermentation and bacteria composition in Hu sheep when consuming high-fat dietary. Front Vet Sci 2023; 10:1001621. [PMID: 36798143 PMCID: PMC9926970 DOI: 10.3389/fvets.2023.1001621] [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: 09/03/2022] [Accepted: 01/05/2023] [Indexed: 02/01/2023] Open
Abstract
Introduction This study aims to investigate the long-term effects of spirulina supplementation in a high-fat diet (HFD) on rumen morphology, rumen fermentation, and the composition of rumen microbiota in lambs. Spirulina is a blue-green microalgae that has been shown to have high nutritional value for livestock. Methods Fifty-four lambs were randomly divided into three groups: a normal chow diet (NCD) group, a high-fat diet (HFD) group, and a high-fat diet supplemented with 3% spirulina (HFD+S) group. Rumen morphology, rumen fermentation, and rumen microbiota were analyzed at the end of the study. Results Spirulina supplementation improved the concentration of volatile fatty acids and rumen papilla length. Additionally, there was a tendency for an increase in rumen weight and an upregulation of the genes Claudin-1, Claudin-4, and Occludin in the HFD+S group. Pyrosequencing of the 16S ribosomal RNA gene also showed that spirulina supplementation significantly changed the rumen microbiota composition in the HFD group, with a decrease in richness and diversity. Specifically, the relative abundance of Prevotella 9 and Megasphaera was significantly increased in the HFD group compared to the NCD group, while spirulina supplementation reversed these changes. Discussion This study suggests that 3% spirulina supplementation can improve rumen development and fermentation, and effectively relieve rumen microbe disorders in lambs caused by a high-fat diet. However, further research is needed to confirm the findings and to examine the long-term effects of spirulina supplementation in different types of livestock and under different dietary conditions.
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Affiliation(s)
- Zhibo Wang
- Institute of Goats and Sheep Science, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Yaxu Liang
- Institute of Goats and Sheep Science, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Jiawei Lu
- Institute of Goats and Sheep Science, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Zongyou Wei
- Agricultural and Rural Science & Technology Service Center, and Enterprise Graduate Workstation, Taicang, China
| | - Yongjin Bao
- Institute of Goats and Sheep Science, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Xiaolei Yao
- Institute of Goats and Sheep Science, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Yixuan Fan
- Institute of Goats and Sheep Science, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Feng Wang
- Institute of Goats and Sheep Science, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Daxiang Wang
- Jiangsu Qianbao Animal Husbandry Co., Ltd, Yancheng, Jiangsu, China
| | - Yanli Zhang
- Institute of Goats and Sheep Science, Nanjing Agricultural University, Nanjing, Jiangsu, China,*Correspondence: Yanli Zhang ✉
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Jiang Z, Li X, Guo L. Binning Metagenomic Contigs Using Unsupervised Clustering and Reference Databases. Interdiscip Sci 2022; 14:795-803. [PMID: 35639335 DOI: 10.1007/s12539-022-00526-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 04/23/2022] [Accepted: 04/27/2022] [Indexed: 06/15/2023]
Abstract
Metagenomics can directly extract the genetic material of all microorganisms from the environment, and obtain metagenomic samples with a large number of unknown DNA sequences. Binning of metagenomic contigs is a hot topic in metagenomics research. There are two key challenges for the current unsupervised metagenomic clustering algorithms. First, unsupervised metagenomic clustering methods rarely use reference databases, causing a certain waste of resources. Second, unsupervised metagenomic clustering methods are restricted by the characteristics of the sequences and the clustering algorithms, and the binning effect is limited. Therefore, a new binning method for metagenomic contigs using unsupervised clustering methods and reference databases is proposed to address these challenges, to make full use of the advantages of unsupervised clustering methods and reference databases constructed by scientists to improve the overall binning effect. This method uses the integrated SVM classification model to further bin the unsupervised clustering parts that do not perform well. Our proposed method was tested on simulated datasets and a real dataset and compared with other state-of-the-art metagenomic clustering methods including CONCOCT, Metabin2.0, Autometa, and MetaBAT. The results show that our method can achieve higher precision rate and improve the binning effect.
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Affiliation(s)
- Zhongjun Jiang
- College of Information Science and Technology, Ningbo University, Ningbo, 315211, China
| | - Xiaobo Li
- College of Mathematics and Computer Science, Zhejiang Normal University, Jinhua, 321004, China.
| | - Lijun Guo
- College of Information Science and Technology, Ningbo University, Ningbo, 315211, China
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20
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Choi JY, Park JE, Choi SH, Kim JS, Lee JS, Lee JH, Kim HB, Lee JH, Kim JK, Kang SW, Park SH. Succinivibrio faecicola sp. nov., isolated from cow faeces. Int J Syst Evol Microbiol 2022; 72. [PMID: 36748461 DOI: 10.1099/ijsem.0.005631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
A Gram-stain-negative, obligately anaerobic, non-motile, non-spore-forming, helical rod-shaped bacterium, designated AGMB01872T, was isolated from faeces of a cow deposited in the National Institute of Animal Science (Wanju, Republic of Korea). Phylogenetic analysis based on the 16S rRNA gene sequences showed that strain AGMB01872T was most closely related to Succinivibrio dextrinosolvens DSM 3072T (= KCTC 25222T, 96.6 %) which belonged to the family Succinivibrionaceae. Growth was occurred at 30-40 °C (optimum, 37 °C), pH 6-7 (optimum, pH 7) and in the presence of 0.5-1.0 % (w/v) NaCl. The genomic DNA G+C content of strain AGMB01872T was 35.9 mol%. The average nucleotide identity value between strain AGMB01872T and S. dextrinosolvens DSM 3072T was 72.1 %. Cells of strain AGMB01872T utilized d-glucose, maltose, d-xylose and l-arabinose. The major fatty acids (>10 %) were C14 : 0 (23.9 %), C16 : 0 (29.4 %), summed feature 5 (10.8 %) and summed feature 10 (30.3 %). The major end-product of glucose fermentation was succinate. Based on the phenotypic, phylogenetic, biochemical, genotypic and chemotaxonomic data, AGMB01872T represents a novel species within the genus Succinivibrio, for which the name Succinivibrio feacicola sp. nov. is proposed. The type strain is AGMB01872T (= KCTC 25201T=NBRC 115007T=GDMCC 1.2573T).
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Affiliation(s)
- Ji Young Choi
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 181 Ipsin-gil, Jeongeup-si, Jeollabuk-do 56212, Republic of Korea
| | - Jam-Eon Park
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 181 Ipsin-gil, Jeongeup-si, Jeollabuk-do 56212, Republic of Korea
| | - Seung-Hyeon Choi
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 181 Ipsin-gil, Jeongeup-si, Jeollabuk-do 56212, Republic of Korea
| | - Ji-Sun Kim
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 181 Ipsin-gil, Jeongeup-si, Jeollabuk-do 56212, Republic of Korea
| | - Jung-Sook Lee
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 181 Ipsin-gil, Jeongeup-si, Jeollabuk-do 56212, Republic of Korea
| | - Ju Huck Lee
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 181 Ipsin-gil, Jeongeup-si, Jeollabuk-do 56212, Republic of Korea
| | - Hyeun Bum Kim
- Department of Animal Resources Science, Dankook University, Cheonan 31116, Republic of Korea
| | - Ju-Hoon Lee
- Department of Food Science and Animal Biotechnology, Seoul National University, Seoul, Republic of Korea.,Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea.,Center for Food and Bioconvergence, Seoul National University, Seoul, Republic of Korea
| | - Jae-Kyung Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup-si 56212, Republic of Korea
| | - Se Won Kang
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 181 Ipsin-gil, Jeongeup-si, Jeollabuk-do 56212, Republic of Korea
| | - Seung-Hwan Park
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 181 Ipsin-gil, Jeongeup-si, Jeollabuk-do 56212, Republic of Korea
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21
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Degradation of Cellulose and Hemicellulose by Ruminal Microorganisms. Microorganisms 2022; 10:microorganisms10122345. [PMID: 36557598 PMCID: PMC9785684 DOI: 10.3390/microorganisms10122345] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 11/19/2022] [Accepted: 11/26/2022] [Indexed: 11/29/2022] Open
Abstract
As major structural components of plant cell walls, cellulose and hemicellulose are degraded and fermented by anaerobic microbes in the rumen to produce volatile fatty acids, the main nutrient source for the host. Cellulose degradation is carried out primarily by specialist bacteria, with additional contributions from protists and fungi, via a variety of mechanisms. Hemicelluloses are hydrolyzed by cellulolytic bacteria and by generalist, non-cellulolytic microbes, largely via extracellular enzymes. Cellulose hydrolysis follows first-order kinetics and its rate is limited by available substrate surface area. Nevertheless, its rate is at least an order of magnitude more rapid than in anaerobic digesters, due to near-obligatory adherence of microbial cells to the cellulose surface, and a lack of downstream inhibitory effects; in the host animal, fiber degradation rate is also enhanced by the unique process of rumination. Cellulolytic and hemicellulolytic microbes exhibit intense competition and amensalism, but they also display mutualistic interactions with microbes at other trophic levels. Collectively, the fiber-degrading community of the rumen displays functional redundancy, partial niche overlap, and convergence of catabolic pathways that all contribute to stability of the ruminal fermentation. The superior hydrolytic and fermentative capabilities of ruminal fiber degraders make them promising candidates for several fermentation technologies.
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22
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Wu Z, Wang Y, Zeng J, Zhou Y. Constructing metagenome-assembled genomes for almost all components in a real bacterial consortium for binning benchmarking. BMC Genomics 2022; 23:746. [DOI: 10.1186/s12864-022-08967-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 10/25/2022] [Indexed: 11/11/2022] Open
Abstract
Abstract
Background
So far, a lot of binning approaches have been intensively developed for untangling metagenome-assembled genomes (MAGs) and evaluated by two main strategies. The strategy by comparison to known genomes prevails over the other strategy by using single-copy genes. However, there is still no dataset with all known genomes for a real (not simulated) bacterial consortium yet.
Results
Here, we continue investigating the real bacterial consortium F1RT enriched and sequenced by us previously, considering the high possibility to unearth all MAGs, due to its low complexity. The improved F1RT metagenome reassembled by metaSPAdes here utilizes about 98.62% of reads, and a series of analyses for the remaining reads suggests that the possibility of containing other low-abundance organisms in F1RT is greatly low, demonstrating that almost all MAGs are successfully assembled. Then, 4 isolates are obtained and individually sequenced. Based on the 4 isolate genomes and the entire metagenome, an elaborate pipeline is then in-house developed to construct all F1RT MAGs. A series of assessments extensively prove the high reliability of the herein reconstruction. Next, our findings further show that this dataset harbors several properties challenging for binning and thus is suitable to compare advanced binning tools available now or benchmark novel binners. Using this dataset, 8 advanced binning algorithms are assessed, giving useful insights for developing novel approaches. In addition, compared with our previous study, two novel MAGs termed FC8 and FC9 are discovered here, and 7 MAGs are solidly unearthed for species without any available genomes.
Conclusion
To our knowledge, it is the first time to construct a dataset with almost all known MAGs for a not simulated consortium. We hope that this dataset will be used as a routine toolkit to complement mock datasets for evaluating binning methods to further facilitate binning and metagenomic studies in the future.
