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Keum GB, Pandey S, Kim ES, Doo H, Kwak J, Ryu S, Choi Y, Kang J, Kim S, Kim HB. Understanding the Diversity and Roles of the Ruminal Microbiome. J Microbiol 2024; 62:217-230. [PMID: 38662310 DOI: 10.1007/s12275-024-00121-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 02/16/2024] [Accepted: 02/16/2024] [Indexed: 04/26/2024]
Abstract
The importance of ruminal microbiota in ruminants is emphasized, not only as a special symbiotic relationship with ruminants but also as an interactive and dynamic ecosystem established by the metabolites of various rumen microorganisms. Rumen microbial community is essential for life maintenance and production as they help decompose and utilize fiber that is difficult to digest, supplying about 70% of the energy needed by the host and 60-85% of the amino acids that reach the small intestine. Bacteria are the most abundant in the rumen, but protozoa, which are relatively large, account for 40-50% of the total microorganisms. However, the composition of these ruminal microbiota is not conserved or constant throughout life and is greatly influenced by the host. It is known that the initial colonization of calves immediately after birth is mainly influenced by the mother, and later changes depending on various factors such as diet, age, gender and breed. The initial rumen microbial community contains aerobic and facultative anaerobic bacteria due to the presence of oxygen, but as age increases, a hypoxic environment is created inside the rumen, and anaerobic bacteria become dominant in the rumen microbial community. As calves grow, taxonomic diversity increases, especially as they begin to consume solid food. Understanding the factors affecting the rumen microbial community and their effects and changes can lead to the early development and stabilization of the microbial community through the control of rumen microorganisms, and is expected to ultimately help improve host productivity and efficiency.
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Affiliation(s)
- Gi Beom Keum
- Department of Animal Biotechnology, Dankook University, Cheonan, 31116, Republic of Korea
| | - Sriniwas Pandey
- Department of Animal Biotechnology, Dankook University, Cheonan, 31116, Republic of Korea
| | - Eun Sol Kim
- Department of Animal Biotechnology, Dankook University, Cheonan, 31116, Republic of Korea
| | - Hyunok Doo
- Department of Animal Biotechnology, Dankook University, Cheonan, 31116, Republic of Korea
| | - Jinok Kwak
- Department of Animal Biotechnology, Dankook University, Cheonan, 31116, Republic of Korea
| | - Sumin Ryu
- Department of Animal Biotechnology, Dankook University, Cheonan, 31116, Republic of Korea
| | - Yejin Choi
- Department of Animal Biotechnology, Dankook University, Cheonan, 31116, Republic of Korea
| | - Juyoun Kang
- Department of Animal Biotechnology, Dankook University, Cheonan, 31116, Republic of Korea
| | - Sheena Kim
- Department of Animal Biotechnology, Dankook University, Cheonan, 31116, Republic of Korea.
| | - Hyeun Bum Kim
- Department of Animal Biotechnology, Dankook University, Cheonan, 31116, Republic of Korea.
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Chen X, Li X, Chen D, Zhao W, Zhang X, Yuan W, Si H, Deng X, Du R, Xu C. Effects of Dietary Alfalfa Meal Supplementation on the Growth Performance, Nutrient Apparent Digestibility, Serum Parameters, and Intestinal Microbiota of Raccoon Dogs ( Nyctereutes procyonoides). Animals (Basel) 2024; 14:623. [PMID: 38396591 PMCID: PMC10886288 DOI: 10.3390/ani14040623] [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: 01/10/2024] [Revised: 01/31/2024] [Accepted: 02/08/2024] [Indexed: 02/25/2024] Open
Abstract
The raccoon dog (Nyctereutes procyonoides) is a typical omnivore possessing wide dietary adaptability and tolerance to rough feeding, which may be attributed to its intestinal microbiota. The study aimed to investigate the effect of dietary alfalfa meal levels on the growth performance, nutrient apparent digestibility, serum parameters, and intestinal microbiota of raccoon dogs. Sixty raccoon dogs were randomly divided into four dietary treatments containing 0% (AM0), 5% (AM5), 10% (AM10), and 15% (AM15) alfalfa meal for a 60-day experiment. The results showed that compared to raccoon dogs fed the AM0 diet, those fed the AM5 and AM10 diets had no significant difference in growth performance, while those fed the AM15 diet experienced a significant decrease. Raccoon dogs fed the AM5 diet had no significant effect on the nutrient apparent digestibility. Dietary supplementation with alfalfa meal significantly decreased serum urea levels and increased the antioxidant capacity of raccoon dogs. The intestinal microbiome analysis showed that the richness and diversity of colonic microbiota significantly increased in the AM15 group. With the increase in dietary alfalfa meal levels, the relative abundance of fiber-degrading bacteria in the colon of raccoon dogs, such as Treponema, Phascolarctobacterium, and Christensenellaceae R-7 group, increased. However, the relative abundance of pathogenic bacteria, including Anaerobiospirillum, decreased. In conclusion, the inclusion of 5% alfalfa meal in the raccoon dogs' diet had no effect on growth performance, but it exhibited the potential to improve serum antioxidant capacity and intestinal microbiota. This indicates that raccoon dogs have a certain tolerance to the addition of alfalfa meal in their diet.
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Affiliation(s)
- Xiaoli Chen
- Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China; (X.C.); (X.L.); (D.C.); (W.Z.); (W.Y.)
| | - Xiao Li
- Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China; (X.C.); (X.L.); (D.C.); (W.Z.); (W.Y.)
| | - Danyang Chen
- Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China; (X.C.); (X.L.); (D.C.); (W.Z.); (W.Y.)
| | - Weigang Zhao
- Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China; (X.C.); (X.L.); (D.C.); (W.Z.); (W.Y.)
| | - Xiuli Zhang
- College of Veterinary Medicine, Jilin University, Changchun 130062, China; (X.Z.); (X.D.)
| | - Weitao Yuan
- Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China; (X.C.); (X.L.); (D.C.); (W.Z.); (W.Y.)
| | - Huazhe Si
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China; (H.S.); (R.D.)
| | - Xuming Deng
- College of Veterinary Medicine, Jilin University, Changchun 130062, China; (X.Z.); (X.D.)
| | - Rui Du
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China; (H.S.); (R.D.)
| | - Chao Xu
- Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China; (X.C.); (X.L.); (D.C.); (W.Z.); (W.Y.)
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China; (H.S.); (R.D.)
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Malik PK, Trivedi S, Kolte AP, Mohapatra A, Biswas S, Bhattar AVK, Bhatta R, Rahman H. Comparative Rumen Metagenome and CAZyme Profiles in Cattle and Buffaloes: Implications for Methane Yield and Rumen Fermentation on a Common Diet. Microorganisms 2023; 12:47. [PMID: 38257874 PMCID: PMC10818812 DOI: 10.3390/microorganisms12010047] [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: 11/09/2023] [Revised: 12/20/2023] [Accepted: 12/21/2023] [Indexed: 01/24/2024] Open
Abstract
A study was undertaken to compare the rumen microbial community composition, methane yield, rumen fermentation, and CAZyme profiles between cattle and buffaloes. The primary aim of this study was to ascertain the impact of the host species on the above when diet and environmental factors are fixed. A total of 43 phyla, 200 orders, 458 families, and 1722 microbial genera were identified in the study. Bacteroidetes was the most prominent bacterial phylum and constituted >1/3rd of the ruminal microbiota; however, their abundances were comparable between cattle and buffaloes. Firmicutes were the second most abundant bacteria, found to be negatively correlated with the Bacteroidetes. The abundances of Firmicutes as well as the F/B ratio were not different between the two host species. In this study, archaea affiliated with the nine phyla were identified, with Euryarchaeota being the most prominent. Like bacterial phyla, the abundances of Euryarchaeota methanogens were also similar between the cattle and buffaloes. At the order level, Methanobacteriales dominated the archaea. Methanogens from the Methanosarcinales, Methanococcales, Methanomicrobiales, and Methanomassiliicoccales groups were also identified, but at a lower frequency. Methanobrevibacter was the most prevalent genus of methanogens, accounting for approximately three percent of the rumen metagenome. However, their distribution was not different between the two host species. CAZymes affiliated with five classes, namely CBM, CE, GH, GT, and PL, were identified in the metagenome, where the GH class was the most abundant and constituted ~70% of the total CAZymes. The protozoal numbers, including Entodiniomorphs and Holotrichs, were also comparable between the cattle and buffaloes. Results from the study did not reveal any significant difference in feed intake, nutrient digestibility, and rumen fermentation between cattle and buffaloes fed on the same diet. As methane yield due to the similar diet composition, feed ingredients, rumen fermentation, and microbiota composition did not vary, these results indicate that the microbiota community structure and methane emissions are under the direct influence of the diet and environment, and the host species may play only a minor role until the productivity does not vary. More studies are warranted to investigate the effect of different diets and environments on microbiota composition and methane yield. Further, the impact of variable productivity on both the cattle and buffaloes when the diet and environmental factors are fixed needs to be ascertained.
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Affiliation(s)
- Pradeep K. Malik
- ICAR-National Institute of Animal Nutrition and Physiology, Bangalore 560030, India; (P.K.M.)
| | - Shraddha Trivedi
- International Livestock Research Institute, South Asia Regional Office, New Delhi 110012, India
| | - Atul P. Kolte
- ICAR-National Institute of Animal Nutrition and Physiology, Bangalore 560030, India; (P.K.M.)
| | - Archit Mohapatra
- ICAR-National Institute of Animal Nutrition and Physiology, Bangalore 560030, India; (P.K.M.)
| | - Siddharth Biswas
- ICAR-National Institute of Animal Nutrition and Physiology, Bangalore 560030, India; (P.K.M.)
| | - Ashwin V. K. Bhattar
- ICAR-National Institute of Animal Nutrition and Physiology, Bangalore 560030, India; (P.K.M.)
| | - Raghavendra Bhatta
- ICAR-National Institute of Animal Nutrition and Physiology, Bangalore 560030, India; (P.K.M.)
| | - Habibar Rahman
- International Livestock Research Institute, South Asia Regional Office, New Delhi 110012, India
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Noronha GN, Hess MK, Dodds KG, Silva AGME, de Souza SM, da Silva JAR, Graças DAD, de Carvalho Rodrigues TCG, da Silva WC, da Silva ÉBR, Janssen PH, Henry HM, Rowe SJ, de Castro VCG, Lourenço-Júnior JDB. Characterization of the Ruminal Microbiome of Water Buffaloes (Bubalus bubalis) Kept in Different Ecosystems in the Eastern Amazon. Animals (Basel) 2023; 13:3858. [PMID: 38136895 PMCID: PMC10740732 DOI: 10.3390/ani13243858] [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: 08/16/2023] [Revised: 09/18/2023] [Accepted: 11/06/2023] [Indexed: 12/24/2023] Open
Abstract
Increasing the efficiency of rumen fermentation is one of the main ways to maximize the production of ruminants. It is therefore important to understand the ruminal microbiome, as well as environmental influences on that community. However, there are no studies that describe the ruminal microbiota in buffaloes in the Amazon. The objective of this study was to characterize the rumen microbiome of the water buffalo (Bubalus bubalis) in the eastern Amazon in the dry and rainy seasons in three grazing ecosystems: Baixo Amazonas (BA), Continente do Pará (CP), Ilha do Marajó (IM), and in a confinement system: Tomé-Açu (TA). Seventy-one crossbred male buffaloes (Murrah × Mediterranean) were used, aged between 24 and 36 months, with an average weight of 432 kg in the rainy season and 409 kg in the dry season, and fed on native or cultivated pastures. In the confinement system, the feed consisted of sorghum silage, soybean meal, wet sorghum premix, and commercial feed. Samples of the diet from each ecosystem were collected for bromatological analysis. The collections of ruminal content were carried out in slaughterhouses, with the rumen completely emptied and homogenized, the solid and liquid fractions separated, and the ruminal pH measured. DNA was extracted from the rumen samples, then sequenced using Restriction Enzyme Reduced Representation Sequencing. The taxonomic composition was largely similar between ecosystems. All 61 genera in the reference database were recognized, including members of the domains Bacteria and Archaea. The abundance of 23 bacterial genera differed significantly (p < 0.01) between the Tomé-Açu confinement and other ecosystems. Bacillus, Ruminococcus, and Bacteroides had lower abundance in samples from the Tomé-Açu system. Among the Archaea, the genus Methanomicrobium was less abundant in Tomé-Açu, while Methanosarcina was more abundant. There was a difference caused by all evaluated factors, but the diet (available or offered) was what most influenced the ruminal microbiota.
