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Xie F, Zhao S, Zhan X, Zhou Y, Li Y, Zhu W, Pope PB, Attwood GT, Jin W, Mao S. Unraveling the phylogenomic diversity of Methanomassiliicoccales and implications for mitigating ruminant methane emissions. Genome Biol 2024; 25:32. [PMID: 38263062 PMCID: PMC10804542 DOI: 10.1186/s13059-024-03167-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 01/07/2024] [Indexed: 01/25/2024] Open
Abstract
BACKGROUND Methanomassiliicoccales are a recently identified order of methanogens that are diverse across global environments particularly the gastrointestinal tracts of animals; however, their metabolic capacities are defined via a limited number of cultured strains. RESULTS Here, we profile and analyze 243 Methanomassiliicoccales genomes assembled from cultured representatives and uncultured metagenomes recovered from various biomes, including the gastrointestinal tracts of different animal species. Our analyses reveal the presence of numerous undefined genera and genetic variability in metabolic capabilities within Methanomassiliicoccales lineages, which is essential for adaptation to their ecological niches. In particular, gastrointestinal tract Methanomassiliicoccales demonstrate the presence of co-diversified members with their hosts over evolutionary timescales and likely originated in the natural environment. We highlight the presence of diverse clades of vitamin transporter BtuC proteins that distinguish Methanomassiliicoccales from other archaeal orders and likely provide a competitive advantage in efficiently handling B12. Furthermore, genome-centric metatranscriptomic analysis of ruminants with varying methane yields reveal elevated expression of select Methanomassiliicoccales genera in low methane animals and suggest that B12 exchanges could enable them to occupy ecological niches that possibly alter the direction of H2 utilization. CONCLUSIONS We provide a comprehensive and updated account of divergent Methanomassiliicoccales lineages, drawing from numerous uncultured genomes obtained from various habitats. We also highlight their unique metabolic capabilities involving B12, which could serve as promising targets for mitigating ruminant methane emissions by altering H2 flow.
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Affiliation(s)
- Fei Xie
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Shengwei Zhao
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Xiaoxiu Zhan
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Yang Zhou
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Yin Li
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Weiyun Zhu
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Phillip B Pope
- Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Graeme T Attwood
- AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - Wei Jin
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China.
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China.
| | - Shengyong Mao
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China.
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China.
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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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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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Effects of Dietary Nonfibrous Carbohydrate/Neutral Detergent Fiber Ratio on Methanogenic Archaea and Cellulose-Degrading Bacteria in the Rumen of Karakul Sheep: a 16S rRNA Gene Sequencing Study. Appl Environ Microbiol 2023; 89:e0129122. [PMID: 36541769 PMCID: PMC9888294 DOI: 10.1128/aem.01291-22] [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] [Indexed: 12/24/2022] Open
Abstract
The study was conducted to investigate the effects of dietary nonfibrous carbohydrate (NFC)/neutral detergent fiber (NDF) ratio on methanogenic archaea and cellulose-degrading bacteria in Karakul sheep by 16S rRNA gene sequencing. Twelve Karakul sheep were randomly divided into four groups, each group with three replicates, and they were fed with four dietary NFC/NDF ratios at 0.54, 0.96, 1.37, and 1.90 as groups 1, 2, 3, and 4, respectively. The experiment lasted for four periods: I (1 to 18 days), II (19 to 36 days), III (37 to 54 days), and IV (55 to 72 days); during each period, rumen contents were collected before morning feeding to investigate on methanogenic archaea and cellulose-degrading bacteria. The results showed that with an increase in dietary NFC/NDF ratio, the number of rumen archaea operational taxonomic units and the diversity of archaea decrease. The most dominant methanogens did not change with dietary NFC/NDF ratio and prolongation of experimental periods. Methanobrevibacter was the most dominant genus. At the species level, the relative abundance of Methanobrevibacter ruminantium first increased and then decreased when the NFC/NDF ratio increased. When the dietary NFC/NDF ratio was 0.96, the structure of archaea was largely changed, and the relative abundance of Fibrobacter sp. strain UWCM, Ruminococcus flavefaciens, and Ruminococcus albus were the highest. When the dietary NFC/NDF ratio was 1.37, the relative abundance of Butyrivibrio fibrisolvens was higher than for other groups. Based on all the data, we concluded that a dietary NFC/NDF ratio of ca. 0.96 to 1.37 was a suitable ratio to support optimal sheep production. IMPORTANCE CH4 produced by ruminants aggravates the greenhouse effect and cause wastage of feed energy, and CH4 emissions are related to methanogens. According to the current literature, there is a symbiotic relationship between methanogens and cellulolytic bacteria, so reducing methane will inevitably affect the degradation of fiber materials. This experiment used 16S rRNA gene high-throughput sequencing technology to explore the balance relationship between methanogens and cellulolytic bacteria for the first time through a long-term feeding period. The findings provide fundamental data, supporting for the diet structures with potential to reduce CH4 emission.