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Liu J, Bai Y, Liu F, Kohn RA, Tadesse DA, Sarria S, Li RW, Song J. Rumen Microbial Predictors for Short-Chain Fatty Acid Levels and the Grass-Fed Regimen in Angus Cattle. Animals (Basel) 2022; 12:2995. [PMID: 36359118 PMCID: PMC9656057 DOI: 10.3390/ani12212995] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/13/2022] [Accepted: 10/20/2022] [Indexed: 10/12/2023] Open
Abstract
The health benefits of grass-fed beef are well documented. However, the rumen microbiome features in beef steers raised in a grass-fed regimen have yet to be identified. This study examined the rumen microbiome profile in the feeding regimes. Our findings show that the rumen microbiome of the grass-fed cattle demonstrated greater species diversity and harbored significantly higher microbial alpha diversity, including multiple species richness and evenness indices, than the grain-fed cattle. Global network analysis unveiled that grass-fed cattle's rumen microbial interaction networks had higher modularity, suggesting a more resilient and stable microbial community under this feeding regimen. Using the analysis of compositions of microbiomes with a bias correction (ANCOM-BC) algorithm, the abundance of multiple unclassified genera, such as those belonging to Planctomycetes, LD1-PB3, SR1, Lachnospira, and Sutterella, were significantly enriched in the rumen of grass-fed steers. Sutterella was also the critical genus able to distinguish the two feeding regimens by Random Forest. A rumen microbial predictor consisting of an unclassified genus in the candidate division SR1 (numerator) and an unclassified genus in the order Bacteroidales (denominator) accurately distinguished the two feeding schemes. Multiple microbial signatures or balances strongly correlated with various levels of SCFA in the rumen. For example, a balance represented by the log abundance ratio of Sutterella to Desulfovibrio was strongly associated with acetate-to-propionate proportions in the rumen (R2 = 0.87), which could be developed as a valuable biomarker for optimizing milk fat yield and cattle growth. Therefore, our findings provided novel insights into microbial interactions in the rumen under different feed schemes and their ecophysiological implications. These findings will help to develop rumen manipulation strategies to improve feed conversion ratios and average daily weight gains for grass- or pasture-fed cattle production.
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Affiliation(s)
- Jianan Liu
- Department of Animal & Avian Sciences, University of Maryland, College Park, MD 20742, USA
| | - Ying Bai
- College of Life Sciences and Food Engineering, Hebei University of Engineering, Handan 056038, China
| | - Fang Liu
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Richard A. Kohn
- Department of Animal & Avian Sciences, University of Maryland, College Park, MD 20742, USA
| | - Daniel A. Tadesse
- Food and Drug Administration, Center for Veterinary Medicine, Office of Research, Laurel, MD 20708, USA
| | - Saul Sarria
- Food and Drug Administration, Center for Veterinary Medicine, Office of Research, Laurel, MD 20708, USA
| | - Robert W. Li
- United States Department of Agriculture, Agriculture Research Service, Animal Genomics and Improvement Laboratory, Beltsville, MD 20705, USA
| | - Jiuzhou Song
- Department of Animal & Avian Sciences, University of Maryland, College Park, MD 20742, USA
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Li LP, Qu L, Li T. Supplemental dietary Selenohomolanthionine affects growth and rumen bacterial population of Shaanbei white cashmere wether goats. Front Microbiol 2022; 13:942848. [PMID: 36338028 PMCID: PMC9632625 DOI: 10.3389/fmicb.2022.942848] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 09/28/2022] [Indexed: 11/27/2022] Open
Abstract
Selenium (Se) is an important trace element for all livestock growth. However, little is known about the dietary supplementation of Selenohomolanthionine (SeHLan) effect on growth and rumen microbiota of cashmere goats. In this study, thirty-two growing Shaanbei white cashmere wether goats with mean body weight (26.18 ± 2.71) kg were randomly assigned into 4 treatments, each with 8 replicates. The goats in 4 experimental groups were fed the basal diet (0.016 mg/kg Se) added with organic Se in the form of SeHLan, namely, control group (CG, added 0 mg/kg Se), low Se group (LSE, added 0.3 mg/kg Se), medium Se group (MSE, added 0.6 mg/kg Se), and high Se group (HSE, added 1.2 mg/kg Se). The feed experiment lasted for 70 days including 10-day adaptation, followed by 11 days digestibility trial including 7-day adaptation and 4-day collection period. On the last day of feeding experiment, rumen fluid was collected for microbial community analysis. The feed, orts, and fecal samples were collected for chemical analysis during digestibility trial. The results showed that average daily feed intake (ADFI) and the apparent digestibility of crude protein (CP) were both quadratic ally increased with increased SeHLan supply (Pquadratic < 0.05), while average daily gain (ADG) and feed conversion ratio (FCR) showed a linear response (Plinear < 0.05). The ADFI and ADG were all highest in the MSE group, which also had the lowest FCR (P < 0.05). Alpha diversity indices of the microbial community did not differ among four treatments. While principal coordinates analysis (PCoA) showed that rumen bacterial population differed among four groups. Taxonomic analysis revealed that Bacteroidetes, Firmicutes, and Euryarchaeota were the dominant phyla. The dominant families were Prevotellaceae, Selenomonadaceae, Methanobacteriaceae, and Bifidobacteriaceae. The significantly different rumen bacterial genera were found to be Methanobrevibacter, Quinella, Christensenellaceae_R-7_group, Veillonellaceae_UCG-001, and Succinivibrionaceae_UCG-002 (P < 0.05). In addition, Tax4fun analysis revealed that SeHLan supplemented groups enhanced the enrichment of genes related to energy metabolism, amino acid metabolism, carbohydrate metabolism, and enzymes. Twenty-eight pathways showed significant differences among four treatment groups (P < 0.05). In conclusion, dietary supplementation of medium SeHLan significantly affects rumen bacterial composition and ultimately promotes Shaanbei white cashmere wether goats nutrient digestibility and growth.
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Affiliation(s)
- Long-Ping Li
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin, China
- *Correspondence: Long-Ping Li,
| | - Lei Qu
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin, China
| | - Tuo Li
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin, China
- College of Life Sciences, Yulin University, Yulin, China
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Dong J, Liu Y, Li S, Sun Z, Chen X, Wang D, Qin G, Zhang X, Aschalew ND, Wang T, Zhen Y. The physiological dissimilarities of Holstein dairy cows with different milk yields. Vet Med Sci 2022; 9:429-442. [PMID: 36251757 PMCID: PMC9857101 DOI: 10.1002/vms3.966] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Even if breed, parity, dietary and environmental management are same, dairy cows still have notable differences in milk yield that may be underpinned by physiologic differences. OBJECTIVES This study aimed to investigate the physiological dissimilarities of dairy cows with different milk yields. METHODS Thirty cows were sorted into high milk-yielding cows (group H: 58.93±2.31 kg/day), moderate milk-yielding cows (group M: 44.99±0.54 kg/day), and low milk-yielding cows (group L: 24.99±6.83 kg/day) according to milk yield. Blood was collected and serum parameters were assessed. Rumen fluid was collected for the evaluation of rumen fermentation parameters (RFPs) and bacterial community composition (BCC). RESULTS Serum prolactin, growth hormone, glutathione peroxidase, immunoglobulin A and non-esterified fatty acid had a significantly positive correlation with milk yield (p < 0.05), whereas serum glucagon and total antioxidant capacity had a significantly negative correlation with milk yield (p < 0.05). The concentration of valeric acid and the ratio of acetic acid to propionic acid in the rumen fluid in group H was significantly lower than that in group L (p < 0.05). The concentration of acetic acid and butyric acid in group H was significantly lower than that in groups M and L (p < 0.05). The relative abundances of Ruminococcaceae_NK4A214_group, Prevotella_1, Rikenellaceae_RC9_gut_group, Christensenellaceae_R-7_group, Muribaculaceae, and Ruminococcus_2 were negatively correlated with milk yield, whereas the relative abundance of Succinivibrionaceae_UCG-001, Lachnospiraceae_NK3A20_group, Shuttleworthia and Dialister were positively correlated with milk yield (p < 0.05). CONCLUSIONS This study indicates that dairy cows with different milk yields have clear divergence in serum indicators, RFPs, BCC and rumen microbial metabolism.
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Affiliation(s)
- Jianan Dong
- College of Animal Science and TechnologyJLAU‐Borui Dairy Science and Technology R&D CenterKey Laboratory of Animal Nutrition and Feed Science of Jilin ProvinceKey Laboratory of Animal Production Product Quality and Security Ministry of EducationJilin Agricultural UniversityChangchunP.R. China
| | - Yongjun Liu
- College of Animal Science and TechnologyJLAU‐Borui Dairy Science and Technology R&D CenterKey Laboratory of Animal Nutrition and Feed Science of Jilin ProvinceKey Laboratory of Animal Production Product Quality and Security Ministry of EducationJilin Agricultural UniversityChangchunP.R. China,Ningxia Agricultural Reclamation Helan Mountain Dairy Co., Ltd.YinchuanP.R. China
| | - Songze Li
- College of Animal Science and TechnologyJLAU‐Borui Dairy Science and Technology R&D CenterKey Laboratory of Animal Nutrition and Feed Science of Jilin ProvinceKey Laboratory of Animal Production Product Quality and Security Ministry of EducationJilin Agricultural UniversityChangchunP.R. China
| | - Zhe Sun
- College of Animal Science and TechnologyJLAU‐Borui Dairy Science and Technology R&D CenterKey Laboratory of Animal Nutrition and Feed Science of Jilin ProvinceKey Laboratory of Animal Production Product Quality and Security Ministry of EducationJilin Agricultural UniversityChangchunP.R. China,Postdoctoral Scientific Research WorkstationFeed Engineering Technology Research Center of Jilin ProvinceChangchun Borui Science & Technology Co., LtdChangchunP.R. China,College of Life ScienceJilin Agricultural UniversityChangchunP.R. China
| | - Xue Chen
- College of Animal Science and TechnologyJLAU‐Borui Dairy Science and Technology R&D CenterKey Laboratory of Animal Nutrition and Feed Science of Jilin ProvinceKey Laboratory of Animal Production Product Quality and Security Ministry of EducationJilin Agricultural UniversityChangchunP.R. China,Postdoctoral Scientific Research WorkstationFeed Engineering Technology Research Center of Jilin ProvinceChangchun Borui Science & Technology Co., LtdChangchunP.R. China
| | - Duojia Wang
- Institute of Animal ScienceJilin Academy of Agricultural SciencesChangchunP.R. China
| | - Guixin Qin
- College of Animal Science and TechnologyJLAU‐Borui Dairy Science and Technology R&D CenterKey Laboratory of Animal Nutrition and Feed Science of Jilin ProvinceKey Laboratory of Animal Production Product Quality and Security Ministry of EducationJilin Agricultural UniversityChangchunP.R. China
| | - Xuefeng Zhang
- College of Animal Science and TechnologyJLAU‐Borui Dairy Science and Technology R&D CenterKey Laboratory of Animal Nutrition and Feed Science of Jilin ProvinceKey Laboratory of Animal Production Product Quality and Security Ministry of EducationJilin Agricultural UniversityChangchunP.R. China,Postdoctoral Scientific Research WorkstationFeed Engineering Technology Research Center of Jilin ProvinceChangchun Borui Science & Technology Co., LtdChangchunP.R. China
| | - Natnael Demelash Aschalew
- College of Animal Science and TechnologyJLAU‐Borui Dairy Science and Technology R&D CenterKey Laboratory of Animal Nutrition and Feed Science of Jilin ProvinceKey Laboratory of Animal Production Product Quality and Security Ministry of EducationJilin Agricultural UniversityChangchunP.R. China
| | - Tao Wang
- College of Animal Science and TechnologyJLAU‐Borui Dairy Science and Technology R&D CenterKey Laboratory of Animal Nutrition and Feed Science of Jilin ProvinceKey Laboratory of Animal Production Product Quality and Security Ministry of EducationJilin Agricultural UniversityChangchunP.R. China,Postdoctoral Scientific Research WorkstationFeed Engineering Technology Research Center of Jilin ProvinceChangchun Borui Science & Technology Co., LtdChangchunP.R. China
| | - Yuguo Zhen
- College of Animal Science and TechnologyJLAU‐Borui Dairy Science and Technology R&D CenterKey Laboratory of Animal Nutrition and Feed Science of Jilin ProvinceKey Laboratory of Animal Production Product Quality and Security Ministry of EducationJilin Agricultural UniversityChangchunP.R. China,Postdoctoral Scientific Research WorkstationFeed Engineering Technology Research Center of Jilin ProvinceChangchun Borui Science & Technology Co., LtdChangchunP.R. China
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Dynamic Variations in Rumen Fermentation Characteristics and Bacterial Community Composition during In Vitro Fermentation. FERMENTATION-BASEL 2022. [DOI: 10.3390/fermentation8060276] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
This study aimed to explore the dynamic variations of rumen fermentation characteristics and bacterial community composition during a 24 h in vitro fermentation. A total of twenty-three samples were collected from original rumen fluid (ORF, n = 3), fermentation at 12 h (R12, n = 10), and fermentation at 24 h (R24, n = 10). Results showed that gas production, concentrations of microbial crude protein, ammonia nitrogen, and individual volatile fatty acids (VFA), as well as total VFA and branched-chain VFA concentrations, were higher in R24 when compared with R12 (p < 0.05). However, no significant differences were observed in acetate to propionate ratio and fermentation efficiency between R12 and R24 (p > 0.05). Bacterial diversity analysis found that Shannon index and Simpson index were higher in R24 (p < 0.05), and obvious clusters were observed in rumen bacterial community between R12 and R24. Taxonomic analysis at the phylum level showed that the abundances of Proteobacteria and Fibrobacteres were higher in R12 than that in R24, and inverse results were observed in Bacteroidetes, Firmicutes, Cyanobacteria, Verrucomicrobia, Lentisphaerae, and Synergistetes abundances. Taxonomic analysis at the genus level revealed that the abundances of Rikenellaceae RC9 gut group, Succiniclasticum, Prevotellaceae UCG-003, Christensenellaceae R-7 group, Ruminococcaceae UCG-002, Veillonellaceae UCG-001, and Ruminococcaceae NK4A214 group were higher in R24, whereas higher abundances of Succinivibrionaceae UCG-002, Ruminobacter, and Fibrobacter, were found in R12. Correlation analysis revealed the negative associations between gas production and abundances of Proteobacteria, Succinivibrionaceae UCG-002, and Ruminobacter. Moreover, the abundances of Firmicutes, Rikenellaceae RC9 gut group, Christensenellaceae R-7 group, and Ruminococcaceae UCG-002 positively correlated with VFA production. These results indicate that both rumen fermentation characteristics and bacterial community composition were dynamic during in vitro fermentation, whereas the fermentation pattern, efficiency, and bacterial richness remained similar. This study provide insight into the dynamics of rumen fermentation characteristics and bacterial composition during in vitro fermentation. This study may also provide a reference for decision-making for the sampling time point when conducting an in vitro fermentation for bacterial community investigation.