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Affiliation(s)
- Gerlane Nunes Noronha
- Postgraduate Program in Animal Science (PPGCAN), Institute of Veterinary Medicine, Brazilian Agricultural Research Corporation (EMBRAPA), Castanhal 68746-360, Brazil; (G.N.N.); (A.G.M.e.S.); (T.C.G.d.C.R.); (É.B.R.d.S.); (V.C.G.d.C.); (J.d.B.L.-J.)
| | - Melanie K. Hess
- Invermay Agriculture Centre, AgResearch, Mosgiel 9053, New Zealand; (M.K.H.); (K.G.D.); (H.M.H.); (S.J.R.)
| | - Ken G. Dodds
- Invermay Agriculture Centre, AgResearch, Mosgiel 9053, New Zealand; (M.K.H.); (K.G.D.); (H.M.H.); (S.J.R.)
| | - André Guimarães Maciel e Silva
- Postgraduate Program in Animal Science (PPGCAN), Institute of Veterinary Medicine, Brazilian Agricultural Research Corporation (EMBRAPA), Castanhal 68746-360, Brazil; (G.N.N.); (A.G.M.e.S.); (T.C.G.d.C.R.); (É.B.R.d.S.); (V.C.G.d.C.); (J.d.B.L.-J.)
| | - Shirley Motta de Souza
- Federal Institute of Education, Science and Technology, South of Minas Gerais, Pouso Alegre 37550-000, Brazil;
| | | | - Diego Assis das Graças
- Laboratory of Biological Engineering, Guamá Science and Technology Park, Belem 66075-750, Brazil;
| | - Thomaz Cyro Guimarães de Carvalho Rodrigues
- Postgraduate Program in Animal Science (PPGCAN), Institute of Veterinary Medicine, Brazilian Agricultural Research Corporation (EMBRAPA), Castanhal 68746-360, Brazil; (G.N.N.); (A.G.M.e.S.); (T.C.G.d.C.R.); (É.B.R.d.S.); (V.C.G.d.C.); (J.d.B.L.-J.)
| | - Welligton Conceição da Silva
- Postgraduate Program in Animal Science (PPGCAN), Institute of Veterinary Medicine, Brazilian Agricultural Research Corporation (EMBRAPA), Castanhal 68746-360, Brazil; (G.N.N.); (A.G.M.e.S.); (T.C.G.d.C.R.); (É.B.R.d.S.); (V.C.G.d.C.); (J.d.B.L.-J.)
| | - Éder Bruno Rebelo da Silva
- Postgraduate Program in Animal Science (PPGCAN), Institute of Veterinary Medicine, Brazilian Agricultural Research Corporation (EMBRAPA), Castanhal 68746-360, Brazil; (G.N.N.); (A.G.M.e.S.); (T.C.G.d.C.R.); (É.B.R.d.S.); (V.C.G.d.C.); (J.d.B.L.-J.)
| | - Peter H. Janssen
- Grasslands Research Centre, AgResearch, Palmerston North 4410, New Zealand;
| | - Hannah M. Henry
- Invermay Agriculture Centre, AgResearch, Mosgiel 9053, New Zealand; (M.K.H.); (K.G.D.); (H.M.H.); (S.J.R.)
| | - Suzanne J. Rowe
- Invermay Agriculture Centre, AgResearch, Mosgiel 9053, New Zealand; (M.K.H.); (K.G.D.); (H.M.H.); (S.J.R.)
| | - Vinicius Costa Gomes de Castro
- Postgraduate Program in Animal Science (PPGCAN), Institute of Veterinary Medicine, Brazilian Agricultural Research Corporation (EMBRAPA), Castanhal 68746-360, Brazil; (G.N.N.); (A.G.M.e.S.); (T.C.G.d.C.R.); (É.B.R.d.S.); (V.C.G.d.C.); (J.d.B.L.-J.)
| | - José de Brito Lourenço-Júnior
- Postgraduate Program in Animal Science (PPGCAN), Institute of Veterinary Medicine, Brazilian Agricultural Research Corporation (EMBRAPA), Castanhal 68746-360, Brazil; (G.N.N.); (A.G.M.e.S.); (T.C.G.d.C.R.); (É.B.R.d.S.); (V.C.G.d.C.); (J.d.B.L.-J.)
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Wang H, Meng L, Mi L. Effects of Leymus chinensis hay and alfalfa hay on growth performance, rumen microbiota, and untargeted metabolomics of meat in lambs. Front Vet Sci 2023; 10:1256903. [PMID: 38033638 PMCID: PMC10687458 DOI: 10.3389/fvets.2023.1256903] [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: 07/11/2023] [Accepted: 10/24/2023] [Indexed: 12/02/2023] Open
Abstract
Objective The objective of this study was to compare the effects of Leymus chinensis hay and alfalfa hay as the roughage on the rumen bacterial and the meat metabolomics in lambs. Methods Fourteen male lambs were randomly assigned to two dietary treatments (one group was fed with concentrate and Leymus chinensis hay; another was fed with concentrate and alfalfa hay) with seven replicates per treatment. The feeding experiment lasted for 60 days. Lambs were slaughtered at the end of the feeding experiment. Growth performance, carcass performance, and weights of various viscera were determined. The longissimus dorsi and rumen contents were collected for untargeted metabolomics and 16S rDNA amplicon sequencing analysis, respectively. Results The lambs fed with alfalfa hay showed a significantly increased in average daily gain, carcass weight, dressing percentage, loin-eye area, and kidney weight. Feeding Leymus chinensis hay and alfalfa hay diets resulted in different meat metabolite deposition and rumen bacterial communities in the lambs. The relative abundance of phyla Fibrobacteres, Bacteroidetes, and Spirochaetes were greater in the Leymus Chinensis hay group, while, the relative abundance of Firmicutes, Proteobacteria, Fusobacteria, and Verrucomicrobia were greater in the alfalfa hay group. Based on untargeted metabolomics, the main altered metabolic pathways included alanine, aspartate and glutamate metabolism, D-glutamine and D-glutamate metabolism, phenylalanine metabolism, nitrogen metabolism, and tyrosine metabolism. Several bacteria genera including BF31, Alistipes, Faecalibacterium, Eggerthella, and Anaeroplasma were significantly correlated with growth performance and meat metabolites. Conclusion Alfalfa hay improved growth performance and carcass characteristics in lambs. Leymus chinensis hay and alfalfa hay caused different meat metabolite deposition by modifying the rumen bacterial community. These findings will be beneficial to future forage utilization for sheep growth, carcass performance, and meat quality improvement.
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Affiliation(s)
| | | | - Lan Mi
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Key Laboratory of Forage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, China
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Malik PK, Trivedi S, Kolte AP, Mohapatra A, Biswas S, Bhattar AVK, Bhatta R, Rahman H. Comparative analysis of rumen metagenome, metatranscriptome, fermentation and methane yield in cattle and buffaloes fed on the same diet. Front Microbiol 2023; 14:1266025. [PMID: 38029196 PMCID: PMC10666647 DOI: 10.3389/fmicb.2023.1266025] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 10/19/2023] [Indexed: 12/01/2023] Open
Abstract
A study to compare the rumen microbial community composition, functional potential of the microbiota, methane (CH4) yield, and rumen fermentation was conducted in adult male cattle and buffaloes fed on the same diet. A total of 41 phyla, 169 orders, 374 families, and 1,376 microbial genera were identified in the study. Bacteroidetes and Firmicutes were the two most dominant bacterial phyla in both cattle and buffaloes. However, there was no difference in the abundance of Bacteroidetes and Firmicutes in the rumen metagenome of cattle and buffaloes. Based on the abundance, the Proteobacteria was the 3rd largest phylum in the metagenome, constituting 18-20% in both host species. Euryarchaeota was the most abundant phylum of the methanogens, whereas Methanobacteriales and Methanobrevibacter were the most abundant orders and genera in both species. The methanogen abundances were not different between the two host species. Like the metagenome, the difference between the compositional and functional abundances (metagenome vs. metatranscriptome) of the Bacteroidetes and Firmicutes was not significant, whereas the proteobacteria were functionally less active than their metagenomic composition. Contrary to the metagenome, the Euryarchaeota was the 3rd most functional phylum in the rumen and constituted ~15% of the metatranscriptome. Methanobacteriales were the most functional methanogens, accounting for more than 2/3rd of the total archaeal functionality. These results indicated that the methanogens from Euryarchaeota were functionally more active as compared to their compositional abundance. The CH4 yield (g/kg DMI), CH4 emission (g/kg DDM), dry matter (DM) intake, and rumen fermentation did not vary between the two host species. Overall, the study established a substantial difference between the compositional abundances and metabolic functionality of the rumen microbiota; however, feeding cattle and buffaloes on the same diet resulted in similar microbiota composition, metabolic functionality, and CH4 yield. Further studies are warranted to investigate the effect of different diets and environments on the composition and metabolic functionality of the rumen microbiota.