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Malik PK, Trivedi S, Mohapatra A, Kolte AP, Sejian V, Bhatta R, Rahman H. Comparison of enteric methane yield and diversity of ruminal methanogens in cattle and buffaloes fed on the same diet. PLoS One 2021; 16:e0256048. [PMID: 34379691 PMCID: PMC8357158 DOI: 10.1371/journal.pone.0256048] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 07/28/2021] [Indexed: 11/19/2022] Open
Abstract
An in vivo study was conducted to compare the enteric methane emissions and diversity of ruminal methanogens in cattle and buffaloes kept in the same environment and fed on the same diet. Six cattle and six buffaloes were fed on a similar diet comprising Napier (Pennisetum purpureum) green grass and concentrate in 70:30. After 90 days of feeding, the daily enteric methane emissions were quantified by using the SF6 technique and ruminal fluid samples from animals were collected for the diversity analysis. The daily enteric methane emissions were significantly greater in cattle as compared to buffaloes; however, methane yields were not different between the two species. Methanogens were ranked at different taxonomic levels against the Rumen and Intestinal Methanogen-Database. The archaeal communities in both host species were dominated by the phylum Euryarchaeota; however, Crenarchaeota represented <1% of the total archaea. Methanogens affiliated with Methanobacteriales were most prominent and their proportion did not differ between the two hosts. Methanomicrobiales and Methanomassillicoccales constituted the second largest group of methanogens in cattle and buffaloes, respectively. Methanocellales (Methanocella arvoryza) were exclusively detected in the buffaloes. At the species level, Methanobrevibacter gottschalkii had the highest abundance (55-57%) in both the host species. The relative abundance of Methanobrevibacter wolinii between the two hosts differed significantly. Methanosarcinales, the acetoclastic methanogens were significantly greater in cattle than the buffaloes. It is concluded that the ruminal methane yield in cattle and buffaloes fed on the same diet did not differ. With the diet used in this study, there was a limited influence (<3.5%) of the host on the structure of the ruminal archaea community at the species level. Therefore, the methane mitigation strategies developed in either of the hosts should be effective in the other. Further studies are warranted to reveal the conjunctive effect of diet and geographical locations with the host on ruminal archaea community composition.
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Affiliation(s)
- P. K. Malik
- Bioenergetics and Environmental Science Division, ICAR-National Institute of Animal Nutrition and Physiology, Bangalore, Karnataka, India
| | - S. Trivedi
- Bioenergetics and Environmental Science Division, ICAR-National Institute of Animal Nutrition and Physiology, Bangalore, Karnataka, India
| | - A. Mohapatra
- Bioenergetics and Environmental Science Division, ICAR-National Institute of Animal Nutrition and Physiology, Bangalore, Karnataka, India
| | - A. P. Kolte
- Animal Nutrition Division, ICAR-National Institute of Animal Nutrition and Physiology, Bangalore, Karnataka, India
| | - V. Sejian
- Animal Physiology Division, ICAR-National Institute of Animal Nutrition and Physiology, Bangalore, Karnataka, India
| | - R. Bhatta
- Bioenergetics and Environmental Science Division, ICAR-National Institute of Animal Nutrition and Physiology, Bangalore, Karnataka, India
| | - H. Rahman
- International Livestock Research Institute, South Asia Regional Office, New Delhi, India
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Lu Z, Xu Z, Kong L, Shen H, Aschenbach JR. Functional Changes of the Community of Microbes With Ni-Dependent Enzyme Genes Accompany Adaptation of the Ruminal Microbiome to Urea-Supplemented Diets. Front Microbiol 2020; 11:596681. [PMID: 33414773 PMCID: PMC7782429 DOI: 10.3389/fmicb.2020.596681] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 11/27/2020] [Indexed: 11/25/2022] Open
Abstract
Urea is an inexpensive non-protein nitrogen source commonly supplemented to the diets of ruminants. It is cleaved to ammonia by bacterial ureases, which require Ni as a catalyst for ureolysis. The key event in the changes of the ruminal microbiome after urea supplementation remains unknown. We have therefore investigated changes in the ruminal microbiome and its community with Ni-dependent enzyme genes following urea supplementation and analyzed the associations of rumen environmental factors, including fermentation variables and Ni concentrations, with the compositional and functional changes of these communities. We found that urea supplementation increased urease activity and the concentrations of ammonia and Ni, and tended to increase concentrations of short chain fatty acids and acetate, whereas it decreased rumen pH and the L-/D-lactate ratio. With standards for genome completeness >60% and strain heterogeneity <10%, 20 bacterial species containing five Ni-dependent enzyme genes were detected in the metagenome sequences. For the five Ni-dependent enzyme genes, urea supplementation increased the relative abundances of genes of urease and acetyl-CoA synthase, whereas it decreased the relative abundances of genes of glyoxalase I, [NiFe]-hydrogenase, and lactate racemase. For the 20 microbes with Ni-dependent enzyme genes, urea supplementation increased the relative abundances of five bacteria exhibiting high capacities for the utilization of hemicellulose and pectin for butyrate and fatty acid biosynthesis. For the ruminal microbiome, urea supplementation increased the metagenomic capacities for hemicellulose and pectin degradation, butyrate generation, fatty acid biosynthesis, and carbon fixation, whereas it decreased the metagenomic capacities for starch degradation, propionate generation, and sulfur and nitrogen metabolism. Constrained correspondence analysis identified rumen ammonia and Ni concentrations as likely driving factors in the reshaping of the ruminal microbiome and, together with pH, of the community of microbes with Ni-dependent enzyme genes. Thus, the functional change of the latter community is probably an important event in the adaptation of the ruminal microbiome to urea-supplemented diets. This result provides a new perspective for the understanding of the effects of urea supplementation on rumen fermentation.