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Gruninger RJ, Zhang XM, Smith ML, Kung L, Vyas D, McGinn SM, Kindermann M, Wang M, Tan ZL, Beauchemin KA. Application of 3-nitrooxypropanol and canola oil to mitigate enteric methane emissions of beef cattle results in distinctly different effects on the rumen microbial community. Anim Microbiome 2022; 4:35. [PMID: 35642048 PMCID: PMC9158287 DOI: 10.1186/s42523-022-00179-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 04/01/2022] [Indexed: 11/20/2022] Open
Abstract
Background The major greenhouse gas from ruminants is enteric methane (CH4) which in 2010, was estimated at 2.1 Gt of CO2 equivalent, accounting for 4.3% of global anthropogenic greenhouse gas emissions. There are extensive efforts being made around the world to develop CH4 mitigating inhibitors that specifically target rumen methanogens with the ultimate goal of reducing the environmental footprint of ruminant livestock production. This study examined the individual and combined effects of supplementing a high-forage diet (90% barley silage) fed to beef cattle with the investigational CH4 inhibitor 3-nitrooxypropanol (3-NOP) and canola oil (OIL) on the rumen microbial community in relation to enteric CH4 emissions and ruminal fermentation. Results 3-NOP and OIL individually reduced enteric CH4 yield (g/kg dry matter intake) by 28.2% and 24.0%, respectively, and the effects were additive when used in combination (51.3% reduction). 3-NOP increased H2 emissions 37-fold, while co-administering 3-NOP and OIL increased H2 in the rumen 20-fold relative to the control diet. The inclusion of 3-NOP or OIL significantly reduced the diversity of the rumen microbiome. 3-NOP resulted in targeted changes in the microbiome decreasing the relative abundance of Methanobrevibacter and increasing the relative abundance of Bacteroidetes. The inclusion of OIL resulted in substantial changes to the microbial community that were associated with changes in ruminal volatile fatty acid concentration and gas production. OIL significantly reduced the abundance of protozoa and fiber-degrading microbes in the rumen but it did not selectively alter the abundance of rumen methanogens. Conclusions Our data provide a mechanistic understanding of CH4 inhibition by 3-NOP and OIL when offered alone and in combination to cattle fed a high forage diet. 3-NOP specifically targeted rumen methanogens and partly inhibited the hydrogenotrophic methanogenesis pathway, which increased H2 emissions and propionate molar proportion in rumen fluid. In contrast, OIL caused substantial changes in the rumen microbial community by indiscriminately altering the abundance of a range of rumen microbes, reducing the abundance of fibrolytic bacteria and protozoa, resulting in altered rumen fermentation. Importantly, our data suggest that co-administering CH4 inhibitors with distinct mechanisms of action can both enhance CH4 inhibition and provide alternative sinks to prevent excessive accumulation of ruminal H2. Supplementary Information The online version contains supplementary material available at 10.1186/s42523-022-00179-8.
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Affiliation(s)
- Robert J Gruninger
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, AB, T1J 4B1, Canada.
| | - Xiu Min Zhang
- CAS Key Laboratory for Agro-Ecological Processes in Subtropical Region, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, South Central Experimental Station of Animal Nutrition and Feed Science in the Ministry of Agriculture, Hunan Provincial Engineering Research Center for Healthy Livestock and Poultry Production, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, Hunan, China.,University of Chinese Academy of Sciences (UCAS), Beijing, 100049, China
| | - Megan L Smith
- Department of Animal and Food Sciences, University of Delaware, Newark, DE, 19716, USA
| | - Limin Kung
- Department of Animal and Food Sciences, University of Delaware, Newark, DE, 19716, USA
| | - Diwakar Vyas
- Department of Animal Sciences, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, 32611, USA
| | - Sean M McGinn
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, AB, T1J 4B1, Canada
| | - Maik Kindermann
- DSM Nutritional Products, Animal Nutrition and Health, CH-4002, Basel, Switzerland
| | - Min Wang
- CAS Key Laboratory for Agro-Ecological Processes in Subtropical Region, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, South Central Experimental Station of Animal Nutrition and Feed Science in the Ministry of Agriculture, Hunan Provincial Engineering Research Center for Healthy Livestock and Poultry Production, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, Hunan, China
| | - Zhi Liang Tan
- CAS Key Laboratory for Agro-Ecological Processes in Subtropical Region, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, South Central Experimental Station of Animal Nutrition and Feed Science in the Ministry of Agriculture, Hunan Provincial Engineering Research Center for Healthy Livestock and Poultry Production, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, Hunan, China
| | - Karen A Beauchemin
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, AB, T1J 4B1, Canada
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28
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Liu S, Moon CD, Zheng N, Huws S, Zhao S, Wang J. Opportunities and challenges of using metagenomic data to bring uncultured microbes into cultivation. MICROBIOME 2022; 10:76. [PMID: 35546409 PMCID: PMC9097414 DOI: 10.1186/s40168-022-01272-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 04/10/2022] [Indexed: 05/12/2023]
Abstract
Although there is now an extensive understanding of the diversity of microbial life on earth through culture-independent metagenomic DNA sequence analyses, the isolation and cultivation of microbes remains critical to directly study them and confirm their metabolic and physiological functions, and their ecological roles. The majority of environmental microbes are as yet uncultured however; therefore, bringing these rare or poorly characterized groups into culture is a priority to further understand microbiome functions. Moreover, cultivated isolates may find utility in a range of applications, such as new probiotics, biocontrol agents, and agents for industrial processes. The growing abundance of metagenomic and meta-transcriptomic sequence information from a wide range of environments provides more opportunities to guide the isolation and cultivation of microbes of interest. In this paper, we discuss a range of successful methodologies and applications that have underpinned recent metagenome-guided isolation and cultivation of microbe efforts. These approaches include determining specific culture conditions to enrich for taxa of interest, to more complex strategies that specifically target the capture of microbial species through antibody engineering and genome editing strategies. With the greater degree of genomic information now available from uncultivated members, such as via metagenome-assembled genomes, the theoretical understanding of their cultivation requirements will enable greater possibilities to capture these and ultimately gain a more comprehensive understanding of the microbiomes. Video Abstract.
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Affiliation(s)
- Sijia Liu
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Haidian, Beijing, 100193, China
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Christina D Moon
- AgResearch Ltd., Grasslands Research Centre, Palmerston North, New Zealand
| | - Nan Zheng
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Haidian, Beijing, 100193, China
| | - Sharon Huws
- School of Biological Sciences and Institute for Global Food Security, 19 Chlorine Gardens, Queen's University Belfast, Belfast, UK
| | - Shengguo Zhao
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Haidian, Beijing, 100193, China.
| | - Jiaqi Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Haidian, Beijing, 100193, China.
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29
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Ostrowski MP, La Rosa SL, Kunath BJ, Robertson A, Pereira G, Hagen LH, Varghese NJ, Qiu L, Yao T, Flint G, Li J, McDonald SP, Buttner D, Pudlo NA, Schnizlein MK, Young VB, Brumer H, Schmidt TM, Terrapon N, Lombard V, Henrissat B, Hamaker B, Eloe-Fadrosh EA, Tripathi A, Pope PB, Martens EC. Mechanistic insights into consumption of the food additive xanthan gum by the human gut microbiota. Nat Microbiol 2022; 7:556-569. [PMID: 35365790 DOI: 10.1038/s41564-022-01093-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 02/24/2022] [Indexed: 12/13/2022]
Abstract
Processed foods often include food additives such as xanthan gum, a complex polysaccharide with unique rheological properties, that has established widespread use as a stabilizer and thickening agent. Xanthan gum's chemical structure is distinct from those of host and dietary polysaccharides that are more commonly expected to transit the gastrointestinal tract, and little is known about its direct interaction with the gut microbiota, which plays a central role in digestion of other dietary fibre polysaccharides. Here we show that the ability to digest xanthan gum is common in human gut microbiomes from industrialized countries and appears contingent on a single uncultured bacterium in the family Ruminococcaceae. Our data reveal that this primary degrader cleaves the xanthan gum backbone before processing the released oligosaccharides using additional enzymes. Some individuals harbour Bacteroides intestinalis that is incapable of consuming polymeric xanthan gum but grows on oligosaccharide products generated by the Ruminococcaceae. Feeding xanthan gum to germfree mice colonized with a human microbiota containing the uncultured Ruminococcaceae supports the idea that the additive xanthan gum can drive expansion of the primary degrader Ruminococcaceae, along with exogenously introduced B. intestinalis. Our work demonstrates the existence of a potential xanthan gum food chain involving at least two members of different phyla of gut bacteria and provides an initial framework for understanding how widespread consumption of a recently introduced food additive influences human microbiomes.