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Affiliation(s)
- Pradeep K. Malik
- ICAR-National Institute of Animal Nutrition and Physiology, Bangalore, India
| | - Shraddha Trivedi
- International Livestock Research Institute, South Asia Regional Office, New Delhi, India
| | - Atul P. Kolte
- ICAR-National Institute of Animal Nutrition and Physiology, Bangalore, India
| | - Archit Mohapatra
- ICAR-National Institute of Animal Nutrition and Physiology, Bangalore, India
| | - Siddharth Biswas
- ICAR-National Institute of Animal Nutrition and Physiology, Bangalore, India
| | | | - Raghavendra Bhatta
- ICAR-National Institute of Animal Nutrition and Physiology, Bangalore, India
| | - Habibar Rahman
- International Livestock Research Institute, South Asia Regional Office, New Delhi, India
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Dixit S, Kumar S, Sharma R, Banakar PS, Deb R, Tyagi AK. Rumen microbial diversity, enteric methane emission and nutrient utilization of crossbred Karan-Fries cattle ( Bos taurus) and Murrah buffalo ( Bubalus bubalis) consuming varied roughage concentrate ratio. Anim Biotechnol 2023; 34:1857-1875. [PMID: 35352616 DOI: 10.1080/10495398.2022.2053696] [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] [Indexed: 02/01/2023]
Abstract
Dietary mix and host species have both been shown to have a significant impact on rumen microbial diversity, enteric methane emission and animal performance. The goal of this study was to see how the roughage concentrate ratio 70:30 (Low concentrate; LC) vs 40:60 (High concentrate; HC) and the host species crossbred cattle vs buffalo affected rumen microbial diversity, enteric methane emissions and nutrient utilization. Dry matter intake (kg/d) and dry matter percent digestibility were considerably (p < 0.05) higher in the HC ration and buffalo compared to LC ration and crossbred cattle, respectively. Both dietary mix and host species had a substantial (p < 0.05) impact on intake of various nutrients, including organic matter (OM), crude protein (CP), ether extract (EE), neutral detergent fiber (NDF), and acid detergent fiber (ADF). Increased concentrate proportion in the ration improved nitrogen balance, resulting in increased average daily gain and considerably reduced methane (g/d) output (p < 0.05). Furthermore, 16S rRNA genes were sequenced using Oxford Nanopore Technology (ONT) and subsequently annotated using the Centrifuge workflow to uncover ruminal bacterial diversity. Firmicutes was considerably (p < 0.01) greater in the LC diet, whereas, Bacteroidetes was higher in the HC ration. Genus Prevotella dominated all rumen samples, and buffalo fed LC ration had significantly (p < 0.01) higher Oscillospira abundance. At the species level, simple sugar-utilizing bacteria such as Prevotella spp. and Selenomonas ruminantium predominated in the crossbred cattle, but fibrolytic bacteria such as Oscillospira guilliermondii were statistically (p < 0.01) more abundant in the buffalo. Overall, dietary mix and host species have both been shown to have a significant impact on rumen microbial diversity, enteric methane emission and animal performance, however, host species remained a major driving force to change ruminal community composition as compared to roughage concentrate ratio under similar environmental conditions.
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Affiliation(s)
- Sonam Dixit
- Rumen Biotechnology Laboratory, Department of Animal Nutrition, National Dairy Research Institute, Karnal, India
| | - Sachin Kumar
- Rumen Biotechnology Laboratory, Department of Animal Nutrition, National Dairy Research Institute, Karnal, India
| | - Ritu Sharma
- Rumen Biotechnology Laboratory, Department of Animal Nutrition, National Dairy Research Institute, Karnal, India
| | - P S Banakar
- Rumen Biotechnology Laboratory, Department of Animal Nutrition, National Dairy Research Institute, Karnal, India
| | - Rajib Deb
- Animal Biotechnology Centre, National Dairy Research Institute, Karnal, India
| | - Amrish Kumar Tyagi
- Rumen Biotechnology Laboratory, Department of Animal Nutrition, National Dairy Research Institute, Karnal, India
- Animal Nutrition and Physiology, Indian Council of Agricultural Research, New Delhi, India
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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: 0] [Impact Index Per Article: 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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9
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Ren Y, Zhaxi Y, Ciwang R, Wang Z, Liu M. Responses of rumen microorganisms and metabolites to different roughage of domesticated Tibetan sheep. Front Microbiol 2023; 14:1247609. [PMID: 37664115 PMCID: PMC10469951 DOI: 10.3389/fmicb.2023.1247609] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 08/07/2023] [Indexed: 09/05/2023] Open
Abstract
Tibetan sheep can utilize high fiber feeds well. However, the mechanisms of rumen microbiota and metabolites in response to different roughage in a housed environment are still unclear. We fed Tibetan sheep with three different roughage diets: 50% whole corn silage (TS), 50% wheatgrass group (TW), and 25% each of whole corn silage and wheatgrass (TM). Subsequently, meat traits, rumen contents 16S rRNA and metabolomics were studied. The results showed that feeding wheat straw to Tibetan sheep significantly increased the abundance of bacteria such as Ruminococcus and Succiniclasticum in the rumen. These microorganisms significantly increased metabolites such as beta-alanyl-L-lysine, butanoic acid and prostaglandin E2. Eventually, production performance, such as carcass weight and intramuscular fat and meat quality characteristics, such as color and tenderness were improved by altering the rumen's amino acid, lipid and carbohydrate metabolism. This study demonstrated that including 25% wheatgrass and 25% whole corn silage in the diet improved the performance of Tibetan sheep, revealing the effect of the diet on the performance of Tibetan sheep through rumen microorganisms and metabolites.
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Affiliation(s)
- Yue Ren
- Institute of Livestock Research, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lhasa, China
| | - Yangzhong Zhaxi
- Institute of Livestock Research, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lhasa, China
| | - Renzeng Ciwang
- Institute of Livestock Research, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lhasa, China
| | - Zhengwen Wang
- Key Laboratory of Grassland Ecosystem, College of Grassland Science, Gansu Agricultural University, Lanzhou, China
| | - Mengjun Liu
- Institute of Livestock Research, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lhasa, China
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10
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Role of Feeding and Novel Ripening System to Enhance the Quality and Production Sustainability of Curd Buffalo Cheeses. Foods 2023; 12:foods12040704. [PMID: 36832779 PMCID: PMC9956207 DOI: 10.3390/foods12040704] [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: 12/24/2022] [Revised: 01/20/2023] [Accepted: 02/03/2023] [Indexed: 02/08/2023] Open
Abstract
The buffalo dairy sector is extending its boundaries to include new buffalo cheese productions beyond mozzarella, overcoming some barriers that make cheeses expensive and unsustainable. This study aimed to evaluate the effects of both the inclusion of green feed in the diet of Italian Mediterranean buffaloes and an innovative ripening system on buffalo cheese quality, providing solutions capable of guaranteeing the production of nutritionally competitive and sustainable products. For this purpose, chemical, rheological, and microbiological analyses were carried out on cheeses. Buffaloes were fed with or without the inclusion of green forage. Their milk was used to produce dry ricotta and semi-hard cheeses, ripened according to both respective traditional (MT) and innovative methods (MI); these are based on automatic adjustments of climatic recipe guided by the continuous control of pH. Green feed enhances the nutritional profile of the final products (high content of MUFAs and PUFAs). As far as the ripening method is concerned, to our knowledge, this is the first study that tests aging chambers, commonly used for meat, for the maturing of buffalo cheeses. Results pointed out the MI validity also in this field of application, as it shortens the ripening period without negatively compromising any of desirable physicochemical properties and the safety and hygiene of the final products. Conclusively, this research highlights the benefits of diets rich in green forage on productions and provides support for the ripening optimization of buffalo semi-hard cheeses.
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11
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Zhang X, Han L, Gui L, Raza SHA, Hou S, Yang B, Wang Z, Ma Y, Makhlof RTM, Alhuwaymil Z, Ibrahim SF. Metabolome and microbiome analysis revealed the effect mechanism of different feeding modes on the meat quality of Black Tibetan sheep. Front Microbiol 2023; 13:1076675. [PMID: 36687606 PMCID: PMC9854131 DOI: 10.3389/fmicb.2022.1076675] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 12/05/2022] [Indexed: 01/09/2023] Open
Abstract
Introduction Black Tibetan sheep is one of the primitive sheep breeds in China that is famous for its great eating quality and nutrient value but with little attention to the relationship between feeding regimes and rumen metabolome along with its impact on the muscle metabolism and meat quality. Methods This study applies metabolomics-based analyses of muscles and 16S rDNA-based sequencing of rumen fluid to examine how feeding regimes influence the composition of rumen microbiota, muscle metabolism and ultimately the quality of meat from Black Tibetan sheep. Twenty-seven rams were randomly assigned to either indoor feeding conditions (SG, n = 9), pasture grazing with indoor feeding conditions (BG, n = 9) or pasture grazing conditions (CG, n = 9) for 120 days. Results The results showed that, compared with BG and CG, SG improved the quality of Black Tibetan sheep mutton by preventing a decline in pH and increasing fat deposition to enhance the color, tenderness and water holding capacity (WHC) of the Longissimus lumborum (LL). Metabolomics and correlation analyses further indicated that the feeding regimes primarily altered amino acid, lipid and carbohydrate metabolism in muscles, thereby influencing the amino acid (AA) and fatty acid (FA) levels as well as the color, tenderness and WHC of the LL. Furthermore, SG increased the abundance of Christensenellaceae R-7 group, [Eubacterium] coprostanoligenes group, Methanobrevibacter, Ruminococcus 2 and Quinella, decreased the abundance of Lactobacillus, Prevotella 1 and Rikenellaceae RC9 gut group, and showed a tendency to decrease the abundance of Succinivibrio and Selenomonas 1. Interestingly, all of these microorganisms participated in the deposition of AAs and FAs and modified the levels of different metabolites involved in the regulation of meat quality (maltotriose, pyruvate, L-ascorbic acid, chenodeoxycholate, D-glucose 6-phosphate, glutathione, etc.). Discussion Overall, the results suggest that feeding Black Tibetan sheep indoors with composite forage diet was beneficial to improve the mouthfeel of meat, its color and its nutritional value by altering the abundance of rumen bacteria which influenced muscle metabolism.
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Affiliation(s)
- Xue Zhang
- Department of Animal Science, College of Agriculture and Animal Husbandry, Qinghai University, Xining, Qinghai, China
| | - Lijuan Han
- Department of Animal Science, College of Agriculture and Animal Husbandry, Qinghai University, Xining, Qinghai, China,*Correspondence: Lijuan Han, ✉
| | - Linsheng Gui
- Department of Animal Science, College of Agriculture and Animal Husbandry, Qinghai University, Xining, Qinghai, China
| | - Sayed Haidar Abbas Raza
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China,Safety of Livestock and Poultry Products, College of Food Science, South China Agricultural University, Guangzhou, China
| | - Shengzhen Hou
- Department of Animal Science, College of Agriculture and Animal Husbandry, Qinghai University, Xining, Qinghai, China
| | - Baochun Yang
- Department of Animal Science, College of Agriculture and Animal Husbandry, Qinghai University, Xining, Qinghai, China
| | - Zhiyou Wang
- Department of Animal Science, College of Agriculture and Animal Husbandry, Qinghai University, Xining, Qinghai, China
| | - Ying Ma
- Department of Animal Science, College of Agriculture and Animal Husbandry, Qinghai University, Xining, Qinghai, China
| | - Raafat T. M. Makhlof
- Department of Parasitology, Faculty of Medicine, Umm Al Qura University, Mecca, Saudi Arabia,Department of Parasitology, Faculty of Medicine, Minia University, Minya, Egypt
| | - Zamzam Alhuwaymil
- Organic Department, College of Science and Humanities at Al-Quway'iyah, Shaqra University, Shaqra, Saudi Arabia
| | - Samah F. Ibrahim
- Department of Clinical Sciences, College of Medicine, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
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12
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Rabee AE, Abd El Rahman T, Lamara M. Changes in the bacterial community colonizing extracted and non-extracted tannin-rich plants in the rumen of dromedary camels. PLoS One 2023; 18:e0282889. [PMID: 36897876 PMCID: PMC10004507 DOI: 10.1371/journal.pone.0282889] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 02/26/2023] [Indexed: 03/11/2023] Open
Abstract
Leguminous trees and saltbushes provide potential alternatives to conventional feeds to overcome feed deficiency in arid and semi-arid countries. However, these plants are rich in antinutritional factors that have adverse effects on rumen microbiota and the host- animal. Some rumen microbiota detoxifies plants' secondary metabolites; thus, understanding plant-microbe interaction in the rumen could improve the plants' utilization. This study investigated the bacterial colonization and degradation of non-extracted and extracted tanniniferous plants: Atriplex halimus, Acacia saligna, and Leucaena leucocephala, in the rumen of three fistulated camels at 6 and 12 hours. The results showed that these plants have high nutritional value and tannins contents. The rumen degradation and microbial diversity of plant-attached bacteria varied according to plant type and phenols' extraction. Atriplex and leucaena showed higher microbial diversity at 6 and 12h, respectively. Bacteroidetes and Firmicutes were the main bacterial phyla, and the main genera were Prevotella, RC9_gut_group, Butyrivibrio that overrepresented in non-extracted plants (P<0.05). Fibrobacteres and Anaerovibrio showed sensitivity to plant toxins and Ruminococcus attached to plants with lower tannins. Several bacterial genera in the camel rumen have the potential to resist antinutritional factors in fodder plants, which could be used to improve the performance of grazing animals.