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Affiliation(s)
- Zhongyan Lu
- Key Laboratory of Animal Physiology and Biochemistry, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Zhihui Xu
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China.,Bioinformatics Center, Nanjing Agricultural University, Nanjing, China
| | - Lingmeng Kong
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Hong Shen
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China.,Bioinformatics Center, Nanjing Agricultural University, Nanjing, China
| | - Jörg R Aschenbach
- Institute of Veterinary Physiology, Freie Universität Berlin, Berlin, Germany
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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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Obata O, Ditchfield A, Hatton A, Akunna J. Investigating the impact of inoculum source on anaerobic digestion of various species of marine macroalgae. ALGAL RES 2020. [DOI: 10.1016/j.algal.2020.101803] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Comparative Analysis of the Gut Microbial Composition and Meat Flavor of Two Chicken Breeds in Different Rearing Patterns. BIOMED RESEARCH INTERNATIONAL 2018; 2018:4343196. [PMID: 30410932 PMCID: PMC6206517 DOI: 10.1155/2018/4343196] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 08/12/2018] [Accepted: 09/04/2018] [Indexed: 01/05/2023]
Abstract
The objective of the study is to compare the effects of free-range (FR) and cage-range (CR) breeding on gut microbiota and flavor compounds of Caoke (C) and Partridge Shank chickens (Q). A total of 120 experimental chickens were assigned to FR group and CR group; each group contain both 30 Caoke chickens and 30 Partridge Shank chickens. At 154 d old, 12 chickens of each group were selected and their cecal contents were extracted and examined for the composition of gut microbiota by illumina sequencing of the V3 region of the 16S rDNA genes, and flavor compounds were analyzed through headspace-solid-phase microextraction (HS-SPME) method. The results showed that, except for acids, the amount of flavor substances in the FR group was higher than those in the CR group, especially the content of Hexanal and D-limonene. Meanwhile, the higher concentrations of carbonyls including (E,E)-2,4-decadienal, (E)-2-decenal, (E)-2-octenal, and pentanal were in the FR chicken meat, but the differences in concentrations compared with CR were not significant. High levels of ethyl hexanoate and β-ocimene were only detected in FR groups. The Firmicutes had the highest proportion of chicken cecal microbiota, whereas the Fusobacteria was only detected in the cecal samples of Q chicken in FR group. Actinobacteria was more prevalent in FR groups than in CR groups. Meanwhile, in Q chickens, the proportions of Bacteroidetes and Proteobacteria in FR group were higher than those in CR group. Using MG-RAST Subsystem Technology, we found that some genes were associated with the formation of precursors of flavor compounds or with the metabolism and degradation of aromatic compounds. Overall, CR and FR breeding influenced the gut microbiota and flavor compounds, potentially because of the changes in diet and living conditions.
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Comparative diversity analysis of ruminal methanogens in Murrah buffaloes (Bubalus bubalis) in four states of North India. Anaerobe 2018; 52:59-63. [PMID: 29859302 DOI: 10.1016/j.anaerobe.2018.05.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Revised: 04/20/2018] [Accepted: 05/27/2018] [Indexed: 11/24/2022]
Abstract
We compared the community structure of methanogens in Murrah breed of buffaloes of four states of north India using 16S rRNA gene clone library method. The results revealed the dominance of methanogens related to Methanobrevibacter in three states, while Methanomicrobium-related methanogens were abundant in one state.
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Zhou M, Peng YJ, Chen Y, Klinger CM, Oba M, Liu JX, Guan LL. Assessment of microbiome changes after rumen transfaunation: implications on improving feed efficiency in beef cattle. MICROBIOME 2018; 6:62. [PMID: 29587855 PMCID: PMC5869788 DOI: 10.1186/s40168-018-0447-y] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 03/15/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Understanding the host impact on its symbiotic microbiota is important in redirecting the rumen microbiota and thus improving animal performance. The current study aimed to understand how rumen microbiota were altered and re-established after being emptied and receiving content from donor, thus to understand the impact of such process on rumen microbial fermentation and to explore the microbial phylotypes with higher manipulation potentials. RESULTS Individual animal had strong effect on the re-establishment of the bacterial community according to the observed profiles detected by both fingerprinting and pyrosequencing. Most of the bacterial profile recovery patterns and extents at genus level varied among steers; and each identified bacterial genus responded to transfaunation differently within each host. Coriobacteriaceae, Coprococcus, and Lactobacillus were found to be the most responsive and tunable genera by exchanging rumen content. Besides, the association of 18 bacterial phylotypes with host fermentation parameters suggest that these phylotypes should also be considered as the regulating targets in improving host feed efficiency. In addition, the archaeal community had different re-establishment patterns for each host as determined by fingerprint profiling: it was altered after receiving non-native microbiome in some animals, while it resumed its original status after the adaptation period in the other ones. CONCLUSIONS The highly individualized microbial re-establishment process suggested the importance of considering host genetics, microbial functional genomics, and host fermentation/performance assessment when developing effective and selective microbial manipulation methods for improving animal feed efficiency.