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Affiliation(s)
- Matthew P Ostrowski
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Sabina Leanti La Rosa
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway.,Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Benoit J Kunath
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Andrew Robertson
- Life Sciences Institute: Natural Products Discovery Core, University of Michigan, Ann Arbor, MI, USA
| | - Gabriel Pereira
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Live H Hagen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | | | - Ling Qiu
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Tianming Yao
- Department of Food Science and Whistler Center for Carbohydrate Research, Purdue University, West Lafayette, IN, USA
| | - Gabrielle Flint
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - James Li
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sean P McDonald
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Duna Buttner
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Nicholas A Pudlo
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Matthew K Schnizlein
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Vincent B Young
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA.,Department of Internal Medicine, Infectious Diseases Division, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Harry Brumer
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Thomas M Schmidt
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Nicolas Terrapon
- Centre National de la Recherche Scientifique, Aix-Marseille Univ, Marseille, France.,Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Marseille, France
| | - Vincent Lombard
- Centre National de la Recherche Scientifique, Aix-Marseille Univ, Marseille, France.,Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Marseille, France
| | - Bernard Henrissat
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.,Technical University of Denmark, DTU Bioengineering, Lyngby, Denmark
| | - Bruce Hamaker
- Department of Food Science and Whistler Center for Carbohydrate Research, Purdue University, West Lafayette, IN, USA
| | | | - Ashootosh Tripathi
- Life Sciences Institute: Natural Products Discovery Core, University of Michigan, Ann Arbor, MI, USA
| | - Phillip B Pope
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway. .,Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway.
| | - Eric C Martens
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA.
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30
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Solomon R, Wein T, Levy B, Eshed S, Dror R, Reiss V, Zehavi T, Furman O, Mizrahi I, Jami E. Protozoa populations are ecosystem engineers that shape prokaryotic community structure and function of the rumen microbial ecosystem. THE ISME JOURNAL 2022; 16:1187-1197. [PMID: 34887549 PMCID: PMC8941083 DOI: 10.1038/s41396-021-01170-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 11/24/2021] [Accepted: 11/30/2021] [Indexed: 01/03/2023]
Abstract
Unicellular eukaryotes are an integral part of many microbial ecosystems where they interact with their surrounding prokaryotic community-either as predators or as mutualists. Within the rumen, one of the most complex host-associated microbial habitats, ciliate protozoa represent the main micro-eukaryotes, accounting for up to 50% of the microbial biomass. Nonetheless, the extent of the ecological effect of protozoa on the microbial community and on the rumen metabolic output remains largely understudied. To assess the role of protozoa on the rumen ecosystem, we established an in-vitro system in which distinct protozoa sub-communities were introduced to the native rumen prokaryotic community. We show that the different protozoa communities exert a strong and differential impact on the composition of the prokaryotic community, as well as its function including methane production. Furthermore, the presence of protozoa increases prokaryotic diversity with a differential effect on specific bacterial populations such as Gammaproteobacteria, Prevotella and Treponema. Our results suggest that protozoa contribute to the maintenance of prokaryotic diversity in the rumen possibly by mitigating the effect of competitive exclusion between bacterial taxa. Our findings put forward the rumen protozoa populations as potentially important ecosystem engineers for future microbiome modulation strategies.
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Affiliation(s)
- Ronnie Solomon
- grid.410498.00000 0001 0465 9329Department of Ruminant Science, Institute of Animal Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel ,grid.7489.20000 0004 1937 0511Institute of Natural Sciences, Department of Life Sciences, Ben-Gurion University of the Negev, Beersheba, Israel
| | - Tanita Wein
- grid.13992.300000 0004 0604 7563Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Bar Levy
- grid.410498.00000 0001 0465 9329Department of Ruminant Science, Institute of Animal Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel ,grid.22098.310000 0004 1937 0503The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Shahar Eshed
- grid.410498.00000 0001 0465 9329Department of Ruminant Science, Institute of Animal Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
| | - Rotem Dror
- grid.410498.00000 0001 0465 9329Department of Ruminant Science, Institute of Animal Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
| | - Veronica Reiss
- grid.410498.00000 0001 0465 9329Department of Ruminant Science, Institute of Animal Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
| | - Tamar Zehavi
- grid.7489.20000 0004 1937 0511Institute of Natural Sciences, Department of Life Sciences, Ben-Gurion University of the Negev, Beersheba, Israel
| | - Ori Furman
- grid.7489.20000 0004 1937 0511Institute of Natural Sciences, Department of Life Sciences, Ben-Gurion University of the Negev, Beersheba, Israel
| | - Itzhak Mizrahi
- grid.7489.20000 0004 1937 0511Institute of Natural Sciences, Department of Life Sciences, Ben-Gurion University of the Negev, Beersheba, Israel
| | - Elie Jami
- Department of Ruminant Science, Institute of Animal Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel.
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31
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Xue MY, Xie YY, Zhong Y, Ma XJ, Sun HZ, Liu JX. Integrated meta-omics reveals new ruminal microbial features associated with feed efficiency in dairy cattle. MICROBIOME 2022; 10:32. [PMID: 35172905 PMCID: PMC8849036 DOI: 10.1186/s40168-022-01228-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Accepted: 01/07/2022] [Indexed: 05/23/2023]
Abstract
BACKGROUND As the global population continues to grow, competition for resources between humans and livestock has been intensifying. Increasing milk protein production and improving feed efficiency are becoming increasingly important to meet the demand for high-quality dairy protein. In a previous study, we found that milk protein yield in dairy cows was associated with the rumen microbiome. The objective of this study was to elucidate the potential microbial features that underpins feed efficiency in dairy cows using metagenomics, metatranscriptomics, and metabolomics. RESULTS Comparison of metagenomic and metatranscriptomic data revealed that the latter was a better approach to uncover the associations between rumen microbial functions and host performance. Co-occurrence network analysis of the rumen microbiome revealed differential microbial interaction patterns between the animals with different feed efficiency, with high-efficiency animals having more and stronger associations than low-efficiency animals. In the rumen of high-efficiency animals, Selenomonas and members of the Succinivibrionaceae family positively interacted with each other, functioning as keystone members due to their essential ecological functions and active carbohydrate metabolic functions. At the metabolic level, analysis using random forest machine learning suggested that six ruminal metabolites (all derived from carbohydrates) could be used as metabolic markers that can potentially differentiate efficient and inefficient microbiomes, with an accuracy of prediction of 95.06%. CONCLUSIONS The results of the current study provided new insights into the new ruminal microbial features associated with feed efficiency in dairy cows, which may improve the ability to select animals for better performance in the dairy industry. The fundamental knowledge will also inform future interventions to improve feed efficiency in dairy cows. Video Abstract.
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Affiliation(s)
- Ming-Yuan Xue
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
- Ministry of Education Key Laboratory of Molecular Animal Nutrition, Zhejiang University, Hangzhou, 310058, China
- Ministry of Education Innovation Team of Development and Function of Animal Digestive System, Zhejiang University, Hangzhou, 310058, China
| | - Yun-Yi Xie
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
- Ministry of Education Key Laboratory of Molecular Animal Nutrition, Zhejiang University, Hangzhou, 310058, China
| | - Yifan Zhong
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
- Ministry of Education Key Laboratory of Molecular Animal Nutrition, Zhejiang University, Hangzhou, 310058, China
| | - Xiao-Jiao Ma
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
- Ministry of Education Key Laboratory of Molecular Animal Nutrition, Zhejiang University, Hangzhou, 310058, China
| | - Hui-Zeng Sun
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China.
- Ministry of Education Key Laboratory of Molecular Animal Nutrition, Zhejiang University, Hangzhou, 310058, China.
- Ministry of Education Innovation Team of Development and Function of Animal Digestive System, Zhejiang University, Hangzhou, 310058, China.
| | - Jian-Xin Liu
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China.
- Ministry of Education Key Laboratory of Molecular Animal Nutrition, Zhejiang University, Hangzhou, 310058, China.
- Ministry of Education Innovation Team of Development and Function of Animal Digestive System, Zhejiang University, Hangzhou, 310058, China.
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32
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Qiu X, Qin X, Chen L, Chen Z, Hao R, Zhang S, Yang S, Wang L, Cui Y, Li Y, Ma Y, Cao B, Su H. Serum Biochemical Parameters, Rumen Fermentation, and Rumen Bacterial Communities Are Partly Driven by the Breed and Sex of Cattle When Fed High-Grain Diet. Microorganisms 2022; 10:microorganisms10020323. [PMID: 35208778 PMCID: PMC8878564 DOI: 10.3390/microorganisms10020323] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 12/28/2021] [Accepted: 01/06/2022] [Indexed: 02/04/2023] Open
Abstract
Hybridization in bovines is practiced with the main aim of improving production performance, which may imply the microbial variations in the rumen from the parental breed cross to their progeny. Besides, the interactions of offspring breed with sex in terms of rumen bacteria are not clear. This study aims to evaluate the variations in rumen bacterial communities in different breeds and sexes, and the correlations among fattening performance, serum biochemical parameters, and rumen fermentation. Forty-two 19.2 ± 0.67-month-old beef cattle (390 ± 95 kg of initial body weight) comprising two genetic lines (Yiling and Angus × Yiling) and two sexes (heifers and steers) were raised under the same high-grain diet for 120 d. On the last two days, blood samples were collected from each animal via the jugular vein before morning feeding for analyzing serum biochemical parameters; rumen fluid samples were obtained via esophageal intubation 2 h after morning feeding for analyzing rumen fermentation parameters and bacterial communities. The results show that both breed and sex had a certain impact on fattening performance, serum biochemical parameters, and rumen fermentation. No differences in the diversity and structure of rumen bacterial communities were observed. Significant interactions (p < 0.05) of breed and sex were observed for Succinivibrionaceae UCG-002 and Prevotellaceae UCG-001. The relative abundances of the Rikenellaceae RC9 gut group, Prevotellaceae UCG-003, and Succinivibrio were different (p < 0.05) between breeds. Heifers had a higher (p = 0.008) relative abundance of the Rikenellaceae RC9 gut group than steers. Correlation analysis showed a significant relationship (p < 0.05) of rumen bacteria with serum biochemical parameters, rumen pH, and rumen fermentation patterns. Additionally, only two genera, Prevotellaceae UCG-003 and Prevotellaceae UCG-001, had positive correlations with feed efficiency. In conclusion, serum biochemical parameters, rumen fermentation, and rumen bacterial communities are partly driven by the breed and sex of cattle fed a high-grain diet.
