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Wang H, Zhan J, Jiang H, Jia H, Pan Y, Zhong X, Huo J, Zhao S. Metagenomics-Metabolomics Exploration of Three-Way-Crossbreeding Effects on Rumen to Provide Basis for Crossbreeding Improvement of Sheep Microbiome and Metabolome of Sheep. Animals (Basel) 2024; 14:2256. [PMID: 39123781 PMCID: PMC11311065 DOI: 10.3390/ani14152256] [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: 06/27/2024] [Revised: 07/30/2024] [Accepted: 07/31/2024] [Indexed: 08/12/2024] Open
Abstract
The objective of this experiment was to explore the effects of three-way hybridization on rumen microbes and metabolites in sheep using rumen metagenomics and metabolomics. Healthy Hu and CAH (Charolais × Australian White × Hu) male lambs of similar birth weight and age were selected for short-term fattening after intensive weaning to collect rumen fluid for sequencing. Rumen metagenomics diversity showed that Hu and CAH sheep were significantly segregated at the species, KEGG-enzyme, and CAZy-family levels. Moreover, the CAH significantly increased the ACE and Chao1 indices. Further, correlation analysis of the abundance of the top 80 revealed that the microorganisms were interrelated at the species, KEGG-enzyme, and CAZy-family levels. Overall, the microbiome significantly affected metabolites of the top five pathways, with the strongest correlation found with succinic acid. Meanwhile, species-level microbial markers significantly affected rumen differential metabolites. In addition, rumen microbial markers in Hu sheep were overall positively correlated with down-regulated metabolites and negatively correlated with up-regulated metabolites. In contrast, rumen microbial markers in CAH lambs were overall negatively correlated with down-regulated metabolites and positively correlated with up-regulated metabolites. These results suggest that three-way crossbreeding significantly affects rumen microbial community and metabolite composition, and that significant interactions exist between rumen microbes and metabolites.
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Affiliation(s)
- Haibo Wang
- Jiangxi Province Key Laboratory of Animal Green and Healthy Breeding, Institute of Animal Husbandry and Veterinary, Jiangxi Academy of Agricultural Science, Nanchang 330200, China; (H.W.); (J.Z.); (H.J.); (H.J.); (Y.P.); (X.Z.)
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Jinshun Zhan
- Jiangxi Province Key Laboratory of Animal Green and Healthy Breeding, Institute of Animal Husbandry and Veterinary, Jiangxi Academy of Agricultural Science, Nanchang 330200, China; (H.W.); (J.Z.); (H.J.); (H.J.); (Y.P.); (X.Z.)
| | - Haoyun Jiang
- Jiangxi Province Key Laboratory of Animal Green and Healthy Breeding, Institute of Animal Husbandry and Veterinary, Jiangxi Academy of Agricultural Science, Nanchang 330200, China; (H.W.); (J.Z.); (H.J.); (H.J.); (Y.P.); (X.Z.)
| | - Haobin Jia
- Jiangxi Province Key Laboratory of Animal Green and Healthy Breeding, Institute of Animal Husbandry and Veterinary, Jiangxi Academy of Agricultural Science, Nanchang 330200, China; (H.W.); (J.Z.); (H.J.); (H.J.); (Y.P.); (X.Z.)
| | - Yue Pan
- Jiangxi Province Key Laboratory of Animal Green and Healthy Breeding, Institute of Animal Husbandry and Veterinary, Jiangxi Academy of Agricultural Science, Nanchang 330200, China; (H.W.); (J.Z.); (H.J.); (H.J.); (Y.P.); (X.Z.)
- College of Animal Science and Veterinary Medicine, Tianjin Agricultural University, Tianjin 300384, China
| | - Xiaojun Zhong
- Jiangxi Province Key Laboratory of Animal Green and Healthy Breeding, Institute of Animal Husbandry and Veterinary, Jiangxi Academy of Agricultural Science, Nanchang 330200, China; (H.W.); (J.Z.); (H.J.); (H.J.); (Y.P.); (X.Z.)
| | - Junhong Huo
- Jiangxi Province Key Laboratory of Animal Green and Healthy Breeding, Institute of Animal Husbandry and Veterinary, Jiangxi Academy of Agricultural Science, Nanchang 330200, China; (H.W.); (J.Z.); (H.J.); (H.J.); (Y.P.); (X.Z.)
| | - Shengguo Zhao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
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Miller S, Hendry M, King J, Sankaranarayanan K, Lawson PA. Bacteroides vicugnae sp. nov. isolated from the fecal material of an alpaca. Anaerobe 2024; 88:102862. [PMID: 38718919 DOI: 10.1016/j.anaerobe.2024.102862] [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: 02/15/2024] [Revised: 04/27/2024] [Accepted: 04/29/2024] [Indexed: 06/10/2024]
Abstract
Two strictly anaerobic, Gram-stain-negative rod-shaped bacterial isolates, A2-P53T and A1-P5, were isolated from an enrichment of fecal material from two alpacas (Vicugna pacos). Based on a comparative 16S rRNA gene sequence analysis, the isolates were assigned to the genus Bacteroides with the highest sequence similarities to Bacteroides koreensis YS-aM39T (A2- P53T 97.7 % and A1-P5 97.9 %). Additionally, the average nucleotide identity and digital DNA-DNA hybridization values between these isolates and their closest relatives within Bacteroides were less than 92.1 % and 49.1 %, respectively. The average nucleotide identity between isolates A2-P53T and A1-P5 was 99.9 %. The predominant cellular fatty acid for isolates A2-P53T and A1-P5 was C15:0 antesio. The G+C % content of the isolates was 41.7 %. Based on biochemical, phylogenetic, genotypic, and chemotaxonomic criteria, these isolates A2-P53T and A1-P5 represent two individual strains of a novel species within the genus Bacteroides for which the name Bacteroides vicugnae sp. nov. is proposed. The type strain of this species is strain A2-P53T (CCUG 77273T = CCM 9377T = NRRL B-65693T).
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Affiliation(s)
- Samuel Miller
- School of Biological Sciences, 730 and 770 Van Vleet Oval, Norman, OK, 73019, USA; Laboratories of Molecular Anthropology and Microbiome Research, Stephenson Research and Technology Center, 101 David L. Boren Blvd, Norman, OK, 73019, USA.
| | - Meredith Hendry
- School of Biological Sciences, 730 and 770 Van Vleet Oval, Norman, OK, 73019, USA.
| | - Jacobey King
- School of Biological Sciences, 730 and 770 Van Vleet Oval, Norman, OK, 73019, USA.
| | - Krithivasan Sankaranarayanan
- School of Biological Sciences, 730 and 770 Van Vleet Oval, Norman, OK, 73019, USA; Laboratories of Molecular Anthropology and Microbiome Research, Stephenson Research and Technology Center, 101 David L. Boren Blvd, Norman, OK, 73019, USA.
| | - Paul A Lawson
- School of Biological Sciences, 730 and 770 Van Vleet Oval, Norman, OK, 73019, USA.
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Zhang C, Jiang X, Wu S, Zhang J, Wang Y, Li Z, Yao J. Dietary fat and carbohydrate-balancing the lactation performance and methane emissions in the dairy cow industry: A meta-analysis. ANIMAL NUTRITION (ZHONGGUO XU MU SHOU YI XUE HUI) 2024; 17:347-357. [PMID: 38800741 PMCID: PMC11127094 DOI: 10.1016/j.aninu.2024.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 01/11/2024] [Accepted: 02/20/2024] [Indexed: 05/29/2024]
Abstract
For the agroecosystems of the dairy cow industry, dietary carbohydrate (starch, neutral detergent fiber [NDF]) and fat could directly affect rumen methane emissions and host energy utilization. However, the relationships among diet, lactation performance, and methane emissions need to be further determined to assist dairy farms to adjust diet formulations and feeding strategies for environmental and production management. A meta-analysis was conducted in the current study to explore quantitative patterns of dietary fat and carbohydrate at different levels in balancing lactation performance and environment sustainability of dairy cows, and to establish a methane emission prediction model using the artificial neural network (ANN) model. The results showed that the regression relationship between dietary fat, carbohydrate and methane emissions could be shown by the following models: methane = 106.78 + (14.86 × DMI), R2 = 0.80; methane = 443.17 - (46.41 × starch/NDF), R2 = 0.76; and methane = 388.91 + (31.40 × fat) - (5.42 × fat2), R2 = 0.80. The regression relationships between dietary fat, carbohydrate and lactation performance could be shown by the following models: milk fat yield = 1.08 + (0.43 × starch/NDF) - [0.34 × (starch/NDF)2], R2 = 0.79; milk protein yield = 0.68 + (0.15 × fat) - (0.016 × fat2), R2 = 0.82. In the structural equation model, we found that when formulating dietary carbohydrates and fats, it was necessary to balance the relationship between methane emissions and lactation performance. Specifically, dietary starch/NDF was lower than 0.63 (extremum point) and dietary fat was between 2.89% and 4.69% (extremum point), it could ensure that the aim of methane emission reduction (methane emissions decrease with increasing dietary starch/NDF and fat) was achieved without losing lactation performance of dairy cows (lactation performance increase with increasing dietary starch/NDF and fat). Finally, we established the ANN model to predict methane emissions (training set: R2 = 0.62; validation set: R2 = 0.61).
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Affiliation(s)
| | | | - Shengru Wu
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Jun Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Yue Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Zongjun Li
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Junhu Yao
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China
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Zhang X, Wang W, Wang Y, Cao Z, Yang H, Li S. Metagenomic and metabolomic analyses reveal differences in rumen microbiota between grass- and grain-fed Sanhe heifers. Front Microbiol 2024; 15:1336278. [PMID: 38803375 PMCID: PMC11128563 DOI: 10.3389/fmicb.2024.1336278] [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: 01/09/2024] [Accepted: 03/26/2024] [Indexed: 05/29/2024] Open
Abstract
Introduction The aim of this study was to investigate the effects of diets on the composition and function of rumen microbiome and metabolites in Sanhe heifers. Methods Metagenomic and metabolomic analyses were performed using rumen fluid samples collected from Sanhe heifers (n = 20) with similar body weights and ages from grass-fed and grain-fed systems. Results The grain-fed group exhibited more intensive rumen fermentation than the grass-fed group. However, the grass-fed group exhibited carbohydrate metabolism and methane production higher than that of the grain-fed group; these increases were observed as a higher abundance of various bacterial phyla (Firmicutes, Bacteroidetes, Actinobacteria, Lentisphaerae, and Verrucomicrobia), families (Lachnospiraceae, Eubacteriaceae, and Eggerthellaceae), and the archaeal family Methanobacteriaceae. A comparison of genes encoding carbohydrate-active enzymes, using Kyoto Encyclopedia of Genes and Genome profiles, revealed noteworthy differences in the functions of rumen microbiota; these differences were largely dependent on the feeding system. Conclusion These results could help manipulate and regulate feed efficiency in Sanhe cattle.
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Affiliation(s)
| | | | | | | | | | - Shengli Li
- State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing, China
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Gao Z, Raza SHA, Ma B, Zhang F, Wang Z, Hou S, Almohaimeed HM, Alhelaify SS, Alzahrani SS, Alharthy OM, Gui L. Effects of dietary wheat supplementation levels on growth performance, rumen bacterial community and fermentation parameters in Chinese Tibetan Sheep. J Anim Physiol Anim Nutr (Berl) 2024; 108:470-479. [PMID: 38014916 DOI: 10.1111/jpn.13907] [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: 04/07/2023] [Revised: 08/31/2023] [Accepted: 11/03/2023] [Indexed: 11/29/2023]
Abstract
The objective of this study was to evaluate various wheat supplementation levels on rumen microbiota and fermentation parameter in Tibetan sheep. A total of ninety ram with an average 12.37 ± 0.92 kg at the age of 2 months were randomly allocated to three treatments: 0% wheat diet (CW, N = 30), 10% wheat diet (LW, N = 30), and 15% wheat diet (HW, N = 30) on a dry matter basis. The experiment was conducted over a period of 127 days, including 7 days of adaption to the diets. Our results showed that sheep fed 10% wheat exhibited optimal average daily gain and feed gain ratio compared with HW group (p < 0.05). The serum alkaline phosphatase concentration was the lowest when fed the 10% wheat diet (p < 0.05), whereas serum aspartate aminotransferase concentration was the highest (p < 0.05). Both acetate and propionate increased with increase in dietary wheat ratio (p < 0.05), while a greater decrease in concentrations of NH3 -N was observed (p < 0.05). In rumen fluid, 3413 OTUs were obtained with 97% consistency. Phylum Firmicutes was the predominant bacteria and accounted for 49.04%. The CW groups supported significantly increased the abundance of Bacteroidetes (p < 0.05), as compared with the HW group. The abundance of Bacteroidales_UCG-001, Ruminococcus, and Mitsuokella possessed a higher relative abundance in HW group (p < 0.05). No differences in the bacterial community and fermentation parameters were observed between the sheep fed 0% and 10% wheat (p > 0.05). Ruminal bacterial community structure was significantly correlated with isobutyrite (r2 = 0.4878, p = 0.035) and valerate (r2 = 0.4878, p = 0.013). In conclusion, supplementation of 10% wheat in diet promoted the average daily gain and never altered microbial community structure and fermentation pattern, which can be effectively replace partial corn in Chinese Tibetan Sheep.