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Affiliation(s)
- Mi Zhou
- Department of Agricultural, Food and Nutritional Science, University of Alberta, 416F Agr/For Centre, Edmonton, Alberta, T6G 2P5, Canada
| | - Yong-Jia Peng
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Yanhong Chen
- Department of Agricultural, Food and Nutritional Science, University of Alberta, 416F Agr/For Centre, Edmonton, Alberta, T6G 2P5, Canada
| | - Christen M Klinger
- Department of Agricultural, Food and Nutritional Science, University of Alberta, 416F Agr/For Centre, Edmonton, Alberta, T6G 2P5, Canada
| | - Masahito Oba
- Department of Agricultural, Food and Nutritional Science, University of Alberta, 416F Agr/For Centre, Edmonton, Alberta, T6G 2P5, Canada
| | - Jian-Xin Liu
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Le Luo Guan
- Department of Agricultural, Food and Nutritional Science, University of Alberta, 416F Agr/For Centre, Edmonton, Alberta, T6G 2P5, Canada.
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Zhao L, Meng Q, Li Y, Wu H, Huo Y, Zhang X, Zhou Z. Nitrate decreases ruminal methane production with slight changes to ruminal methanogen composition of nitrate-adapted steers. BMC Microbiol 2018; 18:21. [PMID: 29554875 PMCID: PMC5859718 DOI: 10.1186/s12866-018-1164-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 03/15/2018] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND This study was conducted to examine effects of nitrate on ruminal methane production, methanogen abundance, and composition. Six rumen-fistulated Limousin×Jinnan steers were fed diets supplemented with either 0% (0NR), 1% (1NR), or 2% (2NR) nitrate (dry matter basis) regimens in succession. Rumen fluid was taken after two-week adaptation for evaluation of in vitro methane production, methanogen abundance, and composition measurements. RESULTS Results showed that nitrate significantly decreased in vitro ruminal methane production at 6 h, 12 h, and 24 h (P < 0.01; P < 0.01; P = 0.01). The 1NR and 2NR regimens numerically reduced the methanogen population by 4.47% and 25.82% respectively. However, there was no significant difference observed between treatments. The alpha and beta diversity of the methanogen community was not significantly changed by nitrate either. However, the relative abundance of the methanogen genera was greatly changed. Methanosphaera (PL = 0.0033) and Methanimicrococcus (PL = 0.0113) abundance increased linearly commensurate with increasing nitration levels, while Methanoplanus abundance was significantly decreased (PL = 0.0013). The population of Methanoculleus, the least frequently identified genus in this study, exhibited quadratic growth from 0% to 2% when nitrate was added (PQ = 0.0140). CONCLUSIONS Correlation analysis found that methane reduction was significantly related to Methanobrevibacter and Methanoplanus abundance, and negatively correlated with Methanosphaera and Methanimicrococcus abundance.
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Affiliation(s)
- Liping Zhao
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Qingxiang Meng
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Yan Li
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Hao Wu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Yunlong Huo
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Xinzhuang Zhang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Zhenming Zhou
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China.