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Affiliation(s)
- Xinjun Qiu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100000, China; (X.Q.); (X.Q.); (Z.C.); (R.H.); (S.Z.); (S.Y.); (L.W.); (Y.C.); (Y.L.); (Y.M.)
| | - Xiaoli Qin
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100000, China; (X.Q.); (X.Q.); (Z.C.); (R.H.); (S.Z.); (S.Y.); (L.W.); (Y.C.); (Y.L.); (Y.M.)
| | - Liming Chen
- Hubei Fulljoywo Agricultural Development Company Limited, Yichang 443000, China;
| | - Zhiming Chen
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100000, China; (X.Q.); (X.Q.); (Z.C.); (R.H.); (S.Z.); (S.Y.); (L.W.); (Y.C.); (Y.L.); (Y.M.)
| | - Rikang Hao
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100000, China; (X.Q.); (X.Q.); (Z.C.); (R.H.); (S.Z.); (S.Y.); (L.W.); (Y.C.); (Y.L.); (Y.M.)
| | - Siyu Zhang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100000, China; (X.Q.); (X.Q.); (Z.C.); (R.H.); (S.Z.); (S.Y.); (L.W.); (Y.C.); (Y.L.); (Y.M.)
| | - Shunran Yang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100000, China; (X.Q.); (X.Q.); (Z.C.); (R.H.); (S.Z.); (S.Y.); (L.W.); (Y.C.); (Y.L.); (Y.M.)
| | - Lina Wang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100000, China; (X.Q.); (X.Q.); (Z.C.); (R.H.); (S.Z.); (S.Y.); (L.W.); (Y.C.); (Y.L.); (Y.M.)
| | - Yafang Cui
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100000, China; (X.Q.); (X.Q.); (Z.C.); (R.H.); (S.Z.); (S.Y.); (L.W.); (Y.C.); (Y.L.); (Y.M.)
| | - Yingqi Li
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100000, China; (X.Q.); (X.Q.); (Z.C.); (R.H.); (S.Z.); (S.Y.); (L.W.); (Y.C.); (Y.L.); (Y.M.)
| | - Yiheng Ma
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100000, China; (X.Q.); (X.Q.); (Z.C.); (R.H.); (S.Z.); (S.Y.); (L.W.); (Y.C.); (Y.L.); (Y.M.)
| | - Binghai Cao
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100000, China; (X.Q.); (X.Q.); (Z.C.); (R.H.); (S.Z.); (S.Y.); (L.W.); (Y.C.); (Y.L.); (Y.M.)
- Correspondence: (B.C.); (H.S.); Tel.: +86-010-6273-3850 (B.C.); +86-010-6281-4346 (H.S.)
| | - Huawei Su
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100000, China; (X.Q.); (X.Q.); (Z.C.); (R.H.); (S.Z.); (S.Y.); (L.W.); (Y.C.); (Y.L.); (Y.M.)
- Correspondence: (B.C.); (H.S.); Tel.: +86-010-6273-3850 (B.C.); +86-010-6281-4346 (H.S.)
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Abstract
Cardiovascular diseases (CVDs) still remain the leading concern of global health, accounting for approximately 17.9 million deaths in 2016. The pathogenetic mechanisms of CVDs are multifactorial and incompletely understood. Recent evidence has shown that alterations in the gut microbiome and its associated metabolites may influence the pathogenesis and progression of CVDs such as atherosclerosis, heart failure, hypertension, and arrhythmia, yet the underlying links are not fully elucidated. Owing to the progress in next-generation sequencing techniques and computational strategies, researchers now are available to explore the emerging links to the genomes, transcriptomes, proteomes, and metabolomes in parallel meta-omics approaches, presenting a panoramic vista of culture-independent microbial investigation. This review aims to outline the characteristics of meta-omics pipelines and provide a brief overview of current applications in CVDs studies which can be practical for addressing crucial knowledge gaps in this field, as well as to shed its light on cardiovascular risk biomarkers and therapeutic intervention in the near future.
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Affiliation(s)
- Jing Xu
- State Key Laboratory of Cardiovascular Diseases, Fuwai Hospital & National Center for Cardiovascular Diseases, Beijing, China,Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Yuejin Yang
- State Key Laboratory of Cardiovascular Diseases, Fuwai Hospital & National Center for Cardiovascular Diseases, Beijing, China,Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China,CONTACT Yuejin Yang State Key Laboratory of Cardiovascular Disease, Fuwai Hospital & National Center for Cardiovascular Disease, Beijing, China; Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
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Pereira AM, de Lurdes Nunes Enes Dapkevicius M, Borba AES. Alternative pathways for hydrogen sink originated from the ruminal fermentation of carbohydrates: Which microorganisms are involved in lowering methane emission? Anim Microbiome 2022; 4:5. [PMID: 34991722 PMCID: PMC8734291 DOI: 10.1186/s42523-021-00153-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 12/17/2021] [Indexed: 12/25/2022] Open
Abstract
Agriculture is responsible for a great share of the anthropogenic sources of greenhouse gases that, by warming the earth, threaten its biodiversity. Among greenhouse gas emissions, enteric CH4 from livestock is an important target to slow down climate changes. The CH4 is originated from rumen fermentation and its concentration is affected by several factors, including genetics and nutrition. Ruminants have an extraordinary symbiosis with microorganisms (bacteria, fungi, and protozoa) that ferment otherwise indigestible carbohydrates, from which they obtain energy to grow and continue actively producing, among other products, volatile fatty acids, CO2 and H2. Detrimental ruminal accumulation of H2 is avoided by methanogenesis carried out by Archaea methanogens. Importantly, methanogenesis is not the only H2 sink pathway. In fact, other bacteria can reduce substrates using metabolic hydrogen formed during carbohydrate fermentation, namely propionate production and reductive acetogenesis, thus lowering the CH4 produced. Although the complexity of rumen poses challenges to mitigate CH4 production, the emergence of sequencing techniques that allow the study of microbial communities, gene expression, and metabolome are largely contributing to unravel pathways and key players in the rumen. Indeed, it is now recognized that in vivo emissions of CH4 are correlated to microbial communities, and particularly with the abundance of methanogens, several bacterial groups, and their genes. The goal of CH4 mitigation is to work in favor of the natural processes, without compromising rumen function, animal health, and productivity. Notwithstanding, the major challenge continues to be the feasibility and affordability of the proposed solutions.
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Affiliation(s)
- Ana Margarida Pereira
- Faculdade de Ciências Agrárias e do Ambiente, Instituto de Investigação em Tecnologias Agrárias e do Ambiente (IITAA), Universidade dos Açores, Campus de Angra do Heroísmo, rua Capitão João d’Ávila, 9700-042 Açores Angra do Heroísmo, Portugal
| | - Maria de Lurdes Nunes Enes Dapkevicius
- Faculdade de Ciências Agrárias e do Ambiente, Instituto de Investigação em Tecnologias Agrárias e do Ambiente (IITAA), Universidade dos Açores, Campus de Angra do Heroísmo, rua Capitão João d’Ávila, 9700-042 Açores Angra do Heroísmo, Portugal
| | - Alfredo E. S. Borba
- Faculdade de Ciências Agrárias e do Ambiente, Instituto de Investigação em Tecnologias Agrárias e do Ambiente (IITAA), Universidade dos Açores, Campus de Angra do Heroísmo, rua Capitão João d’Ávila, 9700-042 Açores Angra do Heroísmo, Portugal
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Perlman D, Martínez-Álvaro M, Moraïs S, Altshuler I, Hagen LH, Jami E, Roehe R, Pope PB, Mizrahi I. Concepts and Consequences of a Core Gut Microbiota for Animal Growth and Development. Annu Rev Anim Biosci 2021; 10:177-201. [PMID: 34941382 DOI: 10.1146/annurev-animal-013020-020412] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Animal microbiomes are occasionally considered as an extension of host anatomy, physiology, and even their genomic architecture. Their compositions encompass variable and constant portions when examined across multiple hosts. The latter, termed the core microbiome, is viewed as more accommodated to its host environment and suggested to benefit host fitness. Nevertheless, discrepancies in its definitions, characteristics, and importance to its hosts exist across studies. We survey studies that characterize the core microbiome, detail its current definitions and available methods to identify it, and emphasize the crucial need to upgrade and standardize the methodologies among studies. We highlight ruminants as a case study and discuss the link between the core microbiome and host physiology and genetics, as well as potential factors that shape it. We conclude with main directives of action to better understand the host-core microbiome axis and acquire the necessary insights into its controlled modulation. Expected final online publication date for the Annual Review of Animal Biosciences, Volume 10 is February 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Daphne Perlman
- Department of Life Sciences, Ben-Gurion University of the Negev and the National Institute for Biotechnology in the Negev, Be'er-Sheva, Israel;
| | - Marina Martínez-Álvaro
- Department of Agriculture, Horticulture and Engineering Sciences, SRUC (Scotland's Rural College), Edinburgh, Scotland, United Kingdom
| | - Sarah Moraïs
- Department of Life Sciences, Ben-Gurion University of the Negev and the National Institute for Biotechnology in the Negev, Be'er-Sheva, Israel;
| | - Ianina Altshuler
- Faculty of Biosciences, Norwegian University of Life Sciences, Aas, Norway;
| | - Live H Hagen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Aas, Norway
| | - Elie Jami
- Department of Ruminant Science, Institute of Animal Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
| | - Rainer Roehe
- Department of Agriculture, Horticulture and Engineering Sciences, SRUC (Scotland's Rural College), Edinburgh, Scotland, United Kingdom
| | - Phillip B Pope
- Faculty of Biosciences, Norwegian University of Life Sciences, Aas, Norway; .,Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Aas, Norway
| | - Itzhak Mizrahi
- Department of Life Sciences, Ben-Gurion University of the Negev and the National Institute for Biotechnology in the Negev, Be'er-Sheva, Israel;
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Hu C, Ding L, Jiang C, Ma C, Liu B, Li D, Degen AA. Effects of Management, Dietary Intake, and Genotype on Rumen Morphology, Fermentation, and Microbiota, and on Meat Quality in Yaks and Cattle. Front Nutr 2021; 8:755255. [PMID: 34859030 PMCID: PMC8632495 DOI: 10.3389/fnut.2021.755255] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Accepted: 10/11/2021] [Indexed: 12/20/2022] Open
Abstract
Traditionally, yaks graze only natural grassland, even in harsh winters. Meat from grazing yaks is considered very healthy; however, feedlot fattening, which includes concentrate, has been introduced. We questioned whether this change in management and diet would have an impact on the rumen and meat quality of yaks. This study examined the morphology, fermentation, and microbiota of the rumen and the quality of meat of three groups of bovines: (1) grazing yaks (GYs, 4-year olds), without dietary supplements; (2) yaks (FYs, 2.5-year olds) feedlot-fattened for 5 months after grazing natural pasture; and (3) feedlot-fattened cattle (FC, Simmental, 2-year olds). This design allowed us to determine the role of diet (with and without concentrate) and genotype (yaks vs. cattle) on variables measured. Ruminal papillae surface area was greater in the FYs than in the GYs (P = 0.02), and ruminal microbial diversity was greater but richness was lesser in the GYs than in the FC and FYs. Concentrations of ruminal volatile fatty acids were greater in the yaks than in the cattle. In addition, both yak groups had higher protein and lower fat contents in meat than the FC. Meat of GY had a lower n6:n3 ratio than FY and FC, and was the only group with a ratio below r, which is recommended for healthy food. Essential amino acids (EAA), as a proportion of total AA and of non-essential AA of yak meat, met WHO criteria for healthy food; whereas FC did not.