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Affiliation(s)
- Alaa Emara Rabee
- Animal and Poultry Nutrition Department, Desert Research Center, Cairo, Egypt
| | - Taha Abd El Rahman
- Genetic Engineering and Biotechnology Research Institute, University of Sadat City, Sadat City, Egypt.,Centre SEVE, Department of Biology, Université de Sherbrooke, Sherbrooke, Canada
| | - Mebarek Lamara
- Forest Research Institute, University of Quebec in Abitibi-Temiscamingue, Rouyn-Noranda, Canada
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13
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Shi M, Ma Z, Tian Y, Ma C, Li Y, Zhang X. Effects of corn straw treated with CaO on rumen degradation characteristics and fermentation parameters and their correlation with microbial diversity in rumen. Anim Feed Sci Technol 2022. [DOI: 10.1016/j.anifeedsci.2022.115403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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14
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Understanding microbial networks of farm animals through genomics, metagenomics and other meta-omic approaches for livestock wellness and sustainability. ANNALS OF ANIMAL SCIENCE 2022. [DOI: 10.2478/aoas-2022-0002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Abstract
The association of microorganisms with livestock as endosymbionts, opportunists, and pathogens has been a matter of debate for a long time. Several livestock-associated bacterial and other microbial species have been identified and characterized through traditional culture-dependent genomic approaches. However, it is imperative to understand the comprehensive microbial network of domestic animals for their wellness, disease management, and disease transmission control. Since it is strenuous to provide a niche replica to any microorganisms while culturing them, thus a substantial number of microbial communities remain obscure. Metagenomics has laid out a powerful lens for gaining insight into the hidden microbial diversity by allowing the direct sequencing of the DNA isolated from any livestock sample like the gastrointestinal tract, udder, or genital system. Through metatranscriptomics and metabolomics, understanding gene expression profiles of the microorganisms and their molecular phenotype has become unchallenging. With large data sets emerging out of the genomic, metagenomic, and other meta-omics methods, several computational tools have also been developed for curation, assembly, gene prediction, and taxonomic profiling of the microorganisms. This review provides a detailed account of the beneficial and pathogenic organisms that dwell within or on farm animals. Besides, it highlights the role of meta-omics and computational tools in a comprehensive analysis of livestock-associated microorganisms.
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15
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Tan P, Liu H, Zhao J, Gu X, Wei X, Zhang X, Ma N, Johnston LJ, Bai Y, Zhang W, Nie C, Ma X. Amino acids metabolism by rumen microorganisms: Nutrition and ecology strategies to reduce nitrogen emissions from the inside to the outside. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 800:149596. [PMID: 34426337 DOI: 10.1016/j.scitotenv.2021.149596] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 08/06/2021] [Accepted: 08/07/2021] [Indexed: 06/13/2023]
Abstract
For the ruminant animal industry, the emission of nitrogenous substances, such as nitrous oxide (N2O) and ammonia (NH3), not only challenges environmental sustainability but also restricts its development. The metabolism of proteins and amino acids by rumen microorganisms is a key factor affecting nitrogen (N) excretion in ruminant animals. Rumen microorganisms that affect N excretion mainly include three types: proteolytic and peptidolytic bacteria (PPB), ureolytic bacteria (UB), and hyper-ammonia-producing bacteria (HAB). Microbes residing in the rumen, however, are influenced by several complex factors, such as diet, which results in fluctuations in the rumen metabolism of proteins and amino acids and ultimately affects N emission. Combining feed nutrition strategies (including ingredient adjustment and feed additives) and ecological mitigation strategies of N2O and NH3 in industrial practice can reduce the emission of nitrogenous pollutants from the ruminant breeding industry. In this review, the characteristics of the rumen microbial community related to N metabolism in ruminants were used as the metabolic basis. Furthermore, an effective strategy to increase N utilisation efficiency in combination with nutrition and ecology was reviewed to provide an inside-out approach to reduce N emissions from ruminants.
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Affiliation(s)
- Peng Tan
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Han Liu
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang 832000, China; College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, Henan 453003, China
| | - Jing Zhao
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang 832000, China; College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, Henan 453003, China
| | - Xueling Gu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Xiaobing Wei
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, Henan 453003, China
| | - Xiaojian Zhang
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, Henan 453003, China
| | - Ning Ma
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Lee J Johnston
- West Central Research & Outreach Center, University of Minnesota, Morris, MN 56267, USA
| | - Yueyu Bai
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, Henan 453003, China
| | - Wenju Zhang
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang 832000, China
| | - Cunxi Nie
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang 832000, China
| | - Xi Ma
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang 832000, China.
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16
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Rabee AE, Forster R, Sabra EA. Lignocelluloytic activities and composition of bacterial community in the camel rumen. AIMS Microbiol 2021; 7:354-367. [PMID: 34708177 PMCID: PMC8500796 DOI: 10.3934/microbiol.2021022] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 09/15/2021] [Indexed: 11/29/2022] Open
Abstract
The camel is well-adapted to utilize the poor-quality forages in the harsh desert conditions as the camel rumen sustains fibrolytic microorganisms, mainly bacteria that are capable of breaking down the lignocellulosic biomass efficiently. Exploring the composition of the bacterial community in the rumen of the camel and quantifying their cellulolytic and xylanolytic activities could lead to understanding and improving fiber fermentation and discovering novel sources of cellulases and xylanases. In this study, Illumina MiSeq sequencing of the V4 region on 16S rRNA was applied to identify the bacterial and archaeal communities in the rumen of three camels fed wheat straw and broom corn. Furthermore, rumen samples were inoculated into bacterial media enriched with xylan and different cellulose sources, including filter paper (FP), wheat straw (WS), and alfalfa hay (AH) to assess the ability of rumen bacteria to produce endo-cellulase and endo-xylanase at different fermentation intervals. The results revealed that the phylum Bacteroidetes dominated the bacterial community and Candidatus Methanomethylophilus dominated the archaeal community. Also, most of the bacterial community has fibrolytic potential and the dominant bacterial genera were Prevotella, RC9_gut_group, Butyrivibrio, Ruminococcus, Fibrobacteres, and Treponema. The highest xylanase production (884.8 mU/mL) was observed at 7 days. The highest cellulase production (1049.5 mU/mL) was observed when rumen samples were incubated with Alfalfa hay for 7 days.
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Affiliation(s)
- Alaa Emara Rabee
- Animal and Poultry Nutrition Department, Desert Research Center, Cairo, Egypt
| | - Robert Forster
- Lethbridge Research and Development Centre, Agriculture and Agrifood Canada, Lethbridge, AB, Canada
| | - Ebrahim A Sabra
- Animal Biotechnology Department, Genetic Engineering and Biotechnology Research Institute, University of Sadat City, Sadat City, Egypt
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Ngu NT, Anh LH, Nhan NTH, Van Hon N, Thiet N, Liang JB, Hung LT, Xuan NH, Chen WL, Lan LTT. Analysis of bacterial community in rumen fluid of cattle supplemented with different protein and energy sources. ANIMAL PRODUCTION SCIENCE 2021. [DOI: 10.1071/an20206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Context Source and composition of feed influence rumen microbial community, which determines efficiency of feed digestion and thus productivity in ruminants. Therefore, changes in the structure, function and diversity of the rumen microbial populations in response to changes in diet provide an understanding in the rumen fermentation process. Aims The present study, consisting of two experiments, was conducted to determine the effects of supplementing different protein and energy sources on the rumen bacterial community in cattle. Methods The dietary treatments of the first experiment, which evaluated the effect of protein sources, were as follows: (i) Hymenachne acutigluma grass, rice straw and rice bran (1.5 kg/head.day; C1), (ii) C1 plus 120 g urea/head.day (C1 + U), (iii) C1 plus 720 g soybean/head.day (C1 + SM), and (iv) C1 plus 720 g of blood and feather meal (in 1:1 ratio)/head.day (C1 + BFM). The treatments in the second experiment were (i) Hymenachne acutigluma grass, rice straw and concentrate (1.5 kg/head.day; C2), (ii) C2 plus 250 g fish oil/head.day (C2 + FO) and (iii) C2 + 250 g soybean oil/head.day (C2 + SO). At the end of the 90-day feeding trial, rumen fluids were extracted for microbial DNA isolation to identify the microbe species by the polymerase chain reaction–denaturing gradient gel electrophoresis method and sequencing of the 16S rRNA region. Key results The sequences of some DNA bands were closely related to the bacteria strains of the Prevotella, Cytophaga, Capnocytophaga, Cyanobacterium, Catonella, Faecalibacterium, Lachnospiraceae, Ruminococcaceae, Propionivibrio, Galbibacter, Moorellaglycerin, Escherichia coli and Klebsiella alba groups, with similarity levels ranging from 73% to 96%. In addition, the Prevotella species was found in both the protein and the energy supplement trials, and irrespective of diet supplements, the Firmicutes and Bacteroidetes were the prominent groups in the rumen. Conclusions Firmicutes and Bacteroidetes are the two dominant groups of rumen microflora, and Bacteroidia and Clostridia classes together with the Prevotella genus are predominant in the rumen irrespective of protein and energy sources. Implications Our findings provided evidence on the effect of diet on the interaction of rumen microbial community and have important implications in establishing optimal diets for cattle.
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Zhu Z, Difford GF, Noel SJ, Lassen J, Løvendahl P, Højberg O. Stability Assessment of the Rumen Bacterial and Archaeal Communities in Dairy Cows Within a Single Lactation and Its Association With Host Phenotype. Front Microbiol 2021; 12:636223. [PMID: 33927700 PMCID: PMC8076905 DOI: 10.3389/fmicb.2021.636223] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 02/28/2021] [Indexed: 01/09/2023] Open
Abstract
Better characterization of changes in the rumen microbiota in dairy cows over the lactation period is crucial for understanding how microbial factors may potentially be interacting with host phenotypes. In the present study, we characterized the rumen bacterial and archaeal community composition of 60 lactating Holstein dairy cows (33 multiparous and 27 primiparous), sampled twice within the same lactation with a 122 days interval. Firmicutes and Bacteroidetes dominated the rumen bacterial community and showed no difference in relative abundance between samplings. Two less abundant bacterial phyla (SR1 and Proteobacteria) and an archaeal order (Methanosarcinales), on the other hand, decreased significantly from the mid-lactation to the late-lactation period. Moreover, between-sampling stability assessment of individual operational taxonomic units (OTUs), evaluated by concordance correlation coefficient (C-value) analysis, revealed the majority of the bacterial OTUs (6,187 out of 6,363) and all the 79 archaeal OTUs to be unstable over the investigated lactation period. The remaining 176 stable bacterial OTUs were mainly assigned to Prevotella, unclassified Prevotellaceae, and unclassified Bacteroidales. Milk phenotype-based screening analysis detected 32 bacterial OTUs, mainly assigned to unclassified Bacteroidetes and Lachnospiraceae, associated with milk fat percentage, and 6 OTUs, assigned to Ruminococcus and unclassified Ruminococcaceae, associated with milk protein percentage. These OTUs were only observed in the multiparous cows. None of the archaeal OTUs was observed to be associated with the investigated phenotypic parameters, including methane production. Co-occurrence analysis of the rumen bacterial and archaeal communities revealed Fibrobacter to be positively correlated with the archaeal genus vadinCA11 (Pearson r = 0.76) and unclassified Methanomassiliicoccaceae (Pearson r = 0.64); vadinCA11, on the other hand, was negatively correlated with Methanobrevibacter (Pearson r = –0.56). In conclusion, the rumen bacterial and archaeal communities of dairy cows displayed distinct stability at different taxonomic levels. Moreover, specific members of the rumen bacterial community were observed to be associated with milk phenotype parameters, however, only in multiparous cows, indicating that dairy cow parity could be one of the driving factors for host–microbe interactions.