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Affiliation(s)
- Zhanhong Gao
- College of Agriculture and Animal Husbandry, Qinghai University, Xining, Qinghai Province, People's Republic of China
| | - Sayed Haidar Abbas Raza
- Research Center for Machining and Safety of Livestock and Poultry Products, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern Region, Shaoguan University, Shaoguan, China
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, PR China
| | - Boyan Ma
- College of Agriculture and Animal Husbandry, Qinghai University, Xining, Qinghai Province, People's Republic of China
| | - Fengshuo Zhang
- College of Agriculture and Animal Husbandry, Qinghai University, Xining, Qinghai Province, People's Republic of China
| | - Zhiyou Wang
- College of Agriculture and Animal Husbandry, Qinghai University, Xining, Qinghai Province, People's Republic of China
| | - Shengzhen Hou
- College of Agriculture and Animal Husbandry, Qinghai University, Xining, Qinghai Province, People's Republic of China
| | - Hailah M Almohaimeed
- Department of Basic Science, College of Medicine, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Seham Sater Alhelaify
- Department of Biotechnology, College of Science, Taif University, Taif, Saudi Arabia
| | - Seham Saeed Alzahrani
- Department of Biotechnology, College of Science, Taif University, Taif, Saudi Arabia
| | - Ohud Muslat Alharthy
- Department of Biotechnology, College of Science, Taif University, Taif, Saudi Arabia
| | - Linsheng Gui
- College of Agriculture and Animal Husbandry, Qinghai University, Xining, Qinghai Province, People's Republic of China
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Jin C, Wu S, Liang Z, Zhang J, Lei X, Bai H, Liang G, Su X, Chen X, Wang P, Wang Y, Guan L, Yao J. Multi-omics reveal mechanisms of high enteral starch diet mediated colonic dysbiosis via microbiome-host interactions in young ruminant. MICROBIOME 2024; 12:38. [PMID: 38395946 PMCID: PMC10893732 DOI: 10.1186/s40168-024-01760-w] [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: 03/29/2023] [Accepted: 01/08/2024] [Indexed: 02/25/2024]
Abstract
BACKGROUND Although rumen development is crucial, hindgut undertakes a significant role in young ruminants' physiological development. High-starch diet is usually used to accelerate rumen development for young ruminants, but always leading to the enteral starch overload and hindgut dysbiosis. However, the mechanism behind remains unclear. The combination of colonic transcriptome, colonic luminal metabolome, and metagenome together with histological analysis was conducted using a goat model, with the aim to identify the potential molecular mechanisms behind the disrupted hindgut homeostasis by overload starch in young ruminants. RESULT Compared with low enteral starch diet (LES), high enteral starch diet (HES)-fed goats had significantly higher colonic pathology scores, and serum diamine oxidase activity, and meanwhile significantly decreased colonic mucosal Mucin-2 (MUC2) protein expression and fecal scores, evidencing the HES-triggered colonic systemic inflammation. The bacterial taxa Prevotella sp. P4-67, Prevotella sp. PINT, and Bacteroides sp. CAG:927, together with fungal taxa Fusarium vanettenii, Neocallimastix californiae, Fusarium sp. AF-8, Hypoxylon sp. EC38, and Fusarium pseudograminearum, and the involved microbial immune pathways including the "T cell receptor signaling pathway" were higher in the colon of HES goats. The integrated metagenome and host transcriptome analysis revealed that these taxa were associated with enhanced pathogenic ability, antigen processing and presentation, and stimulated T helper 2 cell (TH2)-mediated cytokine secretion functions in the colon of HES goats. Further luminal metabolomics analysis showed increased relative content of chenodeoxycholic acid (CDCA) and deoxycholic acid (DCA), and decreased the relative content of hypoxanthine in colonic digesta of HES goats. These altered metabolites contributed to enhancing the expression of TH2-mediated inflammatory-related cytokine secretion including GATA Binding Protein 3 (GATA3), IL-5, and IL-13. Using the linear mixed effect model, the variation of MUC2 biosynthesis explained by the colonic bacteria, bacterial functions, fungi, fungal functions, and metabolites were 21.92, 20.76, 19.43, 12.08, and 44.22%, respectively. The variation of pathology scores explained by the colonic bacterial functions, fungal functions, and metabolites were 15.35, 17.61, and 57.06%. CONCLUSIONS Our findings revealed that enteral starch overload can trigger interrupted hindgut host-microbiome homeostasis that led to impaired mucosal, destroyed colonic water absorption, and TH2-mediated inflammatory process. Except for the colonic metabolites mostly contribute to the impaired mucosa, the nonnegligible contribution from fungi deserves more future studies focused on the fungal functions in hindgut dysbiosis of young ruminants. Video Abstract.
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Affiliation(s)
- Chunjia Jin
- 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, 712100, Shaanxi, 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, 712100, Shaanxi, China.
| | - Ziqi Liang
- 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, 712100, Shaanxi, China
| | - Jun Zhang
- 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, 712100, Shaanxi, 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, 712100, Shaanxi, China
| | - Hanxun Bai
- 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, 712100, Shaanxi, China
| | - Gaofeng Liang
- 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, 712100, Shaanxi, China
| | - Xiaodong Su
- 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, 712100, Shaanxi, China
| | - Xiaodong 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, 712100, Shaanxi, China
| | - Peiyue 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, 712100, Shaanxi, China
| | - Yue 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, 712100, Shaanxi, China
| | - Leluo Guan
- Department of Agricultural, Food and Nutritional Science, University of Alberta, 116 St. and 85 Ave., Edmonton, AB, T6G 2P5, 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, 712100, Shaanxi, China.
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Ma X, La Y, Yang G, Dai R, Zhang J, Zhang Y, Jin J, Ma X, Guo X, Chu M, Yan P, Zhang Q, Liang C. Multi-omics revealed the effects of dietary energy levels on the rumen microbiota and metabolites in yaks under house-feeding conditions. Front Microbiol 2024; 14:1309535. [PMID: 38264487 PMCID: PMC10803511 DOI: 10.3389/fmicb.2023.1309535] [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: 10/08/2023] [Accepted: 12/22/2023] [Indexed: 01/25/2024] Open
Abstract
Yak (Bos grunniens) is a unique large ruminant species in the Qinghai-Tibetan Plateau (QTP). Changing the energy levels of their rations can significantly improve their growth performance. Therefore, studying the effects of dietary energy levels on the rumen microflora and metabolites of yak is crucial for enhancing the development of the yak industry. Currently, there is a lack of understanding regarding the impact of feeding energy diets on rumen fermentation parameters, microbial functions, and metabolites. This study was designed to determine the appropriate energy level for feeding yak. Three test diets with metabolizable energy levels of 7.57 MJ/kg, 9.44 MJ/kg, and 11.9 MJ/kg were used and the concentration of volatile fatty acids (VFA) in rumen fluid was measured. The microbial communities, functions, and metabolites in yaks were studied by 16S rRNA sequencing, metagenome, and LC-MS non-targeted metabolomics to investigate the relationships among rumen fermentation parameters, microbial diversity, and metabolites. Ration energy levels significantly affect total VFA, acetate, propionate, butyrate, iso-valerate, valerate, and acetate/propionate (p < 0.05). At the phylum level, the dominant phyla in all three treatment groups were Bacteroidota, Firmicutes, and Actinobacteriota. At the genus level, the abundance of the unclassified_o__Bacteroidales, norank_f_Muribaculaceae, Lachnospiraceae_NK4A136_group, and Family _XIII_AD3011_group showed significant differences (p < 0.05) and were significantly correlated with differential metabolites screened for phosphatidylcholine [PC(16:0/0:0), PC(18:3/0:0)], uridine 3'-monophosphate, and adenosine monophosphate, etc. CAZymes family analysis showed that GHs and CEs differed significantly among the three groups. In addition, differential metabolites were mainly enriched in the pathways of lipid metabolism, nucleotide metabolism, and biosynthesis of other secondary metabolites, and the concentrations of differential metabolites were correlated with microbial abundance. In summary, this study analyzed the effects of ration energy levels on rumen microorganisms and metabolites of yaks and their relationships. The results provided a scientific basis for the selection of dietary energy for yaks in the house feeding period in the future.
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Affiliation(s)
- Xiaoyong Ma
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
| | - Yongfu La
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
| | - Guowu Yang
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
| | - Rongfeng Dai
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
| | - Juanxiang Zhang
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
| | - Yonghui Zhang
- Gansu Grassland Technical Extension Station, Lanzhou, China
| | - Jiaming Jin
- Gansu Grassland Technical Extension Station, Lanzhou, China
| | - Xiaoming Ma
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
| | - Xian Guo
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
| | - Min Chu
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
| | - Ping Yan
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
| | - Qiang Zhang
- Institute of Animal Husbandry and Veterinary, Tibet Autonomous Regional Academy of Agricultural Sciences, Lhasa, China
| | - Chunnian Liang
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
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Liu H, Zhen F, Wu D, Wang Z, Kong X, Li Y, Xing T, Sun Y. Co-production of lactate and volatile fatty acids through repeated-batch fermentation of fruit and vegetable waste: Effect of cycle time and replacement ratio. BIORESOURCE TECHNOLOGY 2023; 387:129678. [PMID: 37579859 DOI: 10.1016/j.biortech.2023.129678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 08/10/2023] [Accepted: 08/11/2023] [Indexed: 08/16/2023]
Abstract
In this study, repeated-batch fermentation was used to convert fruit and vegetable waste to lactate and volatile fatty acids (VFAs), which are essential carbon sources for medium-chain fatty acids (MCFAs) production. The effect of cycle time and replacement ratio on acidification in long-term fermentation was investigated. The results showed that they had a significant impact on product yield, productivity, and type of products. Considering the yield, productivity, and lactate/VFAs ratio, a replacement ratio of 30% and a cycle time of 2 d may be more suitable for further production of MCFAs. Its productivity and lactate/VFAs ratio were 4.07 ± 0.24 g/(L·d) and 5 ± 0.6, respectively. The lactic acid bacteria, such as Enterococcus (63%) and Lactobacillus (33%), stabilized in the reactor, resulting in the generation of both lactate and VFAs by heterolactic fermentation. The present study demonstrated a new strategy with the potential to recover high-value products from organic waste streams.