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Iqbal MW, Zhang Q, Yang Y, Li L, Zou C, Huang C, Lin B. Comparative study of rumen fermentation and microbial community differences between water buffalo and Jersey cows under similar feeding conditions. JOURNAL OF APPLIED ANIMAL RESEARCH 2017. [DOI: 10.1080/09712119.2017.1394859] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Muhammad Wasim Iqbal
- College of Animal Science, Guangxi University, Nanning, People’s Republic of China
| | - Qin Zhang
- College of Animal Science, Guangxi University, Nanning, People’s Republic of China
| | - Yingbai Yang
- College of Animal Science, Guangxi University, Nanning, People’s Republic of China
| | - Lili Li
- The Chinese Academy of Agricultural Sciences, Buffalo Research Institute, Nanning, China
| | - Caixia Zou
- College of Animal Science, Guangxi University, Nanning, People’s Republic of China
| | - Chunhua Huang
- Guangxi Institute of Animal Husbandry, Nanning, People’s Republic of China
| | - Bo Lin
- College of Animal Science, Guangxi University, Nanning, People’s Republic of China
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Paul SS, Dey A, Baro D, Punia BS. Comparative community structure of archaea in rumen of buffaloes and cattle. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2017; 97:3284-3293. [PMID: 27976411 DOI: 10.1002/jsfa.8177] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Revised: 11/13/2016] [Accepted: 12/06/2016] [Indexed: 06/06/2023]
Abstract
BACKGROUND Detailed knowledge of the community structure of methanogens is essential for amelioration of methane emission from livestock species. Several studies have indicated that predominant methanogens of buffalo rumen are different from those in cattle. However, predominant genera of methanogens reported by individual studies varied primarily because of limited scope of sampling, sequencing of limited number of sequences and potential PCR bias in individual studies. In this study, the collective comparative diversity of methanogenic archaea in the rumen of cattle and buffaloes was examined by performing a meta-analysis of all the 16S rRNA (rrn) sequences deposited in GenBank. RESULTS Ruminal methanogen sequences of buffalo were clustered into 900 species-level operational taxonomic units (OTUs), and ruminal methanogen sequences of cattle were clustered into 1522 species level OTUs. The number of species-level OTUs shared between cattle and buffaloes was 229 (10.4% of all OTUs), comprising 1746 sequences (27% of the total 6447 sequences). According to taxonomic classification by three different classifiers, Methanobrevibacter was found to be the most predominant genus both in cattle (69-71% of sequences) as well as buffaloes (65.1-68.9% of sequences). Percentage of Methanomicrobium was much higher (P < 0.05) in the case of buffalo (18%) than that of cattle (4.5%). On the other hand, percentages of Methanosphaera- and Methanomassiliicoccus-like methanogens were much higher (P < 0.05) in cattle than in buffaloes. CONCLUSION This study indicated that there is a substantial difference in community structure of ruminal methanogens of cattle and buffaloes. The study has also indicated that the percent of species-level operational taxonomic units shared between cattle and buffalo is very low, and thus host species-specific methane mitigation strategies need to be developed for cattle and buffaloes. © 2016 Society of Chemical Industry.
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Affiliation(s)
- Shyam S Paul
- ICAR - Central Institute for Research on Buffaloes, Hisar, 125001, Haryana, India
| | - Avijit Dey
- ICAR - Central Institute for Research on Buffaloes, Hisar, 125001, Haryana, India
| | - Daoharu Baro
- ICAR - Central Institute for Research on Buffaloes, Hisar, 125001, Haryana, India
| | - Balbir S Punia
- ICAR - Central Institute for Research on Buffaloes, Hisar, 125001, Haryana, India
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Sinha SK, Chaturvedi VB, Singh P, Chaudhary LC, Ghosh M, Shivani S. Effect of high and low roughage total mixed ration diets on rumen metabolites and enzymatic profiles in crossbred cattle and buffaloes. Vet World 2017; 10:616-622. [PMID: 28717312 PMCID: PMC5499077 DOI: 10.14202/vetworld.2017.616-622] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2016] [Accepted: 04/19/2017] [Indexed: 11/30/2022] Open
Abstract
Aim:: A comparative study was conducted on crossbred cattle and buffaloes to investigate the effect of feeding high and low roughage total mixed ration (TMR) diets on rumen metabolites and enzymatic profiles. Materials and Methods:: Three rumen-fistulated crossbred cattle and buffalo were randomly assigned as per 3×3 switch over design for 21-days. Three TMR diets consisting of concentrate mixture, wheat straw and green maize fodder in the ratios of (T1) 60:20:20, (T2) 40:30:30, and (T3) 20:40:40, respectively, were fed to the animals ad libitum. Rumen liquor samples were collected at 0, 2, 4, 6, and 8 h post feeding for the estimation of rumen biochemical parameters on 2 consecutive days in each trial. Results:: The lactic acid concentration and pH value were comparable in both species and treatments. Feed intake (99.77±2.51 g/kg body weight), ruminal ammonia nitrogen, and total nitrogen were significantly (p<0.05) higher in buffalo and in treatment group fed with high concentrate diet. Production of total volatile fatty acids (VFAs) was non-significant (p>0.05) among treatments and significantly (p<0.05) greater in crossbred cattle than buffaloes. Molar proportions of individual VFAs propionate (C3), propionate:butyrate (C3:C4), and (acetate+butyrate):propionate ([C2+C4]:C3) ratio in both crossbred cattle and buffalo were not affected by high or low roughage diet, but percentage of acetate and butyrate varied significantly (p<0.05) among treatment groups. Activities of microbial enzymes were comparable among species and different treatment groups. A total number of rumen protozoa were significantly (p<0.05) higher in crossbred cattle than buffaloes along with significantly (p<0.05) higher population in animal fed with high concentrate diet (T1). Conclusion:: Rumen microbial population and fermentation depend on constituents of the treatment diet. However, microbial enzyme activity remains similar among species and different treatments. High concentrate diet increases number of rumen protozoa, and the number is higher in crossbred cattle than buffaloes.