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Affiliation(s)
- Changsheng Hu
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Luming Ding
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, China
- Qinghai Provincial Key Laboratory of Adaptive Management on Alpine Grassland, Qinghai University, Xining, China
| | - Cuixia Jiang
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Chengfang Ma
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Botao Liu
- Gansu Devotion Biotechnology Co., Ltd., Zhangye, China
| | - Donglin Li
- Qinghai Qilian Yida Meat Co., Ltd., Qinghai, China
| | - Abraham Allan Degen
- Desert Animal Adaptations and Husbandry, Wyler Department of Dryland Agriculture, Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Beer Sheva, Israel
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Chagas JC, Ramin M, Exposito RG, Smidt H, Krizsan SJ. Effect of a Low-Methane Diet on Performance and Microbiome in Lactating Dairy Cows Accounting for Individual Pre-Trial Methane Emissions. Animals (Basel) 2021; 11:ani11092597. [PMID: 34573563 PMCID: PMC8468840 DOI: 10.3390/ani11092597] [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: 08/13/2021] [Revised: 08/30/2021] [Accepted: 08/31/2021] [Indexed: 11/16/2022] Open
Abstract
This study examined the effects of partly replacing grass silage (GS) with maize silage (MS), with or without rapeseed oil (RSO) supplementation, on methane (CH4) emissions, production performance, and rumen microbiome in the diets of lactating dairy cows. The effect of individual pre-trial CH4-emitting characteristics on dietary emissions mitigation was also examined. Twenty Nordic Red cows at 71 ± 37.2 (mean ± SD) days in milk were assigned to a replicated 4 × 4 Latin square design with four dietary treatments (GS, GS supplemented with RSO, GS plus MS, GS plus MS supplemented with RSO) applied in a 2 × 2 factorial arrangement. Partial replacement of GS with MS decreased the intake of dry matter (DM) and nutrients, milk production, yield of milk components, and general nutrient digestibility. Supplementation with RSO decreased the intake of DM and nutrients, energy-corrected milk yield, composition and yield of milk fat and protein, and general digestibility of nutrients, except for crude protein. Individual cow pre-trial measurements of CH4-emitting characteristics had a significant influence on gas emissions but did not alter the magnitude of CH4 emissions. Dietary RSO decreased daily CH4, yield, and intensity. It also increased the relative abundance of rumen Methanosphaera and Succinivibrionaceae and decreased that of Bifidobacteriaceae. There were no effects of dietary MS on CH4 emissions in this study, but supplementation with 41 g RSO/kg of DM reduced daily CH4 emissions from lactating dairy cows by 22.5%.
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Affiliation(s)
- Juana C. Chagas
- Department of Agricultural Research for Northern Sweden, Swedish University of Agricultural Sciences (SLU), Skogsmarksgränd, 90183 Umeå, Sweden;
- Correspondence: (J.C.C.); (S.J.K.); Tel.: +46-90-7868748 (J.C.C.)
| | - Mohammad Ramin
- Department of Agricultural Research for Northern Sweden, Swedish University of Agricultural Sciences (SLU), Skogsmarksgränd, 90183 Umeå, Sweden;
| | - Ruth Gomez Exposito
- Laboratory of Microbiology, Wageningen University & Research, 6708 WE Wageningen, The Netherlands; (R.G.E.); (H.S.)
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, 6708 WE Wageningen, The Netherlands; (R.G.E.); (H.S.)
| | - Sophie J. Krizsan
- Department of Agricultural Research for Northern Sweden, Swedish University of Agricultural Sciences (SLU), Skogsmarksgränd, 90183 Umeå, Sweden;
- Correspondence: (J.C.C.); (S.J.K.); Tel.: +46-90-7868748 (J.C.C.)
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Mizrahi I, Wallace RJ, Moraïs S. The rumen microbiome: balancing food security and environmental impacts. Nat Rev Microbiol 2021; 19:553-566. [PMID: 33981031 DOI: 10.1038/s41579-021-00543-6] [Citation(s) in RCA: 107] [Impact Index Per Article: 35.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/09/2021] [Indexed: 02/03/2023]
Abstract
Ruminants produce edible products and contribute to food security. They house a complex rumen microbial community that enables the host to digest their plant feed through microbial-mediated fermentation. However, the rumen microbiome is also responsible for the production of one of the most potent greenhouse gases, methane, and contributes about 18% of its total anthropogenic emissions. Conventional methods to lower methane production by ruminants have proved successful, but to a limited and often temporary extent. An increased understanding of the host-microbiome interactions has led to the development of new mitigation strategies. In this Review we describe the composition, ecology and metabolism of the rumen microbiome, and the impact on host physiology and the environment. We also discuss the most pertinent methane mitigation strategies that emerged to balance food security and environmental impacts.
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Affiliation(s)
- Itzhak Mizrahi
- Department of Life Sciences, Ben-Gurion University of the Negev and the National Institute for Biotechnology in the Negev, Marcus Family Campus, Be'er-Sheva, Israel.
| | - R John Wallace
- The Rowett Institute, University of Aberdeen, Aberdeen, UK
| | - Sarah Moraïs
- Department of Life Sciences, Ben-Gurion University of the Negev and the National Institute for Biotechnology in the Negev, Marcus Family Campus, Be'er-Sheva, Israel
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39
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Salami SA, Valenti B, Luciano G, Lanza M, Umezurike-Amahah NM, Kerry JP, O’Grady MN, Newbold CJ, Priolo A. Dietary cardoon meal modulates rumen biohydrogenation and bacterial community in lambs. Sci Rep 2021; 11:16180. [PMID: 34376766 PMCID: PMC8355377 DOI: 10.1038/s41598-021-95691-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 07/29/2021] [Indexed: 02/08/2023] Open
Abstract
Cardoon meal is a by-product of oil extraction from the seeds of Cynara cardunculus and can serve as a novel alternative feedstuff for ruminants. This study examined the rumen fermentation, biohydrogenation of fatty acids (FA) and microbial community in lambs fed a concentrate diet containing 15% dehydrated lucerne (CON, n = 8) or cardoon meal (CMD, n = 7) for 75 days pre-slaughter. Diets did not influence rumen fermentation characteristics and the abundance of bacteria, methanogens, fungi, or protozoa. Rumen digesta in CMD-fed lambs displayed a higher concentration of total saturated FA and lower total odd- and branched-chain FA and monounsaturated FA. Feeding CMD decreased total trans-18:1 isomer and the ratio of trans-10 to trans-11 C18:1, known as the "trans-10 shift". Amplicon sequencing indicated that the rumen bacterial community in CMD-fed lambs had lower diversity and a higher relative phyla abundance of Proteobacteria at the expense of Bacteroidetes and Fibrobacteres. At the genus level, CMD mediated specific shifts from Prevotella, Alloprevotella, Solobacterium and Fibrobacter to Ruminobacter, suggesting that these genera may play important roles in biohydrogenation. Overall, these results demonstrate that cardoon meal can be used as a feedstuff for ruminants without negatively affecting rumen fermentation and microbiota but its impact on biohydrogenation may influence the FA composition in meat or milk.
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Affiliation(s)
- Saheed A. Salami
- grid.8158.40000 0004 1757 1969Department Di3A, Animal Production Science, University of Catania, Via Valdisavoia 5, 95123 Catania, Italy ,grid.7872.a0000000123318773School of Food and Nutritional Sciences, College of Science, Engineering and Food Science, University College Cork, Cork, Ireland
| | - Bernardo Valenti
- grid.9027.c0000 0004 1757 3630Dipartimento di Scienze Agrarie, Alimentari e Ambientali (DSA3), University of Perugia, Borgo XX Giugno 74, 06121 Perugia, Italy
| | - Giuseppe Luciano
- grid.8158.40000 0004 1757 1969Department Di3A, Animal Production Science, University of Catania, Via Valdisavoia 5, 95123 Catania, Italy
| | - Massimiliano Lanza
- grid.8158.40000 0004 1757 1969Department Di3A, Animal Production Science, University of Catania, Via Valdisavoia 5, 95123 Catania, Italy
| | - Ngozi M. Umezurike-Amahah
- grid.8158.40000 0004 1757 1969Department Di3A, Animal Production Science, University of Catania, Via Valdisavoia 5, 95123 Catania, Italy
| | - Joseph P. Kerry
- grid.7872.a0000000123318773School of Food and Nutritional Sciences, College of Science, Engineering and Food Science, University College Cork, Cork, Ireland
| | - Michael N. O’Grady
- grid.7872.a0000000123318773School of Food and Nutritional Sciences, College of Science, Engineering and Food Science, University College Cork, Cork, Ireland
| | - Charles J. Newbold
- grid.426884.40000 0001 0170 6644Scotland’s Rural College, Peter Wilson Building, King’s Buildings, Edinburgh, EH9 3JG UK
| | - Alessandro Priolo
- grid.8158.40000 0004 1757 1969Department Di3A, Animal Production Science, University of Catania, Via Valdisavoia 5, 95123 Catania, Italy
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Wang Z, Fu H, Zhou Y, Yan M, Chen D, Yang M, Xiao S, Chen C, Huang L. Identification of the gut microbiota biomarkers associated with heat cycle and failure to enter oestrus in gilts. Microb Biotechnol 2021; 14:1316-1330. [PMID: 33305898 PMCID: PMC8313273 DOI: 10.1111/1751-7915.13695] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 10/16/2020] [Accepted: 10/18/2020] [Indexed: 01/09/2023] Open
Abstract
Failed puberty is one of the main reasons for eliminating gilts from production herds. This is often caused by disorders of sex hormones. An increasing number of studies have suggested that the gut microbiota may regulate sex hormones and vice versa. Whether the gut microbiota is involved in the failure of oestrus in gilts remains unknown. We used 16S rRNA gene sequencing, network-based microbiota analysis and prediction of functional capacity from 16S rRNA gene sequences to explore the shifts in the gut microbiota throughout a heat cycle in 22 eight-month-old gilts. We found that a module of co-occurrence networks composed of Sphaerochaeta and Treponema, co-occurred with oestrus during a heat cycle. The mcode score of this module reflecting the stability and importance in the network achieved the highest value at the oestrus stage. We then identified bacterial biosignatures associated with the failure to show puberty in 163 gilts. Prevotella, Treponema, Faecalibacterium, Oribacterium, Succinivibrio and Anaerovibrio were enriched in gilts showing normal heat cycles, while Lachnospiraceae, Ruminococcus, Coprococcus and Oscillospira had higher abundance in gilts failing to show puberty. Prediction of functional capacity of the gut microbiome identified a lesser abundance of the pathway 'retinol metabolism' in gilts that failed to undergo puberty. This pathway was also significantly associated with those bacterial taxa involved in failed puberty identified in this study (P < 0.05). This result suggests that the changed gut bacteria might result in a disorder of retinol metabolism, and this may be an explanation for the failure to enter oestrus.