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Affiliation(s)
- Huiliang Liu
- Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou 510640, China; Guangdong Provincial Key Laboratory of New and Renewable Energy Research and Development, Guangzhou 510640, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Feng Zhen
- Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou 510640, China; Guangdong Provincial Key Laboratory of New and Renewable Energy Research and Development, Guangzhou 510640, China
| | - Di Wu
- Chongqing Institute of Green and Intelligent Technology Chinese Academy of Sciences, Chongqing 400714, China
| | - Zhi Wang
- Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou 510640, China; Guangdong Provincial Key Laboratory of New and Renewable Energy Research and Development, Guangzhou 510640, China; University of Science and Technology of China, Hefei 230026, China
| | - Xiaoying Kong
- Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou 510640, China; Guangdong Provincial Key Laboratory of New and Renewable Energy Research and Development, Guangzhou 510640, China
| | - Ying Li
- Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou 510640, China; Guangdong Provincial Key Laboratory of New and Renewable Energy Research and Development, Guangzhou 510640, China
| | - Tao Xing
- Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou 510640, China; Guangdong Provincial Key Laboratory of New and Renewable Energy Research and Development, Guangzhou 510640, China.
| | - Yongming Sun
- Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou 510640, China; Guangdong Provincial Key Laboratory of New and Renewable Energy Research and Development, Guangzhou 510640, China
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9
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Cao Y, Feng T, Wu Y, Xu Y, Du L, Wang T, Luo Y, Wang Y, Li Z, Xuan Z, Chen S, Yao N, Gao NL, Xiao Q, Huang K, Wang X, Cui K, Rehman SU, Tang X, Liu D, Han H, Li Y, Chen WH, Liu Q. The multi-kingdom microbiome of the goat gastrointestinal tract. MICROBIOME 2023; 11:219. [PMID: 37779211 PMCID: PMC10544373 DOI: 10.1186/s40168-023-01651-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 08/14/2023] [Indexed: 10/03/2023]
Abstract
BACKGROUND Goat is an important livestock worldwide, which plays an indispensable role in human life by providing meat, milk, fiber, and pelts. Despite recent significant advances in microbiome studies, a comprehensive survey on the goat microbiomes covering gastrointestinal tract (GIT) sites, developmental stages, feeding styles, and geographical factors is still unavailable. Here, we surveyed its multi-kingdom microbial communities using 497 samples from ten sites along the goat GIT. RESULTS We reconstructed a goat multi-kingdom microbiome catalog (GMMC) including 4004 bacterial, 71 archaeal, and 7204 viral genomes and annotated over 4,817,256 non-redundant protein-coding genes. We revealed patterns of feeding-driven microbial community dynamics along the goat GIT sites which were likely associated with gastrointestinal food digestion and absorption capabilities and disease risks, and identified an abundance of large intestine-enriched genera involved in plant fiber digestion. We quantified the effects of various factors affecting the distribution and abundance of methane-producing microbes including the GIT site, age, feeding style, and geography, and identified 68 virulent viruses targeting the methane producers via a comprehensive virus-bacterium/archaea interaction network. CONCLUSIONS Together, our GMMC catalog provides functional insights of the goat GIT microbiota through microbiome-host interactions and paves the way to microbial interventions for better goat and eco-environmental qualities. Video Abstract.
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Affiliation(s)
- Yanhong Cao
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, 528225, China
- Guangxi Vocational University of Agriculture, Nanning, Guangxi, 530007, China
| | - Tong Feng
- Department of Bioinformatics and Systems Biology, Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China.
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China.
| | - Yingjian Wu
- Department of Bioinformatics and Systems Biology, Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Yixue Xu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China
| | - Li Du
- Hainan Key Lab of Tropical Animal Reproduction and Breeding and Epidemic Disease Research, College of Animal Science and Technology, Hainan University, Haikou, 570000, Hainan, China
| | - Teng Wang
- Department of Bioinformatics and Systems Biology, Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Yuhong Luo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China
| | - Yan Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China
| | - Zhipeng Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China
| | - Zeyi Xuan
- Animal Husbandry Research Institute of Guangxi Zhuang Autonomous Region, Nanning, 530001, Guangxi, China
| | - Shaomei Chen
- Animal Husbandry Research Institute of Guangxi Zhuang Autonomous Region, Nanning, 530001, Guangxi, China
| | - Na Yao
- Animal Husbandry Research Institute of Guangxi Zhuang Autonomous Region, Nanning, 530001, Guangxi, China
| | - Na L Gao
- Department of Bioinformatics and Systems Biology, Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Qian Xiao
- Hainan Key Lab of Tropical Animal Reproduction and Breeding and Epidemic Disease Research, College of Animal Science and Technology, Hainan University, Haikou, 570000, Hainan, China
| | - Kongwei Huang
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, 528225, China
| | - Xiaobo Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China
| | - Kuiqing Cui
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, 528225, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China
| | - Saif Ur Rehman
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China
| | - Xiangfang Tang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Dewu Liu
- South China Agricultural University, Guangzhou, 510642, China
| | - Hongbing Han
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Ying Li
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, 528225, China
| | - Wei-Hua Chen
- Department of Bioinformatics and Systems Biology, Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China.
- Institution of Medical Artificial Intelligence, Binzhou Medical University, Yantai, 264003, China.
| | - Qingyou Liu
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, 528225, China.
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China.
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10
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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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11
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Liu B, Dai Y, Cheng X, He X, Bei Q, Wang Y, Zhou Y, Zhu B, Zhang K, Tian X, Duan M, Xie X, Wang L. Straw mulch improves soil carbon and nitrogen cycle by mediating microbial community structure and function in the maize field. Front Microbiol 2023; 14:1217966. [PMID: 37533822 PMCID: PMC10391546 DOI: 10.3389/fmicb.2023.1217966] [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: 05/06/2023] [Accepted: 06/26/2023] [Indexed: 08/04/2023] Open
Abstract
This study was conducted to investigate the capability of the microbial community characteristics and soil variables to promote carbon and nitrogen cycles in maize fields under straw mulch. We covered the surface soil of the maize field with different amounts of wheat straw (0 kg/ha, 2,250 kg/ha, and 4,500 kg/ha) and used 16S rRNA and ITS sequencing, Biology ECO-plate, traditional enzymology, TOC analyzer, and HPLC to measure bacterial and fungal community composition and functions, characteristics of microbial carbon source metabolism, carbon and nitrogen fraction, enzyme activity, and organic acid content in the maize rhizosphere and non-rhizosphere. The results indicated that short-term straw mulch insignificantly affected the alpha diversity of bacterial and fungal communities whereas significantly influenced their beta diversity. The results of functional prediction revealed that straw mulch considerably boosted the relative abundances of bacteria belonging to chemoheterotrophy, aerobic chemoheterotrophy, ureolysis, and nitrogen fixation and inhibited fermentation and nitrate reduction in maize rhizosphere soil. These processes primarily drove the C and N cycles in soil. Straw mulch also improved fungal saprotrophs by raising the proportion of Chaetomiaceae and Chaetosphaeriaceae. The Biology ECO-plate results illustrated that straw mulch weakened the metabolism capacity of microbial labile carbon resources. As a result, the labile C and N fractions were raised under straw mulch. Our results also showed that straw mulch primarily regulated the microbial community structure in rhizosphere soil by significantly decreasing Firmicutes and Ascomycota relative abundance while increasing Basidiomycota. The fungal community structure is more than bacterial for affecting soil microbial biomass carbon, readily oxidizable organic carbon, dissolved organic carbon, available nitrogen, ammonium, and nitrate directly and indirectly through malic acid content and cellulase, protease, and amylase activity. Overall, our findings imply that straw mulch might influence the bacterial and fungal community structures, thereby boosting the production of labile C and N components and accelerating the C and N cycle in maize fields.
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Affiliation(s)
- Bangyan Liu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, China
| | - Yisha Dai
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, China
| | - Xin Cheng
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, China
| | - Xian He
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, China
| | - Qicheng Bei
- Department of Soil Ecology, Helmholtz Centre for Environmental Research - UFZ, Halle, Germany
| | - Yifan Wang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, China
| | - Yuling Zhou
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, China
| | - Bo Zhu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, China
| | - Kangping Zhang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, China
| | - Xiaoqin Tian
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, China
| | - Meichun Duan
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, China
| | - Xiaoyu Xie
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, China
| | - Longchang Wang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, China
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12
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Liang J, Chang J, Zhang R, Fang W, Chen L, Ma W, Zhang Y, Yang W, Li Y, Zhang P, Zhang G. Metagenomic analysis reveals the efficient digestion mechanism of corn stover in Angus bull rumen: Microbial community succession, CAZyme composition and functional gene expression. CHEMOSPHERE 2023; 336:139242. [PMID: 37330070 DOI: 10.1016/j.chemosphere.2023.139242] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 06/05/2023] [Accepted: 06/14/2023] [Indexed: 06/19/2023]
Abstract
Ruminant rumen is a biological fermentation system that can efficiently degrade lignocellulosic biomass. The knowledge about mechanisms of efficient lignocellulose degradation with rumen microorganisms is still limited. In this study, composition and succession of bacteria and fungi, carbohydrate-active enzymes (CAZymes), and functional genes involved in hydrolysis and acidogenesis were revealed during fermentation in Angus bull rumen via metagenomic sequencing. Results showed that degradation efficiency of hemicellulose and cellulose reached 61.2% and 50.4% at 72 h fermentation, respectively. Main bacterial genera were composed of Prevotella, Butyrivibrio, Ruminococcus, Eubacterium, and Fibrobacter, and main fungal genera were composed of Piromyces, Neocallimastix, Anaeromyces, Aspergillus, and Orpinomyces. Principal coordinates analysis indicated that community structure of bacteria and fungi dynamically changed during 72 h fermentation. Bacterial networks with higher complexity had stronger stability than fungal networks. Most CAZyme families showed a significant decrease trend after 48 h fermentation. Functional genes related to hydrolysis decreased at 72 h, while functional genes involved in acidogenesis did not change significantly. These findings provide a in-depth understanding of mechanisms of lignocellulose degradation in Angus bull rumen, and may guide the construction and enrichment of rumen microorganisms in anaerobic fermentation of waste biomass.
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Affiliation(s)
- Jinsong Liang
- Beijing Key Lab for Source Control Technology of Water Pollution, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China
| | - Jianning Chang
- Beijing Key Lab for Source Control Technology of Water Pollution, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China
| | - Ru Zhang
- Beijing Key Lab for Source Control Technology of Water Pollution, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China
| | - Wei Fang
- Beijing Key Lab for Source Control Technology of Water Pollution, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China
| | - Le Chen
- Beijing Key Lab for Source Control Technology of Water Pollution, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China
| | - Weifang Ma
- Beijing Key Lab for Source Control Technology of Water Pollution, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China
| | - Yajie Zhang
- Beijing Key Lab for Source Control Technology of Water Pollution, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China
| | - Wenjing Yang
- Beijing Key Lab for Source Control Technology of Water Pollution, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China
| | - Yuehan Li
- Beijing Key Lab for Source Control Technology of Water Pollution, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China
| | - Panyue Zhang
- Beijing Key Lab for Source Control Technology of Water Pollution, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China.
| | - Guangming Zhang
- School of Energy & Environmental Engineering, Hebei University of Technology, Tianjin, 300130, China.
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13
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Bhattacharjee D, Flores C, Woelfel-Monsivais C, Seekatz AM. Diversity and Prevalence of Clostridium innocuum in the Human Gut Microbiota. mSphere 2023; 8:e0056922. [PMID: 36541771 PMCID: PMC9942572 DOI: 10.1128/msphere.00569-22] [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: 11/16/2022] [Accepted: 11/22/2022] [Indexed: 12/24/2022] Open
Abstract
Clostridia are a polyphyletic group of Gram-positive, spore-forming anaerobes in the Firmicutes phylum that significantly impact metabolism and functioning of the human gastrointestinal tract. Recently, Clostridia were divided into two separate classes, Clostridia and Erysipelotrichia, based on phenotypic and 16S rRNA gene-based differences. While Clostridia include many well-known pathogenic bacteria, Erysipelotrichia remain relatively uncharacterized, particularly regarding their role as a pathogen versus commensal. Despite wide recognition as a commensal, the erysipelotrichial species Clostridium innocuum has recently been associated with various disease states. To further understand the ecological and potential virulent role of C. innocuum, we conducted a genomic comparison across 38 C. innocuum isolates and 194 publicly available genomes. Based on colony morphology, we isolated multiple C. innocuum cultivars from the feces of healthy human volunteers (n = 5). Comparison of the 16S rRNA gene of our isolates against publicly available microbiota data sets in healthy individuals suggests a high prevalence of C. innocuum across the human population (>80%). Analysis of single nucleotide polymorphisms (SNPs) across core genes and average nucleotide identify (ANI) revealed the presence of four clades among all available genomes (n = 232 total). Investigation of carbohydrate and protein utilization pathways, including comparison against the carbohydrate-activating enzyme (CAZyme) database, demonstrated inter- and intraclade differences that were further substantiated in vitro. Collectively, these data indicate genetic variance within the C. innocuum species that may help clarify its role in human disease and health. IMPORTANCE Clostridia are a group of medically important anaerobes as both commensals and pathogens. Recently, a new class of Erysipelotrichia containing a number of reassigned clostridial species has emerged, including Clostridium innocuum. Recent studies have implicated C. innocuum as a potential causative agent of diarrhea in patients from whom Clostridioides difficile could not be isolated. Using genomic and in vitro comparison, this study sought to characterize C. innocuum in the healthy human gut. Our analyses suggest that C. innocuum is a highly prevalent and diverse species, demonstrating clade-specific differences in metabolism and potential virulence. Collectively, this study is the first investigation into a broader description of C. innocuum as a human gut inhabitant.