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Affiliation(s)
- S K Sinha
- Division of Animal Nutrition, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly - 243 122, Uttar Pradesh, India.,Department of Animal Nutrition, Ranchi Veterinary College, Birsa Agricultural University, Kanke, Ranchi - 834 006, Jharkhand, India
| | - V B Chaturvedi
- Division of Animal Nutrition, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly - 243 122, Uttar Pradesh, India
| | - Putan Singh
- Division of Animal Nutrition, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly - 243 122, Uttar Pradesh, India
| | - L C Chaudhary
- Division of Animal Nutrition, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly - 243 122, Uttar Pradesh, India
| | - Mayukh Ghosh
- Department of Veterinary Biochemistry, Ranchi Veterinary College, Birsa Agricultural University, Kanke, Ranchi - 834 006, Jharkhand, India
| | - Swati Shivani
- Division of Animal Nutrition, ICAR-National Dairy Research Institute, Karnal - 132 001, Haryana, India
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Zhou Z, Fang L, Meng Q, Li S, Chai S, Liu S, Schonewille JT. Assessment of Ruminal Bacterial and Archaeal Community Structure in Yak ( Bos grunniens). Front Microbiol 2017; 8:179. [PMID: 28223980 PMCID: PMC5293774 DOI: 10.3389/fmicb.2017.00179] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 01/24/2017] [Indexed: 11/13/2022] Open
Abstract
The aim of this study was to determine the microbial community composition in the rumen of yaks under different feeding regimes. Microbial communities were assessed by sequencing bacterial and archaeal 16S ribosomal RNA gene fragments obtained from yaks (Bos grunniens) from Qinghai-Tibetan Plateau, China. Samples were obtained from 14 animals allocated to either pasture grazing (Graze), a grazing and supplementary feeding regime (GSF), or an indoor feeding regime (Feed). The predominant bacterial phyla across feeding regimes were Bacteroidetes (51.06%) and Firmicutes (32.73%). At genus level, 25 genera were shared across all samples. The relative abundance of Prevotella in the graze and GSF regime group were significantly higher than that in the feed regime group. Meanwhile, the relative abundance of Ruminococcus was lower in the graze group than the feed and GSF regime groups. The most abundant archaeal phylum was Euryarchaeota, which accounted for 99.67% of the sequences. Ten genera were detected across feeding regimes, seven genera were shared by all samples, and the most abundant was genus Methanobrevibacter (91.60%). The relative abundance of the most detected genera were similar across feeding regime groups. Our results suggest that the ruminal bacterial community structure differs across yak feeding regimes while the archaeal community structures are largely similar.
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Affiliation(s)
- Zhenming Zhou
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University Beijing, China
| | - Lei Fang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University Beijing, China
| | - Qingxiang Meng
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University Beijing, China
| | - Shengli Li
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University Beijing, China
| | - Shatuo Chai
- Qinghai Academy of Animal and Veterinary Sciences, Qinghai University Xining, China
| | - Shujie Liu
- Qinghai Academy of Animal and Veterinary Sciences, Qinghai University Xining, China
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17
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Dan Xue, Chen H, Chen F, He Y, Zhao C, Zhu D, Zeng L, Li W. Analysis of the rumen bacteria and methanogenic archaea of yak (Bos grunniens) steers grazing on the Qinghai-Tibetan Plateau. Livest Sci 2016. [DOI: 10.1016/j.livsci.2016.04.009] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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18
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Franzolin R, Wright ADG. Microorganisms in the rumen and reticulum of buffalo (Bubalus bubalis) fed two different feeding systems. BMC Res Notes 2016; 9:243. [PMID: 27118203 PMCID: PMC4847366 DOI: 10.1186/s13104-016-2046-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 04/15/2016] [Indexed: 11/10/2022] Open
Abstract
Background The community of microorganisms in the rumen and reticulum is influenced by feeding as well as the species and geographical distribution of ruminant animals. Bacteria, methanogenic archaea and ciliate protozoa existing in the rumen and reticulum were evaluated by real-time polymerase chain reaction and light microscopy in buffalo in two feeding systems, grazing and feedlot. Results No significant differences were observed in the total concentrations of bacteria/mL and archaea between rumen and reticulum, and between pasture and feedlots, or interactions between variables. However, the largest density of bacteria and smallest density of archaea was observed in the rumen of grazing animals. The total ciliates protozoa community was higher in grazing buffalo than those in the feedlot on a concentrated diet. There were significant interactions between location in the gastrointestinal tract (rumen vs reticulum) and types of diets (grazing vs feedlot) in the composition of ciliates. Conclusions Our data showed differences in the microbial community of the rumen and reticulum between grazing and feedlot feeding systems demonstrating relevant changes in the microorganism:host relationship existing on rumen–reticulum ecosystem.
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Affiliation(s)
- Raul Franzolin
- Faculdade de Zootecnia e Engenharia de Alimentos, Universidade de São Paulo, Av. Duque de Caxias Norte, 225, Pirassununga, SP, 13630900, Brazil
| | - André-Denis G Wright
- School of Animal and Comparative Biomedical Sciences, College of Agriculture and Life Sciences, University of Arizona, Tucson, AZ, 85721, USA.