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Affiliation(s)
- Zhong Wang
- State Key Laboratory of Pig Genetic Improvement and Production TechnologyJiangxi Agricultural UniversityNanchangJiangxi330045China
| | - Hao Fu
- State Key Laboratory of Pig Genetic Improvement and Production TechnologyJiangxi Agricultural UniversityNanchangJiangxi330045China
| | - Yunyan Zhou
- State Key Laboratory of Pig Genetic Improvement and Production TechnologyJiangxi Agricultural UniversityNanchangJiangxi330045China
| | - Min Yan
- State Key Laboratory of Pig Genetic Improvement and Production TechnologyJiangxi Agricultural UniversityNanchangJiangxi330045China
| | - Dong Chen
- State Key Laboratory of Pig Genetic Improvement and Production TechnologyJiangxi Agricultural UniversityNanchangJiangxi330045China
| | - Ming Yang
- Zhongkai University of Agriculture and EngineeringGuangzhouGuangdong510225China
| | - Shijun Xiao
- State Key Laboratory of Pig Genetic Improvement and Production TechnologyJiangxi Agricultural UniversityNanchangJiangxi330045China
| | - Congying Chen
- State Key Laboratory of Pig Genetic Improvement and Production TechnologyJiangxi Agricultural UniversityNanchangJiangxi330045China
| | - Lusheng Huang
- State Key Laboratory of Pig Genetic Improvement and Production TechnologyJiangxi Agricultural UniversityNanchangJiangxi330045China
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Han X, Lei X, Yang X, Shen J, Zheng L, Jin C, Cao Y, Yao J. A Metagenomic Insight Into the Hindgut Microbiota and Their Metabolites for Dairy Goats Fed Different Rumen Degradable Starch. Front Microbiol 2021; 12:651631. [PMID: 34163442 PMCID: PMC8216219 DOI: 10.3389/fmicb.2021.651631] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 04/20/2021] [Indexed: 12/12/2022] Open
Abstract
High starch diets have been proven to increase the risk of hindgut acidosis in high-yielding dairy animals. As an effective measurement of dietary carbohydrate for ruminants, studies on rumen degradable starch (RDS) and the effects on the gut microbiota diversity of carbohydrate-active enzymes (CAZymes), and Kyoto Encyclopedia of Genes and Genomes (KEGG) Orthology functional categories are helpful to understand the mechanisms between gut microbiota and carbohydrate metabolism in dairy goats. A total of 18 lactating goats (45.8 ± 1.54 kg) were randomly divided equally into three dietary treatments with low dietary RDS concentrations of 20.52% (LRDS), medium RDS of 22.15% (MRDS), and high RDS of 24.88% (HRDS) on a DM basis for 5 weeks. Compared with the LRDS and MRDS groups, HRDS increased acetate molar proportion in the cecum. For the HRDS group, the abundance of family Ruminococcaceae and genus Ruminococcaceae UCG-010 were significantly increased in the cecum. For the LRDS group, the butyrate molar proportion and the abundance of butyrate producer family Bacteroidale_S24-7, family Lachnospiraceae, and genus Bacteroidale_S24-7_group were significantly increased in the cecum. Based on the BugBase phenotypic prediction, the microbial oxidative stress tolerant and decreased potentially pathogenic in the LRDS group were increased in the cecum compared with the HRDS group. A metagenomic study on cecal bacteria revealed that dietary RDS level could affect carbohydrate metabolism by increasing the glycoside hydrolase 95 (GH95) family and cellulase enzyme (EC 3.2.1.4) in the HRDS group; increasing the GH13_20 family and isoamylase enzyme (EC 3.2.1.68) in the LRDS group. PROBIO probiotics database showed the relative gene abundance of cecal probiotics significantly decreased in the HRDS group. Furthermore, goats fed the HRDS diet had a lower protein expression of Muc2, and greater expression RNA of interleukin-1β and secretory immunoglobulin A in cecal mucosa than did goats fed the LRDS diet. Combined with the information from previous results from rumen, dietary RDS level altered the degradation position of carbohydrates in the gastrointestinal (GI) tract and increased the relative abundance of gene encoded enzymes degrading cellulose in the HRDS group in the cecum of dairy goats. This study revealed that the HRDS diet could bring disturbances to the microbial communities network containing taxa of the Lachnospiraceae and Ruminococcaceae and damage the mucus layer and inflammation in the cecum of dairy goats.
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Affiliation(s)
- Xiaoying Han
- Country College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xinjian Lei
- Country College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xuexin Yang
- Country College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Jing Shen
- Country College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Lixin Zheng
- Country College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Chunjia Jin
- Country College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yangchun Cao
- Country College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Junhu Yao
- Country College of Animal Science and Technology, Northwest A&F University, Yangling, China
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Hashemi S, Hashemi SE, Lien KM, Lamb JJ. Molecular Microbial Community Analysis as an Analysis Tool for Optimal Biogas Production. Microorganisms 2021; 9:microorganisms9061162. [PMID: 34071282 PMCID: PMC8226781 DOI: 10.3390/microorganisms9061162] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 05/17/2021] [Accepted: 05/26/2021] [Indexed: 11/16/2022] Open
Abstract
The microbial diversity in anaerobic digestion (AD) is important because it affects process robustness. High-throughput sequencing offers high-resolution data regarding the microbial diversity and robustness of biological systems including AD; however, to understand the dynamics of microbial processes, knowing the microbial diversity is not adequate alone. Advanced meta-omic techniques have been established to determine the activity and interactions among organisms in biological processes like AD. Results of these methods can be used to identify biomarkers for AD states. This can aid a better understanding of system dynamics and be applied to producing comprehensive models for AD. The paper provides valuable knowledge regarding the possibility of integration of molecular methods in AD. Although meta-genomic methods are not suitable for on-line use due to long operating time and high costs, they provide extensive insight into the microbial phylogeny in AD. Meta-proteomics can also be explored in the demonstration projects for failure prediction. However, for these methods to be fully realised in AD, a biomarker database needs to be developed.
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Affiliation(s)
- Seyedbehnam Hashemi
- Department of Energy and Process Engineering & Enersense, Norwegian University of Science and Technology (NTNU), 7034 Trondheim, Norway; (S.H.); (S.E.H.); (K.M.L.)
| | - Sayed Ebrahim Hashemi
- Department of Energy and Process Engineering & Enersense, Norwegian University of Science and Technology (NTNU), 7034 Trondheim, Norway; (S.H.); (S.E.H.); (K.M.L.)
| | - Kristian M. Lien
- Department of Energy and Process Engineering & Enersense, Norwegian University of Science and Technology (NTNU), 7034 Trondheim, Norway; (S.H.); (S.E.H.); (K.M.L.)
| | - Jacob J. Lamb
- Department of Energy and Process Engineering & Enersense, Norwegian University of Science and Technology (NTNU), 7034 Trondheim, Norway; (S.H.); (S.E.H.); (K.M.L.)
- Department of Electronic Systems, Norwegian University of Science and Technology (NTNU), 7034 Trondheim, Norway
- Correspondence:
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In Vitro Screening of East Asian Plant Extracts for Potential Use in Reducing Ruminal Methane Production. Animals (Basel) 2021; 11:ani11041020. [PMID: 33916571 PMCID: PMC8066825 DOI: 10.3390/ani11041020] [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: 03/11/2021] [Revised: 03/30/2021] [Accepted: 04/02/2021] [Indexed: 11/16/2022] Open
Abstract
Indiscriminate use of antibiotics can result in antibiotic residues in animal products; thus, plant compounds may be better alternative sources for mitigating methane (CH4) production. An in vitro screening experiment was conducted to evaluate the potential application of 152 dry methanolic or ethanolic extracts from 137 plant species distributed in East Asian countries as anti-methanogenic additives in ruminant feed. The experimental material consisted of 200 mg total mixed ration, 20 mg plant extract, and 30 mL diluted ruminal fluid-buffer mixture in 60 mL serum bottles that were sealed with rubber stoppers and incubated at 39 °C for 24 h. Among the tested extracts, eight extracts decreased CH4 production by >20%, compared to the corresponding controls: stems of Vitex negundo var. incisa, stems of Amelanchier asiatica, fruit of Reynoutria sachalinensis, seeds of Tribulus terrestris, seeds of Pharbitis nil, leaves of Alnus japonica, stem and bark of Carpinus tschonoskii, and stems of Acer truncatum. A confirmation assay of the eight plant extracts at a dosage of 10 mg with four replications repeated on 3 different days revealed that the extracts decreased CH4 concentration in the total gas (7-15%) and total CH4 production (17-37%), compared to the control. This is the first report to identify the anti-methanogenic activities of eight potential plant extracts. All extracts decreased ammonia (NH3-N) concentrations. Negative effects on total gas and volatile fatty acid (VFA) production were also noted for all extracts that were rich in hydrolysable tannins and total saponins or fatty acids. The underlying modes of action differed among plants: extracts from P. nil, V. negundo var. incisa, A. asiatica, and R. sachalinensis resulted in a decrease in total methanogen or the protozoan population (p < 0.05) but extracts from other plants did not. Furthermore, extracts from P. nil decreased the population of total protozoa and increased the proportion of propionate among VFAs (p < 0.05). Identifying bioactive compounds in seeds of P. nil by gas chromatography-mass spectrometry analysis revealed enrichment of linoleic acid (18:2). Overall, seeds of P. nil could be a possible alternative to ionophores or oil seeds to mitigate ruminal CH4 production.
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Bailoni L, Carraro L, Cardin M, Cardazzo B. Active Rumen Bacterial and Protozoal Communities Revealed by RNA-Based Amplicon Sequencing on Dairy Cows Fed Different Diets at Three Physiological Stages. Microorganisms 2021; 9:754. [PMID: 33918504 PMCID: PMC8066057 DOI: 10.3390/microorganisms9040754] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/29/2021] [Accepted: 04/01/2021] [Indexed: 12/12/2022] Open
Abstract
Seven Italian Simmental cows were monitored during three different physiological stages, namely late lactation (LL), dry period (DP), and postpartum (PP), to evaluate modifications in their metabolically-active rumen bacterial and protozoal communities using the RNA-based amplicon sequencing method. The bacterial community was dominated by seven phyla: Proteobacteria, Bacteroidetes, Firmicutes, Spirochaetes, Fibrobacteres, Verrucomicrobia, and Tenericutes. The relative abundance of the phylum Proteobacteria decreased from 47.60 to 28.15% from LL to DP and then increased to 33.24% in PP. An opposite pattern in LL, DP, and PP stages was observed for phyla Verrucomicrobia (from 0.96 to 4.30 to 1.69%), Elusimicrobia (from 0.32 to 2.84 to 0.25%), and SR1 (from 0.50 to 2.08 to 0.79%). The relative abundance of families Succinivibrionaceae and Prevotellaceae decreased in the DP, while Ruminococcaceae increased. Bacterial genera Prevotella and Treponema were least abundant in the DP as compared to LL and PP, while Ruminobacter and Succinimonas were most abundant in the DP. The rumen eukaryotic community was dominated by protozoal phylum Ciliophora, which showed a significant decrease in relative abundance from 97.6 to 93.9 to 92.6 in LL, DP, and PP, respectively. In conclusion, the physiological stage-dependent dietary changes resulted in a clear shift in metabolically-active rumen microbial communities.
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Affiliation(s)
- Lucia Bailoni
- Department of Comparative Biomedicine and Food Science (BCA), University of Padova, Viale dell’Universitá 16, 35020 Legnaro, PD, Italy; (L.C.); (M.C.); (B.C.)
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Hitch TCA, Afrizal A, Riedel T, Kioukis A, Haller D, Lagkouvardos I, Overmann J, Clavel T. Recent advances in culture-based gut microbiome research. Int J Med Microbiol 2021; 311:151485. [PMID: 33689954 DOI: 10.1016/j.ijmm.2021.151485] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 01/15/2021] [Accepted: 02/23/2021] [Indexed: 12/16/2022] Open
Abstract
Gut microbes affect the physiology of their hosts. Studying their diversity and functions is thus of utmost importance as it will open new avenues towards the discovery of new biomolecules and the treatment of diseases. Gut microbiome research is currently boosted by the unification of metagenomics, which has dominated the field in the last two decades, and cultivation, which is experiencing a renaissance. Each of these approaches has advantages and drawbacks that can be overcome if used synergistically. In this brief article, we summarize recent literature and own studies on the cultivation of gut microbes, provide a succinct status quo of cultured fractions and collections of isolates, and give short opinions on challenges and next steps to take.