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Affiliation(s)
- Zhigang Zhu
- Department of Animal Science, Faculty of Science and Technology, Aarhus University, Aarhus, Denmark
| | - Gareth Frank Difford
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Faculty of Science and Technology, Aarhus University, Aarhus, Denmark
| | - Samantha Joan Noel
- Department of Animal Science, Faculty of Science and Technology, Aarhus University, Aarhus, Denmark
| | - Jan Lassen
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Faculty of Science and Technology, Aarhus University, Aarhus, Denmark
| | - Peter Løvendahl
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Faculty of Science and Technology, Aarhus University, Aarhus, Denmark
| | - Ole Højberg
- Department of Animal Science, Faculty of Science and Technology, Aarhus University, Aarhus, Denmark
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19
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Wang B, Luo Y, Wang Y, Wang D, Hou Y, Yao D, Tian J, Jin Y. Rumen bacteria and meat fatty acid composition of Sunit sheep reared under different feeding regimens in China. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2021; 101:1100-1110. [PMID: 32767556 DOI: 10.1002/jsfa.10720] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Revised: 07/20/2020] [Accepted: 08/07/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Rumen bacteria play a critical role in feed degradation and productivity. This study evaluated the impact of feeding regimen on the rumen microbial populations and fatty acid composition of the meat of sheep. Twenty-four Sunit sheep were raised on a grass pasture from birth to 9 months of age, at which time they were randomly divided into two feeding groups: pasture feeding (PF) and barn feeding (BF). Sheep in the PF group were allowed to graze freely on wild grassland for 3 months. Sheep in the BF group were confined for 3 months to a dry barn, in which they roamed freely with corn straw and corn. RESULTS Sheep in the PF group had greater rumen bacteria diversity. The relative abundances of the genera Butyrivibrio_2, Saccharofermentans and Succiniclasticum were increased, and that of the genus RC9_gut_group was decreased, in the PF compared to the BF sheep. The n-3 polyunsaturated fatty acid contents were greater in meat from PF sheep than from BF sheep. In addition, the α-linolenic acid (C18:3 n-3, ALA) and conjugated linoleic acid (CLA) contents were positively correlated with the abundance of Butyrivibrio_2. CONCLUSION Grazing may improve the diversity of rumen bacteria and increase the proportion of ALA and CLA in sheep meat. © 2020 Society of Chemical Industry.
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Affiliation(s)
- Bohui Wang
- College of Food Science and Engineering, Inner Mongolia Agricultural University, Hohhot, China
- Ordos City Food Inspection and Testing Center, Ordos, China
| | - Yulong Luo
- College of Food Science and Engineering, Inner Mongolia Agricultural University, Hohhot, China
| | - Yu Wang
- College of Food Science and Engineering, Inner Mongolia Agricultural University, Hohhot, China
| | - Debao Wang
- College of Food Science and Engineering, Inner Mongolia Agricultural University, Hohhot, China
| | - Yanru Hou
- College of Food Science and Engineering, Inner Mongolia Agricultural University, Hohhot, China
| | - Duo Yao
- College of Food Science and Engineering, Inner Mongolia Agricultural University, Hohhot, China
| | - Jianjun Tian
- College of Food Science and Engineering, Inner Mongolia Agricultural University, Hohhot, China
| | - Ye Jin
- College of Food Science and Engineering, Inner Mongolia Agricultural University, Hohhot, China
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20
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Mu YY, Qi WP, Zhang T, Zhang JY, Mao SY. Gene function adjustment for carbohydrate metabolism and enrichment of rumen microbiota with antibiotic resistance genes during subacute rumen acidosis induced by a high-grain diet in lactating dairy cows. J Dairy Sci 2020; 104:2087-2105. [PMID: 33358156 DOI: 10.3168/jds.2020-19118] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 09/25/2020] [Indexed: 12/21/2022]
Abstract
The high-grain diets fed to ruminants generally alters the structure and function of rumen microbiota, resulting in variations of rumen fermentation patterns and the occurrence of subacute rumen acidosis (SARA). To clarify the microbial mechanism for carbohydrate metabolism during SARA, 8 ruminally cannulated Holstein cows in mid lactation were selected for a 3-wk experiment. The cows were randomly divided into 2 groups, fed either a conventional diet (CON; 40% concentrate; dry matter basis) or a high-grain diet (HG; 60% concentrate; dry matter basis). Compared with the CON diet, the HG diet reduced average daily pH (5.71 vs. 6.13), acetate concentration (72.56 vs. 78.44 mM), acetate ratio (54.81 vs. 65.24%), and the ratio of the concentrations of acetate to propionate (1.87 vs. 3.21) but increased the concentrations of total volatile fatty acids (133.03 vs. 120.22 mM), propionate (41.32 vs. 24.71 mM), and valerate (2.46 vs. 1.68 mM) and the propionate ratio (30.51 vs. 20.47%). Taxonomic analysis indicated that the HG cows had a higher relative abundance of Ruminococcus, Eubacterium, Selenomonas, Ruminobacter, Succinimonas, Methanomicrobium, and Methanocaldococcus accompanied by a lower relative abundance of unclassified Firmicutes, unclassified Bacteroidetes, Bacteroides, Fibrobacter, Alistipes, Candidatus Methanoplasma, Methanomassiliicoccus, and Methanolobus. Carbohydrate-active enzyme annotation suggested that there was enriched abundance of glycosyltransferases (GT) 2, glycoside hydrolase (GH) 13, GH24, carbohydrate-binding module (CBM) 26, GH73, GH25, CBM12, GH23, GT8, CBM50, and GT9 and reduced abundance of GH78, GH31, S-layer homology, GH109, carbohydrate esterase 1, GH3, carbohydrate esterase 10, and GH43 in the HG group. Functional profiling revealed that the HG feeding mainly downregulated the pentose phosphate pathway of carbohydrate catabolism, acetate metabolism, propionate metabolism (succinate pathway), and methane metabolism, whereas it upregulated the Embden-Meyerhof-Parnas and Entner-Doudoroff pathways of glycolysis and the citrate cycle. Additionally, the HG feeding promoted the abundance of various antibiotic resistance genes and antimicrobial resistance gene families. These results elucidated the structure and function adjustment of rumen microbiota for carbohydrate metabolism and summarized the enrichment of rumen antibiotic resistance genes under the HG feeding, which expands our understanding of the mechanism underlying the response of rumen microbiota to SARA in dairy cattle.
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Affiliation(s)
- Y Y Mu
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, Centre for Ruminant Nutrition and Feed Engineering Technology Research, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - W P Qi
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, Centre for Ruminant Nutrition and Feed Engineering Technology Research, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - T Zhang
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, Centre for Ruminant Nutrition and Feed Engineering Technology Research, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - J Y Zhang
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, Centre for Ruminant Nutrition and Feed Engineering Technology Research, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - S Y Mao
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, Centre for Ruminant Nutrition and Feed Engineering Technology Research, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China.
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21
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Rabee AE, Forster R, Elekwachi C, Sabra E, Lamara M. Comparative analysis of the metabolically active microbial communities in the rumen of dromedary camels under different feeding systems using total rRNA sequencing. PeerJ 2020; 8:e10184. [PMID: 33194403 PMCID: PMC7603790 DOI: 10.7717/peerj.10184] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 09/23/2020] [Indexed: 11/20/2022] Open
Abstract
Breakdown of plant biomass in rumen depends on interactions between bacteria, archaea, fungi, and protozoa; however, the majority of studies of the microbiome of ruminants, including the few studies of the rumen of camels, only studied one of these microbial groups. In this study, we applied total rRNA sequencing to identify active microbial communities in 22 solid and liquid rumen samples from 11 camels. These camels were reared at three stations that use different feeding systems: clover, hay and wheat straw (G1), fresh clover (G2), and wheat straw (G3). Bacteria dominated the libraries of sequence reads generated from all rumen samples, followed by protozoa, archaea, and fungi respectively. Firmicutes, Thermoplasmatales, Diplodinium, and Neocallimastix dominated bacterial, archaeal, protozoal and fungal communities, respectively in all samples. Libraries generated from camels reared at facility G2, where they were fed fresh clover, showed the highest alpha diversity. Principal co-ordinate analysis and linear discriminate analysis showed clusters associated with facility/feed and the relative abundance of microbes varied between liquid and solid fractions. This provides preliminary evidence that bacteria dominate the microbial communities of the camel rumen and these communities differ significantly between populations of domesticated camels.
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Affiliation(s)
- Alaa Emara Rabee
- Animal and Poultry Nutrition Department, Desert Research Center, Cairo, Cairo, Egypt
| | - Robert Forster
- Lethbridge Research and Development Centre, Agriculture and Agrifood Canada, Lethbridge, AB, Canada
| | - Chijioke Elekwachi
- Lethbridge Research and Development Centre, Agriculture and Agrifood Canada, Lethbridge, AB, Canada
| | - Ebrahim Sabra
- Genetic Engineering and Biotechnology Research Institute, University of Sadat City, Sadat City, Menoufia, Egypt
| | - Mebarek Lamara
- Institut de Recherche sur les Forêts, Université du Québec en Abitibi-Témiscamingue, Rouyn-Noranda, QC, Canada
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22
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Wu J, Yang D, Gong H, Qi Y, Sun H, Liu Y, Liu Y, Qiu X. Multiple omics analysis reveals that high fiber diets promote gluconeogenesis and inhibit glycolysis in muscle. BMC Genomics 2020; 21:660. [PMID: 32972369 PMCID: PMC7513505 DOI: 10.1186/s12864-020-07048-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 09/03/2020] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Meat quality is a complex trait affected by genotypic and environmental factors. In a previous study, it was found that feedstuffs have various effects on the growth rate and meat quality of lambs. However, the underlying mechanisms are still not entirely clear. RESULTS In this study, to investigate the mechanisms that impact meat quality in twin sheep fed either with high fiber low protein (HFLP) forage (Ceratoides) or low fiber high protein (LFHP) forage (alfalfa) diets, multi omics techniques were utilized for integration analysis based on the feed nutritional value and the sheep microbiome, transcriptome, metabolome, and fatty acid profile. Results showed that the production performance and the muscle components of lambs were significantly affected by feeds. The essential fatty acid (linoleic acid and arachidonic acid) content of the muscle, based on gas chromatography-mass spectrometry analysis, was increased when lambs were fed with HFLP. The microbes in the lambs' rumen fed a HFLP diet were more diverse than those of the LFHP fed group. Besides, the ratio of Bacteroidetes and Firmicutes in the rumen of the sheep fed a LFHP diet was 2.6 times higher than that of the HFLP fed group. Transcriptome analysis of the muscle revealed that the genes related to glucose metabolic processes and fatty acid biosynthesis were significantly differentially expressed between the two groups. Potential cross talk was found between the sfour omics data layers, which helps to understand the mechanism by which feedstuffs affect meat quality of lambs. CONCLUSION Feed systems may affect the epigenetic regulation of genes involved in the glucose metabolic pathway. HFLP feeds could induce gluconeogenesis to maintain glucose levels in blood, resulting in decreased fat content in muscle. The multiple omics analysis showed that the microbiota structure is significantly correlated with the metabolome and gene expression in muscle. This study laid a theoretical foundation for controlling the nutrient intake of sheep; it suggested that its fatty acid spectrum modifications and the removal of meat quality detrimental material could guide sheep feeding for functional mutton.