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Affiliation(s)
- Disha Bhattacharjee
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, USA
| | - Clara Flores
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, USA
| | | | - Anna M. Seekatz
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, USA
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14
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Alvarado-Ramírez ER, Maggiolino A, Elghandour MMMY, Rivas-Jacobo MA, Ballesteros-Rodea G, Palo PD, Salem AZM. Impact of Co-Ensiling of Maize with Moringa oleifera on the Production of Greenhouse Gases and the Characteristics of Fermentation in Ruminants. Animals (Basel) 2023; 13:ani13040764. [PMID: 36830550 PMCID: PMC9952511 DOI: 10.3390/ani13040764] [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: 01/17/2023] [Revised: 02/14/2023] [Accepted: 02/16/2023] [Indexed: 02/22/2023] Open
Abstract
The objective of this experiment was to evaluate the impact of maize co-ensiling with increasing percentages of MOL forage on the kinetics of biogas, methane (CH4), carbon monoxide (CO) and hydrogen sulfide (H2S) production, as well as the characteristics of ruminal fermentation and CH4 conversion efficiency, using steers (STI) and sheep (SHI) as inoculum sources. With the STI, the inclusion of MOL reduced (linear: p ≤ 0.0199; quadratic: p ≤ 0.0267) biogas production (mL g-1 DM incubated and degraded), CH4 (mL g-1 DM degraded), CO (mL g-1 DM degraded), and H2S (mL g-1 DM incubated and degraded), without affecting (p > 0.05) the parameters (b = asymptotic gas, c = rate of gas production and Lag = initial delay time before gas production) of CH4 and H2S, and the proportion and production of CH4 per kg of dry matter (DM). In addition, with this inoculum, pH, and dry matter degradation (DMD) increased (linear: p ≤ 0.0060), and although short-chain fatty acids (SCFA) and metabolizable energy (ME) decreased (linear: p < 0.0001; quadratic: p ≤ 0.0015), this did not affect (p > 0.05) the CH4 conversion efficiency. Meanwhile, with the SHI, the inclusion of MOL only decreased (linear: p ≤ 0.0206; quadratic: p ≤ 0.0003) biogas per dry matter (DM) degraded and increased (linear: p ≤ 0.0293; quadratic: p ≤ 0.0325) biogas per DM incubated, as well as the production (mL g-1 DM incubated and degraded and g-1 kg DM) and proportion of CH4, and CO per DM incubated and degraded. In addition, it did not impact (p > 0.05) on the CH4 and H2S parameters, and in the H2S by DM incubated and degraded, and although it increased (linear: p ≤ 0.0292; quadratic: p ≤ 0.0325) the DMD, SCFA, and ME, it was inefficient (quadratic: p ≤ 0.0041) in CH4 conversion. It is concluded that regardless of the percentage of MOL, the STI presented the highest values in the production of biogas, CH4, H2S, DMD, SCFA, and ME, and the lowest pH, so it turned out to be the most efficient in CH4 conversion, while with the SHI only the highest production of CO and pH was obtained, and the lowest DMD, SCFA, and ME, so it was less efficient compared to STI.
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Affiliation(s)
| | - Aristide Maggiolino
- Department of Veterinary Medicine, University of Bari A. Moro, 70010 Bari, Italy
- Correspondence: (A.M.); (A.Z.M.S.)
| | - Mona M. M. Y. Elghandour
- Faculty of Veterinary Medicine and Zootechnics, Autonomous University of the State of Mexico, 50000 Toluca, Mexico
| | - Marco Antonio Rivas-Jacobo
- Faculty of Agronomy and Veterinary, Autonomous University of San Luis Potosí, 78321 San Luis Potosí, Mexico
| | - Gilberto Ballesteros-Rodea
- Faculty of Agronomy and Veterinary, Autonomous University of San Luis Potosí, 78321 San Luis Potosí, Mexico
| | - Pasquale De Palo
- Department of Veterinary Medicine, University of Bari A. Moro, 70010 Bari, Italy
| | - Abdelfattah Z. M. Salem
- Faculty of Veterinary Medicine and Zootechnics, Autonomous University of the State of Mexico, 50000 Toluca, Mexico
- Correspondence: (A.M.); (A.Z.M.S.)
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Jin C, Su X, Wang P, Liang Z, Lei X, Bai H, Liang G, Li J, Cao Y, Yao J. Effects of rumen degradable starch on growth performance, carcass, rumen fermentation, and ruminal VFA absorption in growing goats. Anim Feed Sci Technol 2023. [DOI: 10.1016/j.anifeedsci.2023.115618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
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16
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Apostolakos I, Paramithiotis S, Mataragas M. Comparative Genomic Analysis Reveals the Functional Traits and Safety Status of Lactic Acid Bacteria Retrieved from Artisanal Cheeses and Raw Sheep Milk. Foods 2023; 12:foods12030599. [PMID: 36766127 PMCID: PMC9914385 DOI: 10.3390/foods12030599] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/21/2023] [Accepted: 01/28/2023] [Indexed: 02/05/2023] Open
Abstract
Lactic acid bacteria (LAB) are valuable for the production of fermented dairy products. We investigated the functional traits of LAB isolated from artisanal cheeses and raw sheep milk, assessed their safety status, and explored the genetic processes underlying the fermentation of carbohydrates. Lactiplantibacillus plantarum had the largest and more functional genome compared to all other LAB, while most of its protein-encoding genes had unknown functions. A key finding of our analysis was the overall absence of acquired resistance genes (RGs), virulence genes (VGs), and prophages, denoting that all LAB isolates fulfill safety criteria and can be used as starter or adjunct cultures. In this regard, the identified mobile genetic elements found in LAB, rather than enabling the integration of RGs or VGs, they likely facilitate the uptake of genes involved in beneficial functions and in the adaptation of LAB in dairy matrices. Another important finding of our study was that bacteriocins and CAZymes were abundant in LAB though each species was associated with specific genes, which in turn had different activity spectrums and identified applications. Additionally, all isolates were able to metabolize glucose, lactose, maltose, and sucrose, but Lactiplantibacillus plantarum was strongly associated with the fermentation of rhamnose, mannose, cellobiose, and trehalose whereas Levilactobacillus brevis with the utilization of arabinose and xylose. Altogether these results suggest that to fully exploit the beneficial properties of LAB, a combination of strains as food additives may be necessary. Interestingly, biological processes involved in the metabolism of carbohydrates that are not of direct interest for the dairy industry may yield valuable metabolites or activate pathways associated with beneficial health effects. Our results provide useful information for the development of new probiotic artisanal cheeses and probiotic starter cultures.
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Affiliation(s)
- Ilias Apostolakos
- Department of Dairy Research, Institution of Technology of Agricultural Products, Hellenic Agricultural Organization “DIMITRA”, 3 Ethnikis Antistaseos St., 45221 Ioannina, Greece
| | - Spiros Paramithiotis
- Department of Food Science and Human Nutrition, Agricultural University of Athens, 75 Iera Odos St., 11855 Athens, Greece
| | - Marios Mataragas
- Department of Dairy Research, Institution of Technology of Agricultural Products, Hellenic Agricultural Organization “DIMITRA”, 3 Ethnikis Antistaseos St., 45221 Ioannina, Greece
- Correspondence:
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17
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Ruminal Degradation of Taurine and Its Effects on Rumen Fermentation In Vitro. FERMENTATION-BASEL 2023. [DOI: 10.3390/fermentation9010043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Taurine accounts for approximately 0.1% of an animal’s body. It cannot be used for protein synthesis but plays a wide range of important roles in the animal body. Taurine does not exist in plants, while mammals can only synthesize 30–40% of the taurine they need. Supplementing taurine to beef cattle may be necessary to improve their nutrient utilization and health status. However, no data are available regarding the metabolism of taurine in the rumen. Two in vitro trials were conducted to investigate the ruminal degradability of taurine and its effects on rumen fermentation. In Trial 1, Tilley and Terry’s in vitro rumen fermentation technique was used for incubation. As treatments, two levels of taurine, i.e., 0 and 10 mg, were added into plastic tubes containing 0.4000 g of feed mixture with a calibrated volume of 50 mL. Three adult cattle fitted with rumen cannulas were used as the donors for rumen fluid. The incubation was carried out at 39 °C for 48 h. The results showed that the taurine degradability increased with incubation time (p < 0.001) while its 2 h-degradability reached 99%. Taurine decreased the 48 h-dry matter degradability (DMD) (p = 0.008) and increased the 24 h- and 48 h-pH (p = 0.005; p = 0.018), respectively. In Trial 2, the Hohenheim gas test was used for incubation. Four levels of taurine, i.e., 0, 5, 10 and 20 mg, were added into glass syringes containing 0.2000 g feed mixture with a calibrated volume of 100 mL as treatments. The rumen fluid donors were the same as in Trial 1. The incubation was carried out at 39 °C for 48 h. The results showed that taurine increased the 48 h-pH (p < 0.001) linearly, decreased the cumulative gas production (p < 0.001) and the total volatile fatty acids (VFA) concentration (p = 0.014), and quadratically affected the ammonia–nitrogen (p < 0.001) and microbial crude protein (MCP) concentrations (p < 0.001). It was concluded that taurine was highly degradable in rumen fermentation. Taurine inhibits ruminal fermentation by decreasing DMD, VFA and gas production while improving MCP synthesis on a dose-dependent basis.
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18
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Pittaluga AM, Yang F, Gaffney JR, Embree M, Relling AE. Effect of supplementation with ruminal probiotics on growth performance, carcass characteristics, plasma metabolites, methane emissions, and the associated rumen microbiome changes in beef cattle. J Anim Sci 2023; 101:skac308. [PMID: 36592753 PMCID: PMC9831096 DOI: 10.1093/jas/skac308] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 09/16/2022] [Indexed: 01/04/2023] Open
Abstract
To evaluate the effect of supplementing beef cattle with a ruminal probiotic consisting of native rumen microbes (NRM; Chordicoccus furentiruminis, Prevotella albensis, and Succinivibrio dextrinosolvens) on methane (CH4) emissions, growth performance, carcass characteristics, and plasma metabolites, Angus × SimAngus-crossbred steers (n = 32; 8 per pen) and heifers (n = 48; 12 per pen) with an initial body weight (BW) of 353 ± 64 kg were used in randomized complete block design. Cattle were blocked by sex and BW and randomly assigned to 1 of 2 treatments (2 pens per treatment). Treatments consisted of diets offered for ad libitum intake with (NRM) or without (CON) the inclusion of the ruminal probiotic. Cattle were fed a growing diet for 49 d followed by a ground corn-based diet for 124 ± 27 d until reaching the targeted final BW (635 kg for steers and 590 kg for heifers). Methane emissions were estimated using the GreenFeed system (n = 12 per treatment) prior to trial commencement (baseline; period 1), and on three (2, 3, and 4), and two (5 and 6) different sampling periods throughout the growing and finishing stage, respectively. All data were analyzed using the PROC MIXED procedure of SAS. For CH4 production (g/d), there was a tendency for an NRM supplementation × period interaction (P = 0.07) where cattle-fed diets with NRM had lower production of methane in periods 3 and 4. Including NRM in the diet decreased CH4 yield (g/kg of dry matter intake (DMI)) by 20%. For CH4 emission intensity (g/kg of average daily gain (ADG)), an interaction (P < 0.01) of NRM supplementation × period occurred. In periods 2 and 3, cattle-fed diets with NRM inclusion had lower CH4 emission intensity than CON cattle. During the 84-d period when all cattle were still on the finishing diet, feeding NRM increased (P = 0.02) ADG and tended to increase (P = 0.10) DMI. At the end of the 84-d period, cattle-fed NRM tended to be heavier (P = 0.06) than CON cattle. Cattle supplemented with NRM required less (P = 0.04) days on feed to reach the targeted final BW. No differences (P ≤ 0.11) were detected for gain-to-feed ratio and carcass characteristics. Cattle-fed NRM had greater abundance of uncultured rumen bacteria that may improve rumen digestion when fed a high grain diet and potentially promote the reduction of enteric CH4 production. Results from this study suggest that daily administration of NRM may be a strategy to mitigate methanogenesis and improve the growth performance of beef cattle.