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Affiliation(s)
- Thomas C A Hitch
- Functional Microbiome Research Group, Institute of Medical Microbiology, RWTH University Hospital, Aachen, Germany
| | - Afrizal Afrizal
- Functional Microbiome Research Group, Institute of Medical Microbiology, RWTH University Hospital, Aachen, Germany
| | - Thomas Riedel
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany; German Center for Infection Research (DZIF), Partner site Hannover-Braunschweig, Braunschweig, Germany
| | - Antonios Kioukis
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Greece
| | - Dirk Haller
- ZIEL Institute for Food and Health, Technical University of Munich, Freising, Germany
| | - Ilias Lagkouvardos
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Greece; ZIEL Institute for Food and Health, Technical University of Munich, Freising, Germany
| | - Jörg Overmann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany; German Center for Infection Research (DZIF), Partner site Hannover-Braunschweig, Braunschweig, Germany
| | - Thomas Clavel
- Functional Microbiome Research Group, Institute of Medical Microbiology, RWTH University Hospital, Aachen, Germany; ZIEL Institute for Food and Health, Technical University of Munich, Freising, Germany.
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Vahidi MF, Gharechahi J, Behmanesh M, Ding XZ, Han JL, Hosseini Salekdeh G. Diversity of microbes colonizing forages of varying lignocellulose properties in the sheep rumen. PeerJ 2021; 9:e10463. [PMID: 33510967 PMCID: PMC7808268 DOI: 10.7717/peerj.10463] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 11/10/2020] [Indexed: 01/13/2023] Open
Abstract
Background The rumen microbiota contributes strongly to the degradation of ingested plant materials. There is limited knowledge about the diversity of taxa involved in the breakdown of lignocellulosic biomasses with varying chemical compositions in the rumen. Method We aimed to assess how and to what extent the physicochemical properties of forages influence the colonization and digestion by rumen microbiota. This was achieved by placing nylon bags filled with candidate materials in the rumen of fistulated sheep for a period of up to 96 h, followed by measuring forage's chemical characteristics and community structure of biofilm-embedded microbiota. Results Rumen degradation for all forages appeared to have occurred mainly during the first 24 h of their incubation, which significantly slowed down after 48 h of rumen incubation, depending on their chemical properties. Random Forest analysis predicted the predominant role of Treponema and Butyrivibrio in shaping microbial diversity attached to the forages during the course of rumen incubation. Exploring community structure and composition of fiber-attached microbiota revealed significant differential colonization rates of forages depending on their contents for NDF and cellulose. The correlation analysis highlighted the significant contribution of Lachnospiraceae and Veillonellaceae to fiber degradation in the sheep rumen. Conclusion Our findings suggested that forage cellulose components are critical in shaping the pattern of microbial colonization and thus their final digestibility in the rumen.
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Affiliation(s)
- Mohammad Farhad Vahidi
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Javad Gharechahi
- Human Genetics Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Mehrdad Behmanesh
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Xue-Zhi Ding
- Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Jian-Lin Han
- Livestock Genetics Program, International Livestock Research Institute (ILRI), Nairobi, Kenya.,CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China, Institute of Animal Science, Beijing, China
| | - Ghasem Hosseini Salekdeh
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education, and Extension Organization, Karaj, Iran
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Buffa G, Mangia NP, Cesarani A, Licastro D, Sorbolini S, Pulina G, Nudda A. Agroindustrial by-products from tomato, grape and myrtle given at low dosage to lactating dairy ewes: effects on rumen parameters and microbiota. ITALIAN JOURNAL OF ANIMAL SCIENCE 2020. [DOI: 10.1080/1828051x.2020.1848465] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- G. Buffa
- Dipartimento di Agraria, University of Sassari, Sassari, Italy
| | - N. P. Mangia
- Dipartimento di Agraria, University of Sassari, Sassari, Italy
| | - A. Cesarani
- Dipartimento di Agraria, University of Sassari, Sassari, Italy
| | - D. Licastro
- ARGO Open Lab Platform for Genome sequencing, AREA Science Park, Trieste, Italy
| | - S. Sorbolini
- Dipartimento di Agraria, University of Sassari, Sassari, Italy
| | - G. Pulina
- Dipartimento di Agraria, University of Sassari, Sassari, Italy
| | - A. Nudda
- Dipartimento di Agraria, University of Sassari, Sassari, Italy
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Fan Q, Wanapat M, Hou F. Rumen bacteria influence milk protein yield of yak grazing on the Qinghai-Tibet Plateau. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2020; 34:1466-1478. [PMID: 33332947 PMCID: PMC8495338 DOI: 10.5713/ab.20.0601] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 11/26/2020] [Indexed: 11/27/2022]
Abstract
Objective Ruminants are completely dependent on their microbiota for rumen fermentation, feed digestion, and consequently, their metabolism for productivity. This study aimed to evaluate the rumen bacteria of lactating yaks with different milk protein yields, using high-throughput sequencing technology, in order to understand the influence of these bacteria on milk production. Methods Yaks with similar high milk protein yield (high milk yield and high milk protein content, HH; n = 12) and low milk protein yield (low milk yield and low milk protein content, LL; n = 12) were randomly selected from 57 mid-lactation yaks. Ruminal contents were collected using an oral stomach tube from the 24 yaks selected. High-throughput sequencing of bacterial 16S rRNA gene was used. Results Ruminal ammonia N, total volatile fatty acids, acetate, propionate, and isobutyrate concentrations were found to be higher in HH than LL yaks. Community richness (Chao 1 index) and diversity indices (Shannon index) of rumen microbiota were higher in LL than HH yaks. Relative abundances of the Bacteroidetes and Tenericutes phyla in the rumen fluid were significantly increased in HH than LL yaks, but significantly decreased for Firmicutes. Relative abundances of the Succiniclasticum, Butyrivibrio 2, Prevotella 1, and Prevotellaceae UCG-001 genera in the rumen fluid of HH yaks was significantly increased, but significantly decreased for Christensenellaceae R-7 group and Coprococcus 1. Principal coordinates analysis on unweighted UniFrac distances revealed that the bacterial community structure of rumen differed between yaks with high and low milk protein yields. Furthermore, rumen microbiota were functionally enriched in relation to transporters, ABC transporters, ribosome, and urine metabolism, and also significantly altered in HH and LL yaks. Conclusion We observed significant differences in the composition, diversity, fermentation product concentrations, and function of ruminal microorganisms between yaks with high and low milk protein yields, suggesting the potential influence of rumen microbiota on milk protein yield in yaks. A deeper understanding of this process may allow future modulation of the rumen microbiome for improved agricultural yield through bacterial community design.
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Affiliation(s)
- Qingshan Fan
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730000, China
| | - Metha Wanapat
- Tropical Feed Resources Research and Development Center (TROFREC), Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Fujiang Hou
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730000, China
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Hua D, Zhao Y, Nan X, Xue F, Wang Y, Jiang L, Xiong B. Effect of different glucogenic to lipogenic nutrient ratios on rumen fermentation and bacterial community in vitro. J Appl Microbiol 2020; 130:1868-1882. [PMID: 32998176 PMCID: PMC8247007 DOI: 10.1111/jam.14873] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 09/21/2020] [Accepted: 09/22/2020] [Indexed: 12/22/2022]
Abstract
Aims This study was to investigate the effect of different ratios of glucogenic to lipogenic nutrients on rumen fermentation and the corresponding ruminal bacterial communities. Methods and Results Four diets, including glucogenic diet (G), lipogenic diet (L), two mixed diets: GL1 (G: L = 2 : 1) and GL2 (G:L = 1 : 2), served as substrates and were incubated with rumen fluid in vitro. The results revealed that the gas production, dry matter digestibility and propionate proportion were significantly increased by the G diet than others. The G diet increased the bacterial genera of Succinivibrionaceae_UCG_002, Succinivibrio, Selenomonas_1 and Ruminobacter but decreased some cellulolytic bacteria including the Eubacterium and several genera in family Ruminococcaceae than others. Conclusions When the glucogenic nutrient was above 1/3 of the dietary energy source among the four diets, the in vitro incubation had a higher feed digestibility and lower acetate to propionate ratio. Bacterial genera, including Selenomonas, Succinivibrio, Ruminobacter, certain genera in Ruminococcaceae, Christensenellaceae_R‐7_group and Eubacterium, were more sensitive to the glucogenic to lipogenic nutrients ratio. Significance and Impact of the Study The present study provides a new perspective about the effect of dietary glucogenic to lipogenic ingredient ratios on rumen metabolism by comparing end‐products, gas production and bacterial composition via an in vitro technique.
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Affiliation(s)
- D Hua
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.,Animal Nutrition Group, Department of Animal Sciences, Wageningen University & Research, Wageningen, The Netherlands
| | - Y Zhao
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - X Nan
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - F Xue
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Y Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - L Jiang
- Beijing Key Laboratory for Dairy Cattle Nutrition, Beijing Agricultural College, Beijing, China
| | - B Xiong
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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Hailemariam S, Zhao S, Wang J. Complete Genome Sequencing and Transcriptome Analysis of Nitrogen Metabolism of Succinivibrio dextrinosolvens Strain Z6 Isolated From Dairy Cow Rumen. Front Microbiol 2020; 11:1826. [PMID: 33013723 PMCID: PMC7507024 DOI: 10.3389/fmicb.2020.01826] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 07/10/2020] [Indexed: 02/02/2023] Open
Abstract
The unclassified Succinivibrionaceae lineages are abundant in high yielding multiparous cows, and their presence is positively correlated with milk yield and fat percentage and reduces methane emissions. However, it is still unclear which species are associated with the most efficient feed nutrient utilization and productivity. Here, we used integrated whole genome sequencing and matrix-assisted laser desorption/ionization mass spectrometry, coupled with phenotypic and chemotaxonomic analysis, to characterize S. dextrinosolvens Z6, a species in Succinivibrionaceae isolated from the rumen. To assess the role of S. dextrinosolvens Z6 in nitrogen metabolism, cells grown in different nitrogen sources were analyzed by RNA sequencing. The whole genome sequence result revealed a genome size of 3.47 Mbp with 38.9% of G + C content. A total of 2993 encoding sequences account for 98%. The genes for regulating carbohydrate (10.6%) and amino acid (9%) transport and metabolism were the most abundant. ANI (Average nucleotide identity) showed that SD-Z6 was most closely related to SD-22B (99.96%). The whole genome alignment of SD-Z6 with SD-22B showed a more than 0.34 Mb nucleotide difference. Growth of SD-Z6 occurred at a temperature 36–42°C with an optimum at 39.7°C, pH 6–8; the optimum pH was 6.9 and with 0–1% (w/v) NaCl. The maximum growth (OD600 0.825 ± 0.12) and microbial crude protein (MCP) (178.2 μg/ml) were observed in cells grown in amino acid. The maximum concentration of ammonia (3.96 ± 1.2) was observed in urea containing media and 1.06 mM (26.7% of the produced) remained after 24 h incubation. Activities of urease and glutamine synthase (P < 0.01) and glutamate dehydrogenase (P < 0.05) were significantly different in nitrogen and growth phase. Glutamate synthetase (P < 0.01) was significantly different only at different growth phases. In total, 1246 differentially expressed genes (DEGs) were identified in all nitrogen. Among DEGs, 33 were related to nitrogen metabolism. Their expression correlated with nitrogen sources and the intensity of enzyme activity. This result enhances our understanding of the roles of Succinivibrionaceae in the efficient nitrogen utilization and on environmental protection.
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Affiliation(s)
- Samson Hailemariam
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shengguo Zhao
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jiaqi Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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