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Affiliation(s)
- Jianghong Wu
- College of Animal Science and Technology, Inner Mongolia University for Nationalities, Tongliao, 028000, China. .,Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot, 010031, China.
| | - Ding Yang
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot, 010031, China
| | - Husile Gong
- College of Life Science, Inner Mongolia University for Nationalities, Tongliao, 028000, China
| | - Yunxia Qi
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot, 010031, China
| | - Hailian Sun
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot, 010031, China
| | - Yongbin Liu
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot, 010031, China
| | - Yahong Liu
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot, 010031, China
| | - Xiao Qiu
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot, 010031, China
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23
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Hinsu AT, Patel AB, Pandit RJ, Thakkar JR, Shah RK, Jakhesara SJ, Koringa PG, Joshi CG. MetaRNAseq analysis of surti buffalo rumen content reveals that transcriptionally active microorganisms need not be abundant. Mol Biol Rep 2020; 47:5101-5114. [PMID: 32557173 DOI: 10.1007/s11033-020-05581-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 06/10/2020] [Indexed: 11/26/2022]
Abstract
The present study describes rumen microbiota composition and their functional profiles in Indian Surti buffaloes by metagenomic (MG) and metatranscriptomic (MT) approaches. The study compares samples from buffaloes fed three different proportion of roughages; green and dry type of roughage; and different rumen liquor fractions. Irrespective of sample, Bacteroidetes and Firmicutes were the most predominant bacterial phyla, followed by Proteobacteria, Fibrobacteres and Actinobacteria while, Prevotella, Bacteroides, Ruminococcus and Clostridium were the most abundant genera. Different proportions of taxa were observed in both MG and MT approaches indicating the differences in organisms present and organisms active in the rumen. Higher proportions of fungal taxa were observed in MT while important organisms like Fibrobacter and Butyrivibrio and abundant organisms like Bacteroides and Prevotella were underrepresented in MT data. Functionally, higher proportions of genes involved in Carbohydrate metabolism, Amino acid metabolism and Translation were observed in both data. Genes involved in Metabolism were observed to be underrepresented in MT data while, those involved in Genetic information processing were overrepresented in MT data. Further, genes involved in Carbohydrate metabolism were overexpressed compared to genes involved in Amino acid metabolism in MT data compared to MG data which had higher proportion of genes involved in Amino acid metabolism than Carbohydrate metabolism. In all significant differences were observed between both approaches, different fractions of rumen liquor (liquid and solid) and different proportions of roughage in diet.
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Affiliation(s)
- Ankit T Hinsu
- Department of Animal Genetics & Breeding, College of Veterinary Sciences & A.H, Anand Agricultural University, Anand, Gujarat, India
| | - Avani B Patel
- Department of Animal Genetics & Breeding, College of Veterinary Sciences & A.H, Anand Agricultural University, Anand, Gujarat, India
| | - Ramesh J Pandit
- Department of Animal Biotechnology, College of Veterinary Sciences & A.H, Anand Agricultural University, Anand, Gujarat, India
| | - Jalpa R Thakkar
- Department of Animal Biotechnology, College of Veterinary Sciences & A.H, Anand Agricultural University, Anand, Gujarat, India
| | - Ravi K Shah
- Department of Animal Biotechnology, College of Veterinary Sciences & A.H, Anand Agricultural University, Anand, Gujarat, India
| | - Subhash J Jakhesara
- Department of Animal Biotechnology, College of Veterinary Sciences & A.H, Anand Agricultural University, Anand, Gujarat, India
| | - Prakash G Koringa
- Department of Animal Biotechnology, College of Veterinary Sciences & A.H, Anand Agricultural University, Anand, Gujarat, India
| | - Chaitanya G Joshi
- Department of Animal Biotechnology, College of Veterinary Sciences & A.H, Anand Agricultural University, Anand, Gujarat, India.
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24
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Ribeiro GO, Gruninger RJ, Jones DR, Beauchemin KA, Yang WZ, Wang Y, Abbott DW, Tsang A, McAllister TA. Effect of ammonia fiber expansion-treated wheat straw and a recombinant fibrolytic enzyme on rumen microbiota and fermentation parameters, total tract digestibility, and performance of lambs. J Anim Sci 2020; 98:skaa116. [PMID: 32369600 PMCID: PMC7199887 DOI: 10.1093/jas/skaa116] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 04/28/2020] [Indexed: 12/30/2022] Open
Abstract
The objective of this study was to evaluate the effect of ammonia fiber expansion (AFEX)-treated wheat straw pellets and a recombinant fibrolytic enzyme on the rumen microbiome, rumen fermentation parameters, total tract diet digestibility, and performance of lambs. Eight rumen cannulated wethers and 60 lambs (n = 15 per diet, 8 rams and 7 ewes) were used in a replicated 4 × 4 Latin square design digestibility study and a complete randomized growth performance study, respectively. Four treatment diets were arranged in a 2 × 2 factorial structure with AFEX wheat straw (0% or 30% AFEX straw pellets on a dietary DM basis replacing alfalfa hay pellets) and fibrolytic enzyme (with or without XYL10C, a β-1,4-xylanase, from Aspergillus niger) as main factors. Enzyme was applied at 100 mg/kg of diet DM, 22 h before feeding. Rumen bacteria diversity Pielou evenness decreased (P = 0.05) with AFEX compared with the control diet and increased (P < 0.01) with enzyme. Enzyme increased (P ≤ 0.02) the relative abundancies of Prevotellaceae UCG-004, Christensenellaceae R-7 group, Saccharofermentans, and uncultured Kiritimatiellaeota. Total protozoa counts were greater (P ≤ 0.04) in the rumen of lambs fed AFEX compared with control, with enzyme reducing (P ≤ 0.05) protozoa counts for both diets. Digestibility of DM did not differ (P > 0.10) among diets, but digestibility of CP was reduced (P = 0.001), and digestibility of NDF and ADF increased (P < 0.05) as AFEX replaced alfalfa. Compared with control, AFEX promoted greater DMI (P = 0.003) and improved ADG up to 42 d on feed (P = 0.03), but not (P = 0.51) over the full ~94-d experiment. Consequently, overall G:F was reduced (P = 0.04) for AFEX when compared with control (0.188 vs. 0.199), but days on feed were lower (P = 0.04) for AFEX (97 vs. 91 d). Enzyme improved DMI of AFEX up to day 70 (P = 0.01), but did not affect DMI of the control diet. Enzyme addition improved ADG of lambs fed both diets in the first 28 d (P = 0.02), but not over the entire feeding period (P ≥ 10). As a result, G:F was improved with enzyme for the first 28 d (P = 0.04), but not overall (P = 0.45). This study shows that AFEX-treated wheat straw can replace alfalfa hay with no loss in lamb growth performance. Additionally, the enzyme XYL10C altered the rumen microbiome and improved G:F in the first month of the feeding.
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Affiliation(s)
- Gabriel O Ribeiro
- Department of Animal and Poultry Science, University of Saskatchewan College of Agriculture Bioresources, University of Saskatchewan, Saskatoon, Canada
| | - Robert J Gruninger
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, Canada
| | - Darryl R Jones
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, Canada
| | - Karen A Beauchemin
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, Canada
| | - Wen Zhu Yang
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, Canada
| | - Yuxi Wang
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, Canada
| | - D Wade Abbott
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, Canada
| | - Adrian Tsang
- Centre for Structural and Functional Genomics, Concordia University, Montreal, Canada
| | - Tim A McAllister
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, Canada
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25
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Rabee AE, Forster RJ, Elekwachi CO, Kewan KZ, Sabra E, Mahrous HA, Khamiss OA, Shawket SM. Composition of bacterial and archaeal communities in the rumen of dromedary camel using cDNA-amplicon sequencing. Int Microbiol 2019; 23:137-148. [PMID: 31432356 DOI: 10.1007/s10123-019-00093-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 06/30/2019] [Accepted: 07/21/2019] [Indexed: 11/25/2022]
Abstract
The camel is known to survive in harsh environmental conditions, due to its higher digestive efficiency of high-fiber diets compared with other ruminants. However, limited data are available on the microbial community in the rumen of a camel. In this study, the Illumina sequencing of V4 region of 16S rRNA genes based on RNA isolation was employed to get insight into the bacterial and archaeal communities associated with liquid and solid rumen fractions in eight camels under different feeding systems. Camels in group C1 were fed Egyptian clover hay plus concentrates mixture and camels of group C2 were fed fresh Egyptian clover. The results showed that liquid fraction has higher operational taxonomic units (OTUs) than solid fraction, and camel group C1 showed a higher microbial diversity than C2. The UniFrac analysis indicated that the microbial communities in camel groups are distinct. Moreover, phylum Firmicutes and Bacteroidetes dominated the bacterial community and Candidatus Methanomethylophilus dominated the archaeal community with a significant difference in the relative abundance between camel groups. Dominant bacterial genera were Prevotella, Fibrobacteres, Ruminococcus, and Butyrivibrio. There were many negative and positive correlations between and within bacterial and archaeal genera. The composition of microbial community in the rumen of a camel is similar to other ruminants with differences in the abundance.
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Affiliation(s)
- Alaa E Rabee
- Animal and Poultry Nutrition Department, Desert Research Center, Cairo, Egypt.
| | | | | | - Khaled Z Kewan
- Animal and Poultry Nutrition Department, Desert Research Center, Cairo, Egypt
| | - Ebrahim Sabra
- Genetic Engineering and Biotechnology Research Institute, Sadat City University, Sadat City, Egypt
| | - Hoda A Mahrous
- Genetic Engineering and Biotechnology Research Institute, Sadat City University, Sadat City, Egypt
| | - Omaima A Khamiss
- Genetic Engineering and Biotechnology Research Institute, Sadat City University, Sadat City, Egypt
| | - Safinaze M Shawket
- Animal and Poultry Nutrition Department, Desert Research Center, Cairo, Egypt
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26
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Carreño D, Toral PG, Pinloche E, Belenguer A, Yáñez-Ruiz DR, Hervás G, McEwan NR, Newbold CJ, Frutos P. Rumen bacterial community responses to DPA, EPA and DHA in cattle and sheep: A comparative in vitro study. Sci Rep 2019; 9:11857. [PMID: 31413283 PMCID: PMC6694141 DOI: 10.1038/s41598-019-48294-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 08/02/2019] [Indexed: 11/16/2022] Open
Abstract
The role of marine lipids as modulators of ruminal biohydrogenation of dietary unsaturated fatty acids may be explained by the effects of their n-3 polyunsaturated fatty acids (PUFA) on the bacterial community. However, the impact of individual PUFA has barely been examined, and it is uncertain which bacteria are truly involved in biohydrogenation. In addition, despite interspecies differences in rumen bacterial composition, we are not aware of any direct comparison of bovine and ovine responses to dietary PUFA. Therefore, rumen fluid from cannulated cattle and sheep were used as inocula to examine in vitro the effect of 20:5n-3 (EPA), 22:5n-3 (DPA), and 22:6n-3 (DHA) on the bacterial community. Amplicon 16 S rRNA sequencing suggested that EPA and DHA had a greater contribution to the action of marine lipids than DPA both in cattle and sheep. Certain effects were exclusive to each ruminant species, which underlines the complexity of rumen microbial responses to dietary fatty acids. Based on changes in bacterial abundance, Barnesiella, Prevotella, Paraprevotella, Hallela, Anaerovorax, Succiniclasticum, Ruminococcus and Ruminobacter may be involved in the ruminal response in biohydrogenation to the addition of marine lipids, but further research is necessary to confirm their actual role in ruminal lipid metabolism.