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Affiliation(s)
| | - Fan Yang
- Native Microbials, Inc., San Diego, CA 92121, USA
| | | | | | - Alejandro E Relling
- Department of Animal Sciences/Interdisciplinary PhD Program in Nutrition, The Ohio State University, Columbus 43210, USA
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Osorio-Doblado AM, Feldmann KP, Lourenco JM, Stewart RL, Smith WB, Tedeschi LO, Fluharty FL, Callaway TR. Forages and pastures symposium: forage biodegradation: advances in ruminal microbial ecology. J Anim Sci 2023; 101:skad178. [PMID: 37257501 PMCID: PMC10313095 DOI: 10.1093/jas/skad178] [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: 02/22/2023] [Accepted: 05/26/2023] [Indexed: 06/02/2023] Open
Abstract
The rumen microbial ecosystem provides ruminants a selective advantage, the ability to utilize forages, allowing them to flourish worldwide in various environments. For many years, our understanding of the ruminal microbial ecosystem was limited to understanding the microbes (usually only laboratory-amenable bacteria) grown in pure culture, meaning that much of our understanding of ruminal function remained a "black box." However, the ruminal degradation of plant cell walls is performed by a consortium of bacteria, archaea, protozoa, and fungi that produces a wide variety of carbohydrate-active enzymes (CAZymes) that are responsible for the catabolism of cellulose, hemicellulose, and pectin. The past 15 years have seen the development and implementation of numerous next-generation sequencing (NGS) approaches (e.g., pyrosequencing, Illumina, and shotgun sequencing), which have contributed significantly to a greater level of insight regarding the microbial ecology of ruminants fed a variety of forages. There has also been an increase in the utilization of liquid chromatography and mass spectrometry that revolutionized transcriptomic approaches, and further improvements in the measurement of fermentation intermediates and end products have advanced with metabolomics. These advanced NGS techniques along with other analytic approaches, such as metaproteomics, have been utilized to elucidate the specific role of microbial CAZymes in forage degradation. Other methods have provided new insights into dynamic changes in the ruminal microbial population fed different diets and how these changes impact the assortment of products presented to the host animal. As more omics-based data has accumulated on forage-fed ruminants, the sequence of events that occur during fiber colonization by the microbial consortium has become more apparent, with fungal populations and fibrolytic bacterial populations working in conjunction, as well as expanding understanding of the individual microbial contributions to degradation of plant cell walls and polysaccharide components. In the future, the ability to predict microbial population and enzymatic activity and end products will be able to support the development of dynamic predictive models of rumen forage degradation and fermentation. Consequently, it is imperative to understand the rumen's microbial population better to improve fiber degradation in ruminants and, thus, stimulate more sustainable production systems.
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Affiliation(s)
- A M Osorio-Doblado
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA
| | - K P Feldmann
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA
| | - J M Lourenco
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA
| | - R L Stewart
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA
| | - W B Smith
- Department Animal Science, Auburn University, Auburn, AL, USA
| | - L O Tedeschi
- Department of Animal Science, Texas A&M University, College Station, TX, USA
| | - F L Fluharty
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA
| | - T R Callaway
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA
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20
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Jeilu O, Simachew A, Alexandersson E, Johansson E, Gessesse A. Discovery of novel carbohydrate degrading enzymes from soda lakes through functional metagenomics. Front Microbiol 2022; 13:1059061. [PMID: 36569080 PMCID: PMC9768486 DOI: 10.3389/fmicb.2022.1059061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 11/11/2022] [Indexed: 12/12/2022] Open
Abstract
Extremophiles provide a one-of-a-kind source of enzymes with properties that allow them to endure the rigorous industrial conversion of lignocellulose biomass into fermentable sugars. However, the fact that most of these organisms fail to grow under typical culture conditions limits the accessibility to these enzymes. In this study, we employed a functional metagenomics approach to identify carbohydrate-degrading enzymes from Ethiopian soda lakes, which are extreme environments harboring a high microbial diversity. Out of 21,000 clones screened for the five carbohydrate hydrolyzing enzymes, 408 clones were found positive. Cellulase and amylase, gave high hit ratio of 1:75 and 1:280, respectively. A total of 378 genes involved in the degradation of complex carbohydrates were identified by combining high-throughput sequencing of 22 selected clones and bioinformatics analysis using a customized workflow. Around 41% of the annotated genes belonged to the Glycoside Hydrolases (GH). Multiple GHs were identified, indicating the potential to discover novel CAZymes useful for the enzymatic degradation of lignocellulose biomass from the Ethiopian soda Lakes. More than 73% of the annotated GH genes were linked to bacterial origins, with Halomonas as the most likely source. Biochemical characterization of the three enzymes from the selected clones (amylase, cellulase, and pectinase) showed that they are active in elevated temperatures, high pH, and high salt concentrations. These properties strongly indicate that the evaluated enzymes have the potential to be used for applications in various industrial processes, particularly in biorefinery for lignocellulose biomass conversion.
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Affiliation(s)
- Oliyad Jeilu
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia,Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden,*Correspondence: Oliyad Jeilu,
| | - Addis Simachew
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Erik Alexandersson
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Eva Johansson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Amare Gessesse
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia,Department of Biological Sciences and Biotechnology, Botswana International University of Science and Technology, Palapye, Botswana
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21
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Li Z, Wang X, Zhang Y, Yu Z, Zhang T, Dai X, Pan X, Jing R, Yan Y, Liu Y, Gao S, Li F, Huang Y, Tian J, Yao J, Xing X, Shi T, Ning J, Yao B, Huang H, Jiang Y. Genomic insights into the phylogeny and biomass-degrading enzymes of rumen ciliates. THE ISME JOURNAL 2022; 16:2775-2787. [PMID: 35986094 PMCID: PMC9666518 DOI: 10.1038/s41396-022-01306-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 08/04/2022] [Accepted: 08/09/2022] [Indexed: 12/15/2022]
Abstract
Understanding the biodiversity and genetics of gut microbiomes has important implications for host physiology and industrial enzymes, whereas most studies have been focused on bacteria and archaea, and to a lesser extent on fungi and viruses. One group, still underexplored and elusive, is ciliated protozoa, despite its importance in shaping microbiota populations. Integrating single-cell sequencing and an assembly-and-identification pipeline, we acquired 52 high-quality ciliate genomes of 22 rumen morphospecies from 11 abundant morphogenera. With these genomes, we resolved the taxonomic and phylogenetic framework that revised the 22 morphospecies into 19 species spanning 13 genera and reassigned the genus Dasytricha from Isotrichidae to a new family Dasytrichidae. Comparative genomic analyses revealed that extensive horizontal gene transfers and gene family expansion provided rumen ciliate species with a broad array of carbohydrate-active enzymes (CAZymes) to degrade all major kinds of plant and microbial carbohydrates. In particular, the genomes of Diplodiniinae and Ophryoscolecinae species encode as many CAZymes as gut fungi, and ~80% of their degradative CAZymes act on plant cell-wall. The activities of horizontally transferred cellulase and xylanase of ciliates were experimentally verified and were 2-9 folds higher than those of the inferred corresponding bacterial donors. Additionally, the new ciliate dataset greatly facilitated rumen metagenomic analyses by allowing ~12% of the metagenomic sequencing reads to be classified as ciliate sequences.
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Affiliation(s)
- Zongjun Li
- Center for Ruminant Genetics and Evolution, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Xiangnan Wang
- Center for Ruminant Genetics and Evolution, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Yu Zhang
- Center for Ruminant Genetics and Evolution, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Zhongtang Yu
- Department of Animal Sciences, The Ohio State University, Columbus, OH, 43210, USA
| | - Tingting Zhang
- Center for Ruminant Genetics and Evolution, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Xuelei Dai
- Center for Ruminant Genetics and Evolution, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Xiangyu Pan
- Center for Ruminant Genetics and Evolution, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Ruoxi Jing
- Center for Ruminant Genetics and Evolution, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
- College of Animal Engineering, Yangling Vocational & Technical College, Yangling, 712100, China
| | - Yueyang Yan
- Center for Ruminant Genetics and Evolution, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Yangfan Liu
- Center for Ruminant Genetics and Evolution, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Shan Gao
- Center for Ruminant Genetics and Evolution, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Fei Li
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Youqin Huang
- Center for Ruminant Genetics and Evolution, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Jian Tian
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Junhu Yao
- Center for Ruminant Genetics and Evolution, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - XvPeng Xing
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, China
| | - Tao Shi
- Center for Ruminant Genetics and Evolution, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Jifeng Ning
- College of Information Engineering, Northwest A&F University, Yangling, 712100, China
| | - Bin Yao
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Huoqing Huang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Yu Jiang
- Center for Ruminant Genetics and Evolution, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.
- Center for Functional Genomics, Institute of Future Agriculture, Northwest A&F University, Yangling, 712100, China.
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Yeast Products Mediated Ruminal Subenvironmental Microbiota, and Abnormal Metabolites and Digestive Enzymes Regulated Rumen Fermentation Function in Sheep. Animals (Basel) 2022; 12:ani12223221. [PMID: 36428448 PMCID: PMC9686794 DOI: 10.3390/ani12223221] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/18/2022] [Accepted: 11/19/2022] [Indexed: 11/23/2022] Open
Abstract
Yeast products (YP) are commonly used as rumen regulators, but their mechanisms of action are still unclear. Based on our previous studies, we questioned whether yeast products would have an impact on rumen solid-associated (SA) and liquid-associated (LA) microorganisms and alter rumen fermentation patterns. Thirty 3-month-old male sheep weighing 19.27 ± 0.45 kg were selected and randomized into three groups for 60 days: (1) basal diet group (CON group), (2) basal diet add 20 g YP per day (low YP, LYP group) and (3) basal diet add 40 g YP per day (high YP, HYP group). The results demonstrated that the addition of YP increased rumen cellulase activity, butyrate and total volatile fatty acid (TVFA) concentrations (p < 0.05), while it decreased rumen amylase activity and abnormal metabolites, such as lactate, lipopolysaccharides (LPS) and histamine (HIS) (p < 0.05). Metagenomic analysis of rumen microorganisms in three groups revealed that YP mainly influenced the microbial profiles of the SA system. YP increased the relative abundance of R. flavefaciens and decreased methanogens in the SA system (p < 0.05). With the addition of YP, the abundance of only a few lactate-producing bacteria increased in the SA system, including Streptococcus and Lactobacillus (p < 0.05). However, almost all lactate-utilizing bacteria increased in the LA system, including Megasphaera, Selenomonas, Fusobacterium and Veillonella (p < 0.05). In addition, YP increased the abundance of certain GHs family members, including GH43 and GH98 (p < 0.05), but decreased the abundance of some KEGG metabolic pathways involved in starch and sucrose metabolism, biosynthesis of antibiotics and purine metabolism, among others. In conclusion, the addition of YP to high-concentrate diets can change the abundance of major functional microbiota in the rumen, especially in the solid fraction, which in turn affects rumen fermentation patterns and improves rumen digestibility.
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Hua D, Hendriks WH, Xiong B, Pellikaan WF. Starch and Cellulose Degradation in the Rumen and Applications of Metagenomics on Ruminal Microorganisms. Animals (Basel) 2022; 12:ani12213020. [PMID: 36359144 PMCID: PMC9653558 DOI: 10.3390/ani12213020] [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: 09/16/2022] [Revised: 10/31/2022] [Accepted: 11/01/2022] [Indexed: 11/06/2022] Open
Abstract
Simple Summary Starch and cellulose are the principal components in diets for dairy cows worldwide, providing the primary energy to the rumen microorganisms as well as the host. Starch and cellulose degradation in the rumen have always been of key importance for dairy cows to obtain high production performance. To improve the starch- and cellulose-degrading activities in the rumen, the amylolytic and cellulolytic microbes and the related enzymes need to be well understood. As the rapid development of sequencing technologies, bioinformatic tools and reference databases, the rumen metagenomics have made great progress in mining the rumen microbial community for novel enzymes, such as the carbohydrate active enzymes (CAZymes). This review will summarize the ruminal microbes and enzymes involved in starch and cellulose degradation. Recent studies with metagenomics techniques on CAZymes related to starch and cellulose degradation will be discussed. Abstract Carbohydrates (e.g., starch and cellulose) are the main energy source in the diets of dairy cows. The ruminal digestion of starch and cellulose is achieved by microorganisms and digestive enzymes. In order to improve their digestibility, the microbes and enzymes involved in starch and cellulose degradation should be identified and their role(s) and activity known. As existing and new analytical techniques are continuously being developed, our knowledge of the amylolytic and cellulolytic microbial community in the rumen of dairy cows has been evolving rapidly. Using traditional culture-based methods, the main amylolytic and cellulolytic bacteria, fungi and protozoa in the rumen of dairy cows have been isolated. These culturable microbes have been found to only account for a small fraction of the total population of microorganisms present in the rumen. A more recent application of the culture-independent approach of metagenomics has acquired a more complete genetic structure and functional composition of the rumen microbial community. Metagenomics can be divided into functional metagenomics and sequencing-based computational metagenomics. Both approaches have been applied in determining the microbial composition and function in the rumen. With these approaches, novel microbial species as well as enzymes, especially glycosyl hydrolases, have been discovered. This review summarizes the current state of knowledge regarding the major amylolytic and cellulolytic microorganisms present in the rumen of dairy cows. The ruminal amylases and cellulases are briefly discussed. The application of metagenomics technology in investigating glycosyl hydrolases is provided and the novel enzymes are compared in terms of glycosyl hydrolase families related to amylolytic and cellulolytic activities.
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Affiliation(s)
- Dengke Hua
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Animal Nutrition Group, Department of Animal Sciences, Wageningen University & Research, 6708 PB Wageningen, The Netherlands
| | - Wouter H. Hendriks
- Animal Nutrition Group, Department of Animal Sciences, Wageningen University & Research, 6708 PB Wageningen, The Netherlands
| | - Benhai Xiong
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Correspondence: ; Tel.: +86-(10)-62811680
| | - Wilbert F. Pellikaan
- Animal Nutrition Group, Department of Animal Sciences, Wageningen University & Research, 6708 PB Wageningen, The Netherlands
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Shi T, Zhang T, Wang X, Wang X, Shen W, Guo X, Liu Y, Li Z, Jiang Y. Metagenomic Analysis of in Vitro Ruminal Fermentation Reveals the Role of the Copresent Microbiome in Plant Biomass Degradation. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:12095-12106. [PMID: 36121066 DOI: 10.1021/acs.jafc.2c03522] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
In vitro ruminal fermentation is considered an efficient way to degrade crop residue. To better understand the microbial communities and their functions during in vitro ruminal fermentation, the microbiome and short chain fatty acid (SCFA) production were investigated using the metagenomic sequencing and rumen simulation technique (RUSITEC) system. A total of 1677 metagenome-assembled genomes (MAGs) were reconstructed, and 298 MAGs were found copresenting in metagenomic data of the current work and 58 previously ruminal representative samples. Additionally, the domains related to pectin and xylan degradation were overrepresented in the copresent MAGs compared with total MAGs. Among the copresent MAGs, we obtained 14 MAGs with SCFA-synthesis-related genes positively correlated with SCFA concentrations. The MAGs obtained from this study enable a better understanding of dominant microbial communities across in vivo and in vitro ruminal fermentation and show promise for pointing out directions for further research on in vitro ruminal fermentation.
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Affiliation(s)
- Tao Shi
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi Province, P.R. China
| | - Tingting Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi Province, P.R. China
| | - Xihong Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi Province, P.R. China
| | - Xiangnan Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi Province, P.R. China
| | - Weijun Shen
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, Hunan Province, P.R. China
| | - Xi Guo
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi Province, P.R. China
| | - Yuqin Liu
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi Province, P.R. China
| | - Zongjun Li
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi Province, P.R. China
| | - Yu Jiang
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi Province, P.R. China
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Effects of Barley Starch Level in Diet on Fermentation and Microflora in Rumen of Hu Sheep. Animals (Basel) 2022; 12:ani12151941. [PMID: 35953930 PMCID: PMC9367498 DOI: 10.3390/ani12151941] [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] [Received: 05/22/2022] [Revised: 07/20/2022] [Accepted: 07/27/2022] [Indexed: 01/19/2023] Open
Abstract
This study aimed to explore the effects of different levels of barley starch instead of corn starch on the rumen fermentation and microflora when feeding a corn-based diet to Hu sheep. Thirty-two male Hu sheep equipped with permanent rumen fistulas were selected and fed in individual metabolic cages. All sheep were randomly divided into four groups (eight sheep in each group) and fed with four diets containing a similar starch content, but from different starch sources, including 100% of starch derived from corn (CS), 33% of starch derived from barley + 67% of starch derived from corn (33 BS), 67% of starch derived from barley + 33% of starch derived from corn (67 BS) and 100% of starch derived from barley (100 BS). The experimental period included a 14 d adaptation period and a 2 d continuous data collection period. The results showed that the molar proportions of acetate, isobutyrate, butyrate and isovalerate and the ratio of acetate to propionate in the 67 BS and 100 BS groups decreased compared with the CS and 33 BS groups (p < 0.001), while the molar proportions of propionate and valerate increased (p < 0.001). The combination of 33% barley starch and 67% corn starch in the diet improved the production of TVFAs (p = 0.007). The OTUs and Shannon indexes of the CS and 33 BS groups were higher than the 67 BS and 100 BS groups (p < 0.001), and the Chao1 and Ace indexes were higher than the 100 BS group (p < 0.05). In addition, the 33 BS group had increased the relative abundances of Bacteroidetes, Prevotella and Ruminococcus and the abundances of Fibrobacter succinogenes, Ruminococcus flavefaciens, Streptococcus bovis, Selenomonas ruminantium and Prevotella brevis relative to the CS group (p < 0.05). These results indicate that the substitution of 33% of the CS with BS did not change the rumen fermentation pattern relative to the CS group, and increased the richness and diversity of the rumen microbes in Hu sheep compared with other two starch substitute groups.
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Wang Q, Ren Y, Cui Y, Gao B, Zhang H, Jiang Q, Loor JJ, Deng Z, Xu C. Bacillus subtilis Produces Amino Acids to Stimulate Protein Synthesis in Ruminal Tissue Explants via the Phosphatidylinositol-4,5-Bisphosphate 3-Kinase Catalytic Subunit Beta–Serine/Threonine Kinase–Mammalian Target of Rapamycin Complex 1 Pathway. Front Vet Sci 2022; 9:852321. [PMID: 35832333 PMCID: PMC9272757 DOI: 10.3389/fvets.2022.852321] [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: 01/11/2022] [Accepted: 05/03/2022] [Indexed: 11/29/2022] Open
Abstract
Background Bacillus subtilis is a probiotic strain that is widely used as a feed supplement for ruminants. In this study, one B. subtilis strain isolated from the ruminal fluid of Holstein dairy cows was used for an ex vivo study with ruminal tissue explants. The main goal was to assess the potential endosymbiotic links between B. subtilis and the ruminal epithelium using molecular analyses and amino acid profiling. The explant culture protocol was first optimized to determine the ideal conditions in terms of tissue viability before performing the actual experiments involving active and inactive bacteria with or without protein synthesis inhibitors, such as LY294002 (phosphatidylinositol 3-kinase inhibitor) or rapamycin [mammalian target of rapamycin (mTOR) inhibitor]. Results The mRNA levels of phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit beta (PIK3CB), serine/threonine kinase (AKT), mTOR, P70S6K1, and eukaryotic translation initiation factor 4E binding protein 1 were the highest (p < 0.01), while those of programmed cell death 4 were the lowest when the tissue was incubated with 107 of B. subtilis. Compared with the inactivated bacteria, the expression levels of PIK3CB and AKT, and overall changes in mTOR and P70S6K1 were greater in rumen explants with living bacteria (p < 0.05). With an increase in B. subtilis concentration, the trends of protein and corresponding gene changes were consistent. There were differences in the concentrations of individual amino acids in the supernatants of living and inactivated bacterial culture groups, with most amino acids enriched in pathways, such as aminoacyl tRNA biosynthesis, cyanoamino acid metabolism, monobactam biosynthesis, or glycine, serine, and threonine metabolism. The addition of psilocybin upregulated the expression levels of PIK3CB and AKT. A significant decrease (p < 0.05) in PIK3CB and mTOR protein expression levels was detected after the addition of LY294002 and rapamycin. In addition, These responses were associated with the downregulation (p < 0.05) of AKT and P70S6K protein expression levels. Conclusions We confirmed that the in vivo ruminal tissue culture system is a suitable model for studying probiotic-induced alterations in tissue function. As such, this study provides a means for future mechanistic studies related to microbial regulation and the dietary supply of proteins. In addition, living and inactivated B. subtilis can promote protein synthesis in ruminal tissue explants by altering the expression levels of related factors in the PIK3CB–AKT–mTORC1 pathway, which could further aid in optimizing the feed efficiency and increasing the use of inactivated bacteria as additives in dairy cow farming.
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Affiliation(s)
- Qiuju Wang
- College of Animal Science and Veterinary, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Yulong Ren
- College of Animal Science and Veterinary, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Yizhe Cui
- College of Animal Science and Veterinary, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Bingnan Gao
- College of Animal Science and Veterinary, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Hao Zhang
- College of Animal Science and Veterinary, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Qianming Jiang
- Department of Animal Sciences and Division of Nutritional Sciences, University of Illinois, Urbana, IL, United States
| | - Juan J. Loor
- Department of Animal Sciences and Division of Nutritional Sciences, University of Illinois, Urbana, IL, United States
| | - Zhaoju Deng
- College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Chuang Xu
- College of Animal Science and Veterinary, Heilongjiang Bayi Agricultural University, Daqing, China
- *Correspondence: Chuang Xu ;
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Meng H, Song J, Li Y, Li X, Li X, Gou J, Nie Z, Wang J, Zheng Y, Wang M. Monascus vinegar protects against liver inflammation in high-fat-diet rat by alleviating intestinal microbiota dysbiosis and enteritis. J Funct Foods 2022. [DOI: 10.1016/j.jff.2022.105078] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
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28
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Su M, Hao Z, Shi H, Li T, Wang H, Li Q, Zhang Y, Ma Y. Metagenomic Analysis Revealed Differences in Composition and Function Between Liquid-Associated and Solid-Associated Microorganisms of Sheep Rumen. Front Microbiol 2022; 13:851567. [PMID: 35711780 PMCID: PMC9197192 DOI: 10.3389/fmicb.2022.851567] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 04/11/2022] [Indexed: 11/24/2022] Open
Abstract
The rumen microbiota plays a key role in the utilization of plant materials by ruminants, yet little is known about the key taxa and their genetic functions of the rumen sub-environment involved in the ruminal degradation process. Understanding the differences in the composition and function of ruminal microbiota in the liquid-associated (LA) and solid-associated (SA) systems is needed to further study and regulate rumen function and health. In this study, rumen contents of nine sheep were collected to separate LA and SA systems with elution and centrifugal precipitation. Metagenome sequencing was used to investigate the differences in microbial composition and genetic functions of LA and SA systems, with special emphasis on their degradational potential toward carbohydrates. Results showed that the dominant species composition was similar between the two systems, but SA microorganisms had a higher relative abundance than LA microorganisms in all taxa. The concentration of fiber-degrading bacteria, such as Ruminococcus, Treponema, and Fibrobacter, was higher and Prevotella was lower in the SA vs. LA system. Additionally, SA microorganisms dominated in cellulose degradation, while LA microorganisms were more important in starch utilization based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) Orthology (KO)'s functional categories and Carbohydrate-Active Enzymes (CAZymes). In general, SA microorganisms are more abundant and important in metabolic functions than LA, such as carbohydrate and amino acid metabolisms. In summary, the key differential biomarkers between LA and SA systems were Prevotella, Ruminococcus, Treponema, and Fibrobacter. Ruminal microbes degraded carbohydrates synergistically with SA, thus, more focusing on cellulose and hemicellulose, while LA is more important to starch.
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Affiliation(s)
- Manchun Su
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
- Gansu Key Laboratory of Animal Generational Physiology and Reproductive Regulation, Lanzhou, China
- School of Agriculture and Forestry Technology, Longnan Teachers College, Longnan, China
| | - Ziyun Hao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
- Gansu Key Laboratory of Animal Generational Physiology and Reproductive Regulation, Lanzhou, China
| | - Huibin Shi
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
- Gansu Key Laboratory of Animal Generational Physiology and Reproductive Regulation, Lanzhou, China
| | - Taotao Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
- Gansu Key Laboratory of Animal Generational Physiology and Reproductive Regulation, Lanzhou, China
| | - Huihui Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
- Gansu Key Laboratory of Animal Generational Physiology and Reproductive Regulation, Lanzhou, China
| | - Qiao Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
- Gansu Key Laboratory of Animal Generational Physiology and Reproductive Regulation, Lanzhou, China
| | - Yong Zhang
- Gansu Key Laboratory of Animal Generational Physiology and Reproductive Regulation, Lanzhou, China
| | - Youji Ma
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
- Gansu Key Laboratory of Animal Generational Physiology and Reproductive Regulation, Lanzhou, China
- *Correspondence: Youji Ma
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Kheirandish P, Petri RM, Sener-Aydemir A, Schwartz-Zimmermann HE, Berthiller F, Zebeli Q, Pacífico C. Characterization of Microbial Intolerances and Ruminal Dysbiosis Towards Different Dietary Carbohydrate Sources Using an in vitro Model. J Appl Microbiol 2022; 133:458-476. [PMID: 35396778 PMCID: PMC9545568 DOI: 10.1111/jam.15573] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 03/15/2022] [Accepted: 04/01/2022] [Indexed: 11/30/2022]
Abstract
AIM This study aimed to characterize the critical points for determining the development of dysbiosis associated with feed intolerances and ruminal acidosis. METHODS AND RESULTS A metabologenomics approach was used to characterize dynamic microbial and metabolomics shifts using the rumen simulation technique (RUSITEC) by feeding native cornstarch (ST), chemically-modified cornstarch (CMS), or sucrose (SU). SU and CMS elicited the most drastic changes as rapidly as 4 h after feeding. This was accompanied by a swift accumulation of D-lactate, and the decline of benzoic and malonic acid. A consistent increase in Bifidobacterium and Lactobacillus as well as a decrease in fibrolytic bacteria was observed for both CMS and ST after 24 h, indicating intolerances within the fiber degrading populations. However, an increase in Lactobacillus was already evident in SU after 8 h. An inverse relationship between Fibrobacter and Bifidobacterium was observed in ST. In fact, Fibrobacter was positively correlated with several short-chain fatty acids (SCFA), while Lactobacillus was positively correlated with lactic acid, hexoses, hexose-phosphates, pentose phosphate pathway (PENTOSE-P-PWY) and heterolactic fermentation (P122-PWY). CONCLUSIONS The feeding of sucrose and modified starches, followed by native cornstarch, had a strong disruptive effect in the ruminal microbial community. Feed intolerances were shown to develop at different rates based on the availability of glucose for ruminal microorganisms. SIGNIFICANCE OF THE STUDY These results can be used to establish patterns of early dysbiosis (biomarkers) and develop strategies for preventing undesirable shifts in the ruminal microbial ecosystem.
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Affiliation(s)
- Parisa Kheirandish
- Christian Doppler Laboratory for Innovative Gut Health Concepts of Livestock, Institute of Animal Nutrition and Functional Plant Compounds, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
| | - Renee Maxine Petri
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, Sherbrooke, Canada
| | - Arife Sener-Aydemir
- Christian Doppler Laboratory for Innovative Gut Health Concepts of Livestock, Institute of Animal Nutrition and Functional Plant Compounds, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
| | - Heidi Elisabeth Schwartz-Zimmermann
- Christian Doppler Laboratory for Innovative Gut Health Concepts of Livestock, Institute of Bioanalytics and Agro-Metabolomics, Department of Agrobiotechnology (IFA-Tulln), University of Natural Resources and Life Sciences, Vienna, Austria
| | - Franz Berthiller
- Christian Doppler Laboratory for Innovative Gut Health Concepts of Livestock, Institute of Bioanalytics and Agro-Metabolomics, Department of Agrobiotechnology (IFA-Tulln), University of Natural Resources and Life Sciences, Vienna, Austria
| | - Qendrim Zebeli
- Christian Doppler Laboratory for Innovative Gut Health Concepts of Livestock, Institute of Animal Nutrition and Functional Plant Compounds, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
| | - Cátia Pacífico
- Christian Doppler Laboratory for Innovative Gut Health Concepts of Livestock, Institute of Animal Nutrition and Functional Plant Compounds, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
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Bhujbal SK, Ghosh P, Vijay VK, Rathour R, Kumar M, Singh L, Kapley A. Biotechnological potential of rumen microbiota for sustainable bioconversion of lignocellulosic waste to biofuels and value-added products. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 814:152773. [PMID: 34979222 DOI: 10.1016/j.scitotenv.2021.152773] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 12/05/2021] [Accepted: 12/25/2021] [Indexed: 06/14/2023]
Abstract
Lignocellulosic biomass is an abundant resource with untapped potential for biofuel, enzymes, and chemical production. Its complex recalcitrant structure obstructs its bioconversion into biofuels and other value-added products. For improving its bioconversion efficiency, it is important to deconstruct its complex structure. In natural systems like rumen, diverse microbial communities carry out hydrolysis, acidogenesis, acetogenesis, and methanogenesis of lignocellulosic biomass through physical penetration, synergistic and enzymatic actions enhancing lignocellulose degradation activity. This review article aims to discuss comprehensively the rumen microbial ecosystem, their interactions, enzyme production, and applications for efficient bioconversion of lignocellulosic waste to biofuels. Furthermore, meta 'omics' approaches to elucidate the structure and functions of rumen microorganisms, fermentation mechanisms, microbe-microbe interactions, and host-microbe interactions have been discussed thoroughly. Additionally, feed additives' role in improving ruminal fermentation efficiency and reducing environmental nitrogen losses has been discussed. Finally, the current status of rumen microbiota applications and future perspectives for the development of rumen mimic bioreactors for efficient bioconversion of lignocellulosic wastes to biofuels and chemicals have been highlighted.
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Affiliation(s)
- Sachin Krushna Bhujbal
- Centre for Rural Development and Technology, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Pooja Ghosh
- Centre for Rural Development and Technology, Indian Institute of Technology Delhi, New Delhi 110016, India.
| | - Virendra Kumar Vijay
- Centre for Rural Development and Technology, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Rashmi Rathour
- CSIR-National Environmental and Engineering Research Institute (CSIR-NEERI), Nagpur 440020, India
| | - Manish Kumar
- CSIR-National Environmental and Engineering Research Institute (CSIR-NEERI), Nagpur 440020, India
| | - Lal Singh
- CSIR-National Environmental and Engineering Research Institute (CSIR-NEERI), Nagpur 440020, India
| | - Atya Kapley
- CSIR-National Environmental and Engineering Research Institute (CSIR-NEERI), Nagpur 440020, India
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Xie Y, Sun H, Xue M, Liu J. Metagenomics reveals differences in microbial composition and metabolic functions in the rumen of dairy cows with different residual feed intake. Anim Microbiome 2022; 4:19. [PMID: 35260198 PMCID: PMC8902708 DOI: 10.1186/s42523-022-00170-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Accepted: 02/21/2022] [Indexed: 12/25/2022] Open
Abstract
Background Rumen microbial composition and functions have vital roles in feed digestion and fermentation and are linked to feed efficiency in cattle. This study selected Holstein cows, which are high in both milk protein content and milk yield, to analyse the relationship between the rumen microbiota and residual feed intake (RFI). Eighteen multiparous lactating cows were divided into low RFI (LRFI, high efficiency, n = 9) and high RFI (HRFI, low efficiency, n = 9) groups to investigate the differences in microbial composition and functions. Results The relative abundances of butyrate producers, including the Clostridium, Butyrivibrio, Eubacterium and Blautia genera, were higher in HRFI cows than in LRFI cows (P < 0.05). Four carbohydrate metabolic pathways (glycolysis/gluconeogenesis, pentose phosphate pathway, fructose and mannose metabolism, and butanoate metabolism) and one energy metabolism pathway (methane metabolism), were more abundant in HRFI animals (P < 0.05). Quorum sensing and DNA replication pathways were more abundant in HRFI cows. For CAZyme profiles, 14 out of 19 genes encoding carbohydrates-deconstructing enzymes were more abundant in HRFI cows (P < 0.05). Seven Lachnospiraceae species associated with carbohydrate metabolism and quorum sensing may contribute to the difference in feed efficiency. Moreover, the LRFI cows had lower abundances of Methanosphaera (P < 0.01), Methanobrevibacter ruminantium (P = 0.09) and methanogenesis functions (P = 0.04). Conclusions The rumen microbiota of low-efficiency cows has stronger abilities to degrade carbohydrates and produce methane, and quorum sensing pathways could also be associated with differences in feed efficiency. This study provides a deeper understanding of the microbial ecology of dairy cows with different feed efficiencies and highlights the possibility of modulating the rumen microbiome or microbial functions to improve the feed efficiency of dairy cows. Supplementary Information The online version contains supplementary material available at 10.1186/s42523-022-00170-3.
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Affiliation(s)
- Yunyi 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
| | - Huizeng 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
| | - Mingyuan 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
| | - Jianxin 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.
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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: 19] [Impact Index Per Article: 9.5] [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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Integrated metagenomics-metabolomics analysis reveals the cecal microbial composition, function, and metabolites of pigs fed diets with different starch sources. Food Res Int 2022; 154:110951. [DOI: 10.1016/j.foodres.2022.110951] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 12/14/2021] [Accepted: 01/09/2022] [Indexed: 01/10/2023]
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Gonçalves MFM, Hilário S, Tacão M, Van de Peer Y, Alves A, Esteves AC. Genome and Metabolome MS-Based Mining of a Marine Strain of Aspergillus affinis. J Fungi (Basel) 2021; 7:1091. [PMID: 34947073 PMCID: PMC8709101 DOI: 10.3390/jof7121091] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 12/17/2021] [Accepted: 12/17/2021] [Indexed: 01/09/2023] Open
Abstract
Aspergillus section Circumdati encompasses several species that express both beneficial (e.g., biochemical transformation of steroids and alkaloids, enzymes and metabolites) and harmful compounds (e.g., production of ochratoxin A (OTA)). Given their relevance, it is important to analyze the genetic and metabolic diversity of the species of this section. We sequenced the genome of Aspergillus affinis CMG 70, isolated from sea water, and compared it with the genomes of species from section Circumdati, including A. affinis's strain type. The A. affinis genome was characterized considering secondary metabolites biosynthetic gene clusters (BGCs), carbohydrate-active enzymes (CAZymes), and transporters. To uncover the biosynthetic potential of A. affinis CMG 70, an untargeted metabolomics (LC-MS/MS) approach was used. Cultivating the fungus in the presence and absence of sea salt showed that A. affinis CMG 70 metabolite profiles are salt dependent. Analyses of the methanolic crude extract revealed the presence of both unknown and well-known Aspergillus compounds, such as ochratoxin A, anti-viral (e.g., 3,5-Di-tert-butyl-4-hydroxybenzoic acid and epigallocatechin), anti-bacterial (e.g., 3-Hydroxybenzyl alcohol, l-pyroglutamic acid, lecanoric acid), antifungal (e.g., lpyroglutamic acid, 9,12,13-Trihydroxyoctadec-10-enoic acid, hydroxyferulic acid), and chemotherapeutic (e.g., daunomycinone, mitoxantrone) related metabolites. Comparative analysis of 17 genomes from 16 Aspergillus species revealed abundant CAZymes (568 per species), secondary metabolite BGCs (73 per species), and transporters (1359 per species). Some BGCs are highly conserved in this section (e.g., pyranonigrin E and UNII-YC2Q1O94PT (ACR toxin I)), while others are incomplete or completely lost among species (e.g., bikaverin and chaetoglobosins were found exclusively in series Sclerotiorum, while asperlactone seemed completely lost). The results of this study, including genome analysis and metabolome characterization, emphasize the molecular diversity of A. affinis CMG 70, as well as of other species in the section Circumdati.
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Affiliation(s)
- Micael F. M. Gonçalves
- CESAM, Department of Biology, University of Aveiro, 3810-193 Aveiro, Portugal; (M.F.M.G.); (S.H.); (M.T.); (A.C.E.)
| | - Sandra Hilário
- CESAM, Department of Biology, University of Aveiro, 3810-193 Aveiro, Portugal; (M.F.M.G.); (S.H.); (M.T.); (A.C.E.)
| | - Marta Tacão
- CESAM, Department of Biology, University of Aveiro, 3810-193 Aveiro, Portugal; (M.F.M.G.); (S.H.); (M.T.); (A.C.E.)
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium;
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0028, South Africa
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Artur Alves
- CESAM, Department of Biology, University of Aveiro, 3810-193 Aveiro, Portugal; (M.F.M.G.); (S.H.); (M.T.); (A.C.E.)
| | - Ana C. Esteves
- CESAM, Department of Biology, University of Aveiro, 3810-193 Aveiro, Portugal; (M.F.M.G.); (S.H.); (M.T.); (A.C.E.)
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Li Z, Lei X, Chen X, Yin Q, Shen J, Yao J. Long-term and combined effects of N-[2-(nitrooxy)ethyl]-3-pyridinecarboxamide and fumaric acid on methane production, rumen fermentation, and lactation performance in dairy goats. J Anim Sci Biotechnol 2021; 12:125. [PMID: 34865657 PMCID: PMC8647438 DOI: 10.1186/s40104-021-00645-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 10/26/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In recent years, nitrooxy compounds have been identified as promising inhibitors of methanogenesis in ruminants. However, when animals receive a nitrooxy compound, a high portion of the spared hydrogen is eructated as gas, which partly offsets the energy savings of CH4 mitigation. The objective of the present study was to evaluate the long-term and combined effects of supplementation with N-[2-(nitrooxy)ethyl]-3-pyridinecarboxamide (NPD), a methanogenesis inhibitor, and fumaric acid (FUM), a hydrogen sink, on enteric CH4 production, rumen fermentation, bacterial populations, apparent nutrient digestibility, and lactation performance of dairy goats. RESULTS Twenty-four primiparous dairy goats were used in a randomized complete block design with a 2 × 2 factorial arrangement of treatments: supplementation without or with FUM (32 g/d) or NPD (0.5 g/d). All samples were collected every 3 weeks during a 12-week feeding experiment. Both FUM and NPD supplementation persistently inhibited CH4 yield (L/kg DMI, by 18.8% and 18.1%, respectively) without negative influence on DMI or apparent nutrient digestibility. When supplemented in combination, no additive CH4 suppression was observed. FUM showed greater responses in increasing the molar proportion of propionate when supplemented with NPD than supplemented alone (by 10.2% vs. 4.4%). The rumen microbiota structure in the animals receiving FUM was different from that of the other animals, particularly changed the structure of phylum Firmicutes. Daily milk production and serum total antioxidant capacity were improved by NPD, but the contents of milk fat and protein were decreased, probably due to the bioactivity of absorbed NPD on body metabolism. CONCLUSIONS Supplementing NPD and FUM in combination is a promising way to persistently inhibit CH4 emissions with a higher rumen propionate proportion. However, the side effects of this nitrooxy compound on animals and its residues in animal products need further evaluation before it can be used as an animal feed additive.
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Affiliation(s)
- Zongjun Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Xinjian Lei
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Xiaoxu Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Qingyan Yin
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Jing Shen
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Junhu Yao
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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Sato Y, Takebe H, Tominaga K, Oishi K, Kumagai H, Yoshida T, Hirooka H. Taxonomic and functional characterization of the rumen microbiome of Japanese Black cattle revealed by 16S rRNA gene amplicon and metagenome shotgun sequencing. FEMS Microbiol Ecol 2021; 97:6447535. [PMID: 34864967 DOI: 10.1093/femsec/fiab152] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 11/28/2021] [Indexed: 01/04/2023] Open
Abstract
This study aimed to determine the taxonomic and functional characteristics of the Japanese Black (JB) steer rumen microbiome. The rumen microbiomes of six JB steers (age 14.7 ± 1.44 months) and six JB sires × Holstein dams crossbred (F1) steers (age 11.1 ± 0.39 months), fed the same diet, were evaluated. Based on 16S rRNA gene sequencing, the beta diversity revealed differences in microbial community structures between the JB and F1 rumen. Shotgun sequencing showed that Fibrobacter succinogenes and two Ruminococcus spp., which are related to cellulose degradation were relatively more abundant in the JB steer rumen than in the F1 rumen. Furthermore, the 16S rRNA gene copy number of F. succinogenes was significantly higher in the JB steer rumen than in the F1 rumen according to quantitative real-time polymerase chain reaction analysis. Genes encoding the enzymes that accelerate cellulose degradation and those associated with hemicellulose degradation were enriched in the JB steer rumen. Although Prevotella spp. were predominant both in the JB and F1 rumen, the genes encoding carbohydrate-active enzymes of Prevotella spp. may differ between JB and F1.
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Affiliation(s)
- Yoshiaki Sato
- Laboratory of Animal Husbandry Resources, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake, Kyoto 606-8502, Japan
| | - Hiroaki Takebe
- Laboratory of Marine Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake, Kyoto 606-8502, Japan
| | - Kento Tominaga
- Laboratory of Marine Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake, Kyoto 606-8502, Japan
| | - Kazato Oishi
- Laboratory of Animal Husbandry Resources, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake, Kyoto 606-8502, Japan
| | - Hajime Kumagai
- Laboratory of Animal Husbandry Resources, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake, Kyoto 606-8502, Japan
| | - Takashi Yoshida
- Laboratory of Marine Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake, Kyoto 606-8502, Japan
| | - Hiroyuki Hirooka
- Laboratory of Animal Husbandry Resources, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake, Kyoto 606-8502, Japan
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Liang J, Fang W, Wang Q, Zubair M, Zhang G, Ma W, Cai Y, Zhang P. Metagenomic analysis of community, enzymes and metabolic pathways during corn straw fermentation with rumen microorganisms for volatile fatty acid production. BIORESOURCE TECHNOLOGY 2021; 342:126004. [PMID: 34583109 DOI: 10.1016/j.biortech.2021.126004] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 09/16/2021] [Accepted: 09/19/2021] [Indexed: 06/13/2023]
Abstract
Anaerobic fermentation of corn straw with rumen microorganisms as inoculum to produce volatile fatty acids (VFAs) is important for biomass valorization. In this study, dynamic variation in bacterial and fungal community composition, carbohydrate-active enzymes (CAZymes) and key functional genes related with VFA production was explored via metagenomic sequencing. Rumen microorganisms efficiently hydrolyzed and acidified corn straw, and VFA concentration reached 8.99 g/L in 72 h. Bacterial and fungal community significantly changed, but the core genera kept stable. Low pH and VFA accumulation were the main factors affecting bacterial and fungal communities. The positive correlations between bacteria were more complex than those between fungi. Most CAZyme abundance significantly decreased after 72 h fermentation, and functional gene abundance participating in VFA generation also decreased. This study provided new insights into dynamic variation of bacteria and fungi during anaerobic ruminal fermentation in vitro, promoting the application of rumen microorganisms in practice.
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Affiliation(s)
- Jinsong Liang
- College of Environmental Science & Engineering, Beijing Forestry University, Beijing 100083, PR China
| | - Wei Fang
- College of Environmental Science & Engineering, Beijing Forestry University, Beijing 100083, PR China
| | - Qingyan Wang
- College of Environmental Science & Engineering, Beijing Forestry University, Beijing 100083, PR China
| | - Muhammad Zubair
- College of Environmental Science & Engineering, Beijing Forestry University, Beijing 100083, PR China
| | - Guangming Zhang
- School of Energy & Environmental Engineering, Hebei University of Technology, Tianjin 300130, PR China
| | - Weifang Ma
- College of Environmental Science & Engineering, Beijing Forestry University, Beijing 100083, PR China
| | - Yajing Cai
- College of Environmental Science & Engineering, Beijing Forestry University, Beijing 100083, PR China
| | - Panyue Zhang
- College of Environmental Science & Engineering, Beijing Forestry University, Beijing 100083, PR China.
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Barraza A, Montes-Sánchez JJ, Caamal-Chan MG, Loera-Muro A. Characterization of microbial communities from rumen and large intestine of lactating creole goats grazing in arid plant communities. MICROBIOLOGY-SGM 2021; 167. [PMID: 34661515 DOI: 10.1099/mic.0.001092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Arid plant communities provide variable diets that can affect digestive microbial communities of free-foraging ruminants. Thus, we used next-generation sequencing of 16S and 18S rDNA to characterize microbial communities in the rumen (regurgitated digesta) and large intestine (faeces) and diet composition of lactating creole goats from five flocks grazing in native plant communities in the Sonoran Desert in the rainy season. The bacterial communities in the rumen and large intestine of the five flocks had similar alpha diversity (Chao1, Shannon, and Simpson indices). However, bacterial community compositions were different: a bacterial community dominated by Proteobacteria in the rumen transitioned to a community dominated by Firmicutes in the large intestine. Bacterial communities of rumen were similar across flocks; similarly occurred with large-intestine communities. Archaea had a minimum presence in the goat digestive tract. We detected phylum Basidiomycota, Ascomycota, and Apicomplexa as the main fungi and protozoa. Analyses suggested different diet compositions; forbs and grasses composed the bulk of plants in the rumen and forbs and shrubs in faeces. Therefore, lactating goats consuming different diets in the Sonoran Desert in the rainy season share a similar core bacterial community in the rumen and another in the large intestine and present low archaeal communities.
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Affiliation(s)
- Aarón Barraza
- CONACYT-Centro de Investigaciones Biológicas del Noroeste, SC. La Paz, BCS, 23096, Mexico
| | - Juan J Montes-Sánchez
- CONACYT-Centro de Investigaciones Biológicas del Noroeste, SC. Guerrero Negro, BCS, 23940, Mexico
| | - M Goretty Caamal-Chan
- CONACYT-Centro de Investigaciones Biológicas del Noroeste, SC. La Paz, BCS, 23096, Mexico
| | - Abraham Loera-Muro
- CONACYT-Centro de Investigaciones Biológicas del Noroeste, SC. La Paz, BCS, 23096, Mexico
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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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Real-time monitoring of ruminal microbiota reveals their roles in dairy goats during subacute ruminal acidosis. NPJ Biofilms Microbiomes 2021; 7:45. [PMID: 33990613 PMCID: PMC8121909 DOI: 10.1038/s41522-021-00215-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 04/09/2021] [Indexed: 02/08/2023] Open
Abstract
Ruminal microbiota changes frequently with high grain diets and the occurrence of subacute ruminal acidosis (SARA). A grain-induced goat model of SARA, with durations of a significant decrease in the rumen pH value to less than 5.6 and an increase in the rumen lipopolysaccharides concentration, is constructed for real-time monitoring of bacteria alteration. Using 16 S rRNA gene sequencing, significant bacterial differences between goats from the SARA and healthy groups are identified at every hour for six continuous hours after feeding. Moreover, 29 common differential genera between two groups over 6 h after feeding are all related to the altered pH and lipopolysaccharides. Transplanting the microbiota from donor goats with SARA could induce colonic inflammation in antibiotic-pretreated mice. Overall, significant differences in the bacterial community and rumen fermentation pattern between the healthy and SARA dairy goats are real-time monitored, and then tested using ruminal microbe transplantation to antibiotic-treated mice.
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Njokweni SG, Weimer PJ, Botes M, van Zyl WH. Effects of preservation of rumen inoculum on volatile fatty acids production and the community dynamics during batch fermentation of fruit pomace. BIORESOURCE TECHNOLOGY 2021; 321:124518. [PMID: 33316699 DOI: 10.1016/j.biortech.2020.124518] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 11/30/2020] [Accepted: 12/04/2020] [Indexed: 06/12/2023]
Abstract
Rumen fluid (RF) as inocula is useful for evaluating biomass digestibility and has potential for producing volatile fatty acids (VFA) via the carboxylate platform. However, RF is not readily available, necessitating evaluation of potential preservation methods. Glycerol (50% v/v) and DMSO (5% v/v) were used to preserve rumen inocula for 3 months at -80 °C. Effects of cryo-preservation on digestibility, VFA production and community composition with β-diversity distance metrics were compared to fresh RF using apple, citrus and grape pomace as substrates. For all substrates, DMSO cryo-preserved rumen digestibility parameters, VFA yield and product distribution were more significantly comparable to fresh RF (P > 0.05) than was glycerol cryo-preserved RF. Similarly, β-diversity coefficient (unweighted unifrac) between DMSO cryo-preserved RF and fresh RF was 0.250 while the coefficient was 0.359 for the glycerol cryo-preserved RF compared to fresh RF. This showed that a DMSO cryo-preserved RF is less affected by preservation effects and is a more promising alternative to fresh RF.
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Affiliation(s)
- Sesethu G Njokweni
- Department of Microbiology, University of Stellenbosch, Stellenbosch 7600, South Africa
| | - Paul J Weimer
- Department of Bacteriology, University of Wisconsin, Madison, WI, United States
| | - Marelize Botes
- Department of Microbiology, University of Stellenbosch, Stellenbosch 7600, South Africa.
| | - Willem H van Zyl
- Department of Microbiology, University of Stellenbosch, Stellenbosch 7600, South Africa
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