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Tapio I, Shingfield KJ, McKain N, Bonin A, Fischer D, Bayat AR, Vilkki J, Taberlet P, Snelling TJ, Wallace RJ. Oral Samples as Non-Invasive Proxies for Assessing the Composition of the Rumen Microbial Community. PLoS One 2016; 11:e0151220. [PMID: 26986467 PMCID: PMC4795602 DOI: 10.1371/journal.pone.0151220] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 02/23/2016] [Indexed: 11/19/2022] Open
Abstract
Microbial community analysis was carried out on ruminal digesta obtained directly via rumen fistula and buccal fluid, regurgitated digesta (bolus) and faeces of dairy cattle to assess if non-invasive samples could be used as proxies for ruminal digesta. Samples were collected from five cows receiving grass silage based diets containing no additional lipid or four different lipid supplements in a 5 x 5 Latin square design. Extracted DNA was analysed by qPCR and by sequencing 16S and 18S rRNA genes or the fungal ITS1 amplicons. Faeces contained few protozoa, and bacterial, fungal and archaeal communities were substantially different to ruminal digesta. Buccal and bolus samples gave much more similar profiles to ruminal digesta, although fewer archaea were detected in buccal and bolus samples. Bolus samples overall were most similar to ruminal samples. The differences between both buccal and bolus samples and ruminal digesta were consistent across all treatments. It can be concluded that either proxy sample type could be used as a predictor of the rumen microbial community, thereby enabling more convenient large-scale animal sampling for phenotyping and possible use in future animal breeding programs aimed at selecting cattle with a lower environmental footprint.
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Affiliation(s)
- Ilma Tapio
- Green Technology, Natural Resources Institute Finland, Jokioinen, Finland
| | | | - Nest McKain
- Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, United Kingdom
| | - Aurélie Bonin
- Laboratoire d'Ecologie Alpine, CNRS, Grenoble, France
| | - Daniel Fischer
- Green Technology, Natural Resources Institute Finland, Jokioinen, Finland
| | - Ali R. Bayat
- Green Technology, Natural Resources Institute Finland, Jokioinen, Finland
| | - Johanna Vilkki
- Green Technology, Natural Resources Institute Finland, Jokioinen, Finland
| | | | - Timothy J. Snelling
- Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, United Kingdom
| | - R. John Wallace
- Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, United Kingdom
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Characterization of the rumen microbial community composition of buffalo breeds consuming diets typical of dairy production systems in Southern China. Anim Feed Sci Technol 2015. [DOI: 10.1016/j.anifeedsci.2015.06.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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21
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Qiao J, Tan Z, Guan L, Tang S, Zhou C, Han X, Wang M, Kang J, He Z. Effects of hydrogen in headspace and bicarbonate in media on rumen fermentation, methane production and methanogenic population using in vitro gas production techniques. Anim Feed Sci Technol 2015. [DOI: 10.1016/j.anifeedsci.2015.05.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
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St-Pierre B, Cersosimo LM, Ishaq SL, Wright ADG. Toward the identification of methanogenic archaeal groups as targets of methane mitigation in livestock animalsr. Front Microbiol 2015; 6:776. [PMID: 26284054 PMCID: PMC4519756 DOI: 10.3389/fmicb.2015.00776] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 07/14/2015] [Indexed: 02/06/2023] Open
Abstract
In herbivores, enteric methane is a by-product from the digestion of plant biomass by mutualistic gastrointestinal tract (GIT) microbial communities. Methane is a potent greenhouse gas that is not assimilated by the host and is released into the environment where it contributes to climate change. Since enteric methane is exclusively produced by methanogenic archaea, the investigation of mutualistic methanogen communities in the GIT of herbivores has been the subject of ongoing research by a number of research groups. In an effort to uncover trends that would facilitate the development of efficient methane mitigation strategies for livestock species, we have in this review summarized and compared currently available results from published studies on this subject. We also offer our perspectives on the importance of pursuing current research efforts on the sequencing of gut methanogen genomes, as well as investigating their cellular physiology and interactions with other GIT microorganisms.
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Affiliation(s)
- Benoit St-Pierre
- Department of Animal Science, South Dakota State University, Brookings SD, USA
| | - Laura M Cersosimo
- Department of Animal and Veterinary Sciences, The University of Vermont, Burlington VT, USA
| | - Suzanne L Ishaq
- Department of Animal and Range Sciences, Montana State University, Bozeman MT, USA
| | - André-Denis G Wright
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson AZ, USA
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23
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Cersosimo LM, Lachance H, St-Pierre B, van Hoven W, Wright ADG. Examination of the rumen bacteria and methanogenic archaea of wild impalas (Aepyceros melampus melampus) from Pongola, South Africa. MICROBIAL ECOLOGY 2015; 69:577-585. [PMID: 25351144 DOI: 10.1007/s00248-014-0521-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2014] [Accepted: 10/15/2014] [Indexed: 06/04/2023]
Abstract
Although the rumen microbiome of domesticated ruminants has been evaluated, few studies have explored the rumen microbiome of wild ruminants, and no studies have identified the rumen microbiome in the impala (Aepyceros melampus melampus). In the present study, next-generation sequencing and real-time polymerase chain reaction were used to investigate the diversity and density of the bacteria and methanogenic archaea residing in the rumen of five adult male impalas, culled during the winter dry season in Pongola, South Africa. A total of 15,323 bacterial 16S rRNA gene sequences (from five impala), representing 3,892 different phylotypes, were assigned to 1,902 operational taxonomic units (OTUs). A total of 20,124 methanogen 16S rRNA gene sequence reads (from four impala), of which 5,028 were unique, were assigned to 344 OTUs. From the total sequence reads, Bacteroidetes, Proteobacteria, and Firmicutes were the most abundant bacterial phyla. While the majority of the bacterial genera found were unclassified, Prevotella and Cupriavidus were the most abundant classified genera. For methanogens, the genera Methanobrevibacter and Methanosphaera represented 94.3% and 4.0% of the classified sequences, respectively. Most notable was the identification of Methanobrevibacter thaueri-like 16S rRNA gene sequence reads in all four impala samples, representing greater than 30% of each individual's total sequences. Both data sets are accessible through NCBI's Sequence Read Archive (SRA), under study accession number SRP [048619]. The densities of bacteria (1.26 × 10(10)-3.82 × 10(10) cells/ml whole rumen contents) and methanogens (4.48 × 10(8)-7.2 × 10(9) cells/ml of whole rumen contents) from five individual impala were similar to those typically observed in domesticated ruminants.
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Affiliation(s)
- Laura M Cersosimo
- Department of Animal Science, The University of Vermont, 570 Main Street, Burlington, VT, 05405, USA
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Snelling TJ, Genç B, McKain N, Watson M, Waters SM, Creevey CJ, Wallace RJ. Diversity and community composition of methanogenic archaea in the rumen of Scottish upland sheep assessed by different methods. PLoS One 2014; 9:e106491. [PMID: 25250654 PMCID: PMC4175461 DOI: 10.1371/journal.pone.0106491] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Accepted: 05/28/2014] [Indexed: 12/27/2022] Open
Abstract
Ruminal archaeomes of two mature sheep grazing in the Scottish uplands were analysed by different sequencing and analysis methods in order to compare the apparent archaeal communities. All methods revealed that the majority of methanogens belonged to the Methanobacteriales order containing the Methanobrevibacter, Methanosphaera and Methanobacteria genera. Sanger sequenced 1.3 kb 16S rRNA gene amplicons identified the main species of Methanobrevibacter present to be a SGMT Clade member Mbb. millerae (≥91% of OTUs); Methanosphaera comprised the remainder of the OTUs. The primers did not amplify ruminal Thermoplasmatales-related 16S rRNA genes. Illumina sequenced V6–V8 16S rRNA gene amplicons identified similar Methanobrevibacter spp. and Methanosphaera clades and also identified the Thermoplasmatales-related order as 13% of total archaea. Unusually, both methods concluded that Mbb. ruminantium and relatives from the same clade (RO) were almost absent. Sequences mapping to rumen 16S rRNA and mcrA gene references were extracted from Illumina metagenome data. Mapping of the metagenome data to16S rRNA gene references produced taxonomic identification to Order level including 2–3% Thermoplasmatales, but was unable to discriminate to species level. Mapping of the metagenome data to mcrA gene references resolved 69% to unclassified Methanobacteriales. Only 30% of sequences were assigned to species level clades: of the sequences assigned to Methanobrevibacter, most mapped to SGMT (16%) and RO (10%) clades. The Sanger 16S amplicon and Illumina metagenome mcrA analyses showed similar species richness (Chao1 Index 19–35), while Illumina metagenome and amplicon 16S rRNA analysis gave lower richness estimates (10–18). The values of the Shannon Index were low in all methods, indicating low richness and uneven species distribution. Thus, although much information may be extracted from the other methods, Illumina amplicon sequencing of the V6–V8 16S rRNA gene would be the method of choice for studying rumen archaeal communities.
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Affiliation(s)
- Timothy J. Snelling
- Rowett Institute of Nutrition and Health, University of Aberdeen, Bucksburn, Aberdeen, United Kingdom
| | - Buğra Genç
- Department of Animal Nutrition and Nutritional Diseases, Faculty of Veterinary Medicine, Ondokuz Mayis University, Samsun, Turkey
| | - Nest McKain
- Rowett Institute of Nutrition and Health, University of Aberdeen, Bucksburn, Aberdeen, United Kingdom
| | - Mick Watson
- ARK Genomics, The Roslin Institute, Easter Bush, Midlothian, United Kingdom
| | - Sinéad M. Waters
- Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc, Grange, Dunsany, Co. Meath, Ireland
| | - Christopher J. Creevey
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, Ceredigion, United Kingdom
| | - R. John Wallace
- Rowett Institute of Nutrition and Health, University of Aberdeen, Bucksburn, Aberdeen, United Kingdom
- * E-mail:
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Dominance of Methanosarcinales Phylotypes and Depth-Wise Distribution of Methanogenic Community