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Affiliation(s)
- D Carreño
- Instituto de Ganadería de Montaña (CSIC-Universidad de León), Finca Marzanas s/n, 24346 Grulleros, León, Spain.,Institute of Biological, Environmental and Rural Sciences (IBERS), Animal and Microbial Sciences, Aberystwyth University, Aberystwyth, Ceredigion, SY23 3EB, United Kingdom
| | - P G Toral
- Instituto de Ganadería de Montaña (CSIC-Universidad de León), Finca Marzanas s/n, 24346 Grulleros, León, Spain.
| | - E Pinloche
- Institute of Biological, Environmental and Rural Sciences (IBERS), Animal and Microbial Sciences, Aberystwyth University, Aberystwyth, Ceredigion, SY23 3EB, United Kingdom
| | - A Belenguer
- Instituto de Ganadería de Montaña (CSIC-Universidad de León), Finca Marzanas s/n, 24346 Grulleros, León, Spain
| | - D R Yáñez-Ruiz
- Estación Experimental del Zaidín (CSIC), Profesor Albareda 1, 18008, Granada, Spain
| | - G Hervás
- Instituto de Ganadería de Montaña (CSIC-Universidad de León), Finca Marzanas s/n, 24346 Grulleros, León, Spain
| | - N R McEwan
- Institute of Biological, Environmental and Rural Sciences (IBERS), Animal and Microbial Sciences, Aberystwyth University, Aberystwyth, Ceredigion, SY23 3EB, United Kingdom.,School of Pharmacy and Life Sciences, Robert Gordon University, Aberdeen, AB10 7GJ, United Kingdom
| | - C J Newbold
- Institute of Biological, Environmental and Rural Sciences (IBERS), Animal and Microbial Sciences, Aberystwyth University, Aberystwyth, Ceredigion, SY23 3EB, United Kingdom.,Scotland's Rural College (SRUC), Kings Buildings, Edinburgh, EH9 3JG, United Kingdom
| | - P Frutos
- Instituto de Ganadería de Montaña (CSIC-Universidad de León), Finca Marzanas s/n, 24346 Grulleros, León, Spain
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27
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Reddy B, Pandey J, Dubey SK. Assessment of environmental gene tags linked with carbohydrate metabolism and chemolithotrophy associated microbial community in River Ganga. Gene 2019; 704:31-41. [DOI: 10.1016/j.gene.2019.04.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Revised: 03/19/2019] [Accepted: 04/01/2019] [Indexed: 10/27/2022]
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28
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Vasta V, Daghio M, Cappucci A, Buccioni A, Serra A, Viti C, Mele M. Invited review: Plant polyphenols and rumen microbiota responsible for fatty acid biohydrogenation, fiber digestion, and methane emission: Experimental evidence and methodological approaches. J Dairy Sci 2019; 102:3781-3804. [PMID: 30904293 DOI: 10.3168/jds.2018-14985] [Citation(s) in RCA: 168] [Impact Index Per Article: 33.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 01/13/2019] [Indexed: 12/29/2022]
Abstract
The interest of the scientific community in the effects of plant polyphenols on animal nutrition is increasing. These compounds, in fact, are ubiquitous in the plant kingdom, especially in some spontaneous plants exploited as feeding resources alternative to cultivated crops and in several agro-industry by-products. Polyphenols interact with rumen microbiota, affecting carbohydrate fermentation, protein degradation, and lipid metabolism. Some of these aspects have been largely reviewed, especially for tannins; however, less information is available about the direct effect of polyphenols on the composition of rumen microbiota. In the present paper, we review the most recent literature about the effect of plant polyphenols on rumen microbiota responsible for unsaturated fatty acid biohydrogenation, fiber digestion, and methane production, taking into consideration the advances in microbiota analysis achieved in the last 10 yr. Key aspects, such as sample collection, sample storage, DNA extraction, and the main phylogenetic markers used in the reconstruction of microbial community structure, are examined. Furthermore, a summary of the new high-throughput methods based on next generation sequencing is reviewed. Several effects can be associated with dietary polyphenols. Polyphenols are able to depress or modulate the biohydrogenation of unsaturated fatty acids by a perturbation of ruminal microbiota composition. In particular, condensed tannins have an inhibitory effect on biohydrogenation, whereas hydrolyzable tannins seem to have a modulatory effect on biohydrogenation. With regard to fiber digestion, data from literature are quite consistent about a general depressive effect of polyphenols on gram-positive fibrolytic bacteria and ciliate protozoa, resulting in a reduction of volatile fatty acid production (mostly acetate molar production). Methane production is also usually reduced when tannins are included in the diet of ruminants, probably as a consequence of the inhibition of fiber digestion. However, some evidence suggests that hydrolyzable tannins may reduce methane emission by directly interacting with rumen microbiota without affecting fiber digestion.
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Affiliation(s)
- V Vasta
- Food Scientist, viale delle Alpi 40, 90144, Palermo, Italy
| | - M Daghio
- Dipartimento di Scienze delle Produzioni Agro-Alimentari e dell'Ambiente, University of Florence, Piazzale delle Cascine 18, 50144 Firenze, Italy
| | - A Cappucci
- Dipartimento di Scienze Agrarie, Alimentari e Agro-ambientali, University of Pisa, Via del Borghetto 80, 56124 Pisa, Italy
| | - A Buccioni
- Dipartimento di Scienze delle Produzioni Agro-Alimentari e dell'Ambiente, University of Florence, Piazzale delle Cascine 18, 50144 Firenze, Italy
| | - A Serra
- Dipartimento di Scienze Agrarie, Alimentari e Agro-ambientali, University of Pisa, Via del Borghetto 80, 56124 Pisa, Italy
| | - C Viti
- Dipartimento di Scienze delle Produzioni Agro-Alimentari e dell'Ambiente, University of Florence, Piazzale delle Cascine 18, 50144 Firenze, Italy
| | - M Mele
- Dipartimento di Scienze Agrarie, Alimentari e Agro-ambientali, University of Pisa, Via del Borghetto 80, 56124 Pisa, Italy; Centro di Ricerche Agro-ambientali "E. Avanzi," University of Pisa, Via Vecchia di Masrina, 6, 56100 Pisa, Italy.
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29
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Al-Masaudi S, El Kaoutari A, Drula E, Redwan EM, Lombard V, Henrissat B. A metagenomics investigation of carbohydrate-active enzymes along the goat and camel intestinal tract. Int Microbiol 2019; 22:429-435. [PMID: 30875036 DOI: 10.1007/s10123-019-00068-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 02/25/2019] [Accepted: 02/26/2019] [Indexed: 12/14/2022]
Abstract
Studies of the digestive microbiota of ruminant animals most often focus on the bacterial diversity in the rumen or the feces of the animals, but little is known about the diversity and functions of their distal intestine. Here, the bacterial microbiota of the distal intestinal tract of two goats and two camels was investigated by metagenomics techniques. The bacterial taxonomic diversity and carbohydrate-active enzyme profile were estimated for samples taken from the small intestine, the large intestine, and the rectum of each animal. The bacterial diversity and abundance in the small intestine were lower than in the rectal and large intestinal samples. Analysis of the carbohydrate-active enzyme profiles at each site revealed a comparatively low abundance of enzymes targeting xylan and cellulose in all animals examined, similar to what has been reported earlier for sheep and therefore suggesting that plant cell wall digestion probably takes place elsewhere, such as in the rumen.
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Affiliation(s)
- Saad Al-Masaudi
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Abdessamad El Kaoutari
- Marseille Cancer Research Center, Institut Paoli-Calmettes, INSERM, CNRS, Aix-Marseille University, Marseille, France
| | - Elodie Drula
- CNRS UMR 7257, Aix-Marseille University, 13288, Marseille, France
- INRA, USC 1408 AFMB, 13288, Marseille, France
| | - Elrashdy M Redwan
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Vincent Lombard
- CNRS UMR 7257, Aix-Marseille University, 13288, Marseille, France
- INRA, USC 1408 AFMB, 13288, Marseille, France
| | - Bernard Henrissat
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.
- CNRS UMR 7257, Aix-Marseille University, 13288, Marseille, France.
- INRA, USC 1408 AFMB, 13288, Marseille, France.
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30
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Zhang J, Shi H, Wang Y, Cao Z, Yang H, Li S. Effect of Limit-Fed Diets With Different Forage to Concentrate Ratios on Fecal Bacterial and Archaeal Community Composition in Holstein Heifers. Front Microbiol 2018; 9:976. [PMID: 29867879 PMCID: PMC5962747 DOI: 10.3389/fmicb.2018.00976] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 04/25/2018] [Indexed: 11/25/2022] Open
Abstract
Limit-feeding of a high concentrate diet has been proposed as an effective method for improving feed efficiency and reducing total manure output of dairy heifers; meanwhile the effects of this method on hindgut microbiota are still unclear. This study investigated the effects of a wide range of dietary forage:concentrate ratios (F:C) on the fecal composition of bacteria and archaea in heifers using next-generation sequencing. Four diets with different F:C (80:20, 60:40, 40:60, and 20:80) were limit-fed to 24 Holstein heifers, and the fecal fermentation parameters and bacterial and archaeal communities were investigated. With increasing dietary concentrate levels, the fecal dry matter output, neutral detergent fiber (NDF) content, and proportion of acetate decreased linearly (P < 0.01), while the fecal starch content and proportions of propionate, butyrate, and total branched-chain volatile fatty acids (TBCVFAs) were increased (P ≤ 0.05). An increased concentrate level linearly increased (P = 0.02) the relative abundance of Proteobacteria, and linearly decreased (P = 0.02) the relative abundance of Bacteroidetes in feces. At the genus level, the relative abundance of unclassified Ruminococcaceae and Paludibacter which may have the potential to degrade forage decreased linearly (q ≤ 0.02) with increasing dietary concentrate levels, while the relative abundance of Roseburia and Succinivibrio which may be non-fibrous carbohydrate degrading bacteria increased linearly (q ≤ 0.05). Some core microbiota operational taxonomic units (OTUs) also showed significant association with fecal VFAs, NDF, and/or acid detergent fiber (ADF) content. Meanwhile, the relative abundance of most detected taxa in archaea were similar across different F:C, and only Methanosphaera showed a linear decrease (P = 0.01) in high concentrate diets. Our study provides a better understanding of fecal fermentation parameters and microbiota under a wide range of dietary F:C. These findings support the potential for microbial manipulation by diet, which could enhance feed digestibility and relieve environmental problems associated with heifer rearing.
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Affiliation(s)
- Jun Zhang
- 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
| | - Haitao Shi
- 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.,Department of Animal and Poultry Science, University of Saskatchewan, Saskatoon, SK, Canada
| | - Yajing Wang
- 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
| | - Zhijun Cao
- 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
| | - Hongjian Yang
- 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
| | - 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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Pandit RJ, Hinsu AT, Patel SH, Jakhesara SJ, Koringa PG, Bruno F, Psifidi A, Shah SV, Joshi CG. Microbiota composition, gene pool and its expression in Gir cattle (Bos indicus) rumen under different forage diets using metagenomic and metatranscriptomic approaches. Syst Appl Microbiol 2018; 41:374-385. [PMID: 29555111 DOI: 10.1016/j.syapm.2018.02.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Revised: 02/01/2018] [Accepted: 02/01/2018] [Indexed: 01/17/2023]
Abstract
Zebu (Bos indicus) is a domestic cattle species originating from the Indian subcontinent and now widely domesticated on several continents. In this study, we were particularly interested in understanding the functionally active rumen microbiota of an important Zebu breed, the Gir, under different dietary regimes. Metagenomic and metatranscriptomic data were compared at various taxonomic levels to elucidate the differential microbial population and its functional dynamics in Gir cattle rumen under different roughage dietary regimes. Different proportions of roughage rather than the type of roughage (dry or green) modulated microbiome composition and the expression of its gene pool. Fibre degrading bacteria (i.e. Clostridium, Ruminococcus, Eubacterium, Butyrivibrio, Bacillus and Roseburia) were higher in the solid fraction of rumen (P<0.01) compared to the liquid fraction, whereas bacteria considered to be utilizers of the degraded product (i.e. Prevotella, Bacteroides, Parabacteroides, Paludibacter and Victivallis) were dominant in the liquid fraction (P<0.05). Likewise, expression of fibre degrading enzymes and related carbohydrate binding modules (CBMs) occurred in the solid fraction. When metagenomic and metatranscriptomic data were compared, it was found that some genera and species were transcriptionally more active, although they were in low abundance, making an important contribution to fibre degradation and its further metabolism in the rumen. This study also identified some of the transcriptionally active genera, such as Caldicellulosiruptor and Paludibacter, whose potential has been less-explored in rumen. Overall, the comparison of metagenomic shotgun and metatranscriptomic sequencing appeared to be a much richer source of information compared to conventional metagenomic analysis.
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Affiliation(s)
- Ramesh J Pandit
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand 388 001, Gujarat, India
| | - Ankit T Hinsu
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand 388 001, Gujarat, India
| | - Shriram H Patel
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand 388 001, Gujarat, India
| | - Subhash J Jakhesara
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand 388 001, Gujarat, India
| | - Prakash G Koringa
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand 388 001, Gujarat, India
| | - Fosso Bruno
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), National Research Council, Via Amendola 165/A, 70126 Bari, Italy
| | - Androniki Psifidi
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, UK; Department of Clinical Science and Services, Royal Veterinary College, North Mymms, Hertfordshire, UK
| | - S V Shah
- Livestock Research Station, College of Veterinary Science & Animal Husbandry, Anand Agricultural University, Anand 388 001, Gujarat, India
| | - Chaitanya G Joshi
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand 388 001, Gujarat, India.
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Li Y, Sun Y, Yang G, Hu K, Lv P, Li L. Vertical distribution of microbial community and metabolic pathway in a methanogenic propionate degradation bioreactor. BIORESOURCE TECHNOLOGY 2017; 245:1022-1029. [PMID: 28946204 DOI: 10.1016/j.biortech.2017.09.028] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 08/30/2017] [Accepted: 09/04/2017] [Indexed: 06/07/2023]
Abstract
The methanogenic propionate degradation consortia were enriched in a propionate-fed semi-continuous bioreactor. The microbial community shift with depth, the microbial network and its correlation with metabolic pathway were also investigated. The results demonstrated that the maximum organic loading rate (OLR) of the reactor was 2.5g propionic acid (HPr) L-1d-1 with approximately 1.20LL-1d-1 of volumetric methane production (VMP). The organisms in the enrichment were spanning 36 bacterial phyla and 7 archaeal orders. Syntrophobacter, the main Hpr oxidizer in the digester, dominated bacteria with relative abundance changing from 63% to 37% with depth. The predominant methanogens shift from hydrogenotrophic Methanoculleus (∼60%) at the upper liquid layer to acetoclastic Methanothrix (∼51%) at the lower sediment layer in the bioreactor. These methanogens syntrophically support Syntrophobacter by degrading HPr catabolism by-products (H2 and acetate). Other bacteria could scavenge anabolic products (carbohydrate and protein) presumably derived from detrital biomass produced by the HPr-degrading community.
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Affiliation(s)
- Ying Li
- Laboratory of Biomass Bio-chemical Conversion, GuangZhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou 510640, PR China; Key Laboratory of Renewable Energy, Chinese Academy of Sciences, Guangzhou 510640, PR China
| | - Yongming Sun
- Laboratory of Biomass Bio-chemical Conversion, GuangZhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou 510640, PR China
| | - Gaixiu Yang
- Laboratory of Biomass Bio-chemical Conversion, GuangZhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou 510640, PR China
| | - Keqin Hu
- Wuhan Kaidi Electric Power Engineering Co. Ltd, Wuhan 430073, PR China
| | - Pengmei Lv
- Laboratory of Biomass Bio-chemical Conversion, GuangZhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou 510640, PR China
| | - Lianhua Li
- Laboratory of Biomass Bio-chemical Conversion, GuangZhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou 510640, PR China; Guangdong Provincial Key Laboratory of New and Renewable Energy Research and Development, Guangzhou 510640, PR China.
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33
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Palma M, Hernández-Castellano LE, Castro N, Arguëllo A, Capote J, Matzapetakis M, de Almeida AM. NMR-metabolomics profiling of mammary gland secretory tissue and milk serum in two goat breeds with different levels of tolerance to seasonal weight loss. MOLECULAR BIOSYSTEMS 2017; 12:2094-107. [PMID: 27001028 DOI: 10.1039/c5mb00851d] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Goats are of special importance in the Mediterranean and tropical regions for producing a variety of dairy products. The scarcity of pastures during the dry season leads to seasonal weight loss (SWL), which affects milk production. In this work, we studied the effect of feed-restriction on two dairy goat breeds, with different tolerance levels to SWL: the Majorera breed (tolerant) and the Palmera breed (susceptible). Nuclear magnetic resonance (NMR) was used to compare the metabolome of an aqueous fraction of the mammary gland and milk serum from both breeds. Goats in mid-lactation were divided by breed, and each in two feed-regime groups: the control group and the restricted-fed group (to achieve 15-20% reduction of body weight at the end of the experiment). Milk and mammary gland samples were collected at the end of the experimental period (23rd day). (1)H NMR spectra were collected from the aqueous extract of the mammary gland biopsies and the milk serum. Profiling analysis has led to the identification of 46 metabolites in the aqueous extract of the mammary gland. Lactose, glutamate, glycine and lactate were found to be the most abundant. Analysis of milk serum allowed the identification of 50 metabolites, the most abundant being lactose, citrate and creatine. Significant differences were observed, in mammary gland biopsies and milk serum, between control and restricted-fed groups in both breeds, albeit with no differences between the breeds. Variations seem to be related to metabolism adaptation to the low-energy diet and are indicative of breed-specific microflora. Milk serum showed more metabolites varying between control and restricted groups, than the mammary gland. The Majorera breed also showed more variations than the Palmera breed in milk samples, which could be an indication of a prompt adaptation to SWL by the Majorera breed.
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Affiliation(s)
- Mariana Palma
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.
| | | | - Noemí Castro
- Department of Animal Science, Universidad de Las Palmas de Gran Canaria, Arucas, Gran Canaria, Spain
| | - Anastasio Arguëllo
- Department of Animal Science, Universidad de Las Palmas de Gran Canaria, Arucas, Gran Canaria, Spain
| | - Juan Capote
- ICIA - Instituto Canario de Investigaciones Agrarias, Valle Guerra, Tenerife, Spain
| | - Manolis Matzapetakis
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.
| | - André Martinho de Almeida
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal. and Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal and Centro Interdisciplinar de Investigação em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, Lisboa, Portugal
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34
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Suriya J, Chandra Shekar M, Nathani NM, Suganya T, Bharathiraja S, Krishnan M. Assessment of bacterial community composition in response to uranium levels in sediment samples of sacred Cauvery River. Appl Microbiol Biotechnol 2016; 101:831-841. [PMID: 27812801 DOI: 10.1007/s00253-016-7945-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Revised: 10/09/2016] [Accepted: 10/13/2016] [Indexed: 01/20/2023]
Abstract
Global industrialization is a major cause of effluent discharge from industries up to alarming concentrations. Especially, uranium concentrations in water bodies are of great concern, as its radioactivity significantly affects the persistent diversity of microbiota. Recently, continuous application of pesticides in the agricultural lands and accumulation of quartz that enter the Cauvery River has significantly increased the concentration of uranium (U) and other heavy metals. To perceive the impact of uranium on bacterial diversity in Cauvery River, sediment samples collected from polluted (UP) site with 32.4 Bq/K of U concentration and control (UNP) site were scrutinized for bacterial diversity through metagenomic analysis of the V3 region of 16S rDNA by Illumina sequencing. Taxonomic assignment revealed that the unpolluted sample was dominated by Bacteroidetes (27.7 %), and Firmicutes (25.9 %), while sediment sample from the highly polluted site revealed abundance of Proteobacteria (47.5 %) followed by Bacteroidetes (22.4 %) and Firmicutes (14.6 %). Among Proteobacteria, Gammaproteobacteria was the most prevalent group followed by alpha, delta, epsilon, and beta in the uranium-polluted sample. Rare and abundant species analysis revealed that species like Idiomarina loihiensis was abundant in the pollutant sample; however, it was rare (<0.1 %) in the sample from pristine environment. Similarly, the species distribution in both the samples varied, with the bacteria potentially active in redox activity and biosorption potential dominating in the polluted sample. Outcomes of the present study demonstrated the impact of uranium and metal accumulation on the bacterial communities and further confirmed the promising candidature of specific bacterial species as bioindicators of contamination.
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Affiliation(s)
- Jayaraman Suriya
- Department of Environmental Biotechnology, School of Environmental Sciences, Bharathidasan University, Tiruchirappalli, Tamil Nadu, 620024, India.
| | - Mootapally Chandra Shekar
- CAS in Marine Biology, Annamalai University, Porto Novo, Tamil Nadu, 608502, India.,Department of Marine Science, Maharaja Krishnakumarsinhji Bhavnagar University, Bhavnagar, Gujarat, 364002, India
| | - Neelam Mustakali Nathani
- Department of Biosciences, Saurashtra University, Rajkot, Gujarat, 360005, India.,Department of Life Sciences, Maharaja Krishnakumarsinhji Bhavnagar University, Bhavnagar, Gujarat, 364002, India
| | - Thangaiyan Suganya
- Department of Environmental Biotechnology, School of Environmental Sciences, Bharathidasan University, Tiruchirappalli, Tamil Nadu, 620024, India
| | | | - Muthukalingan Krishnan
- Department of Environmental Biotechnology, School of Environmental Sciences, Bharathidasan University, Tiruchirappalli, Tamil Nadu, 620024, India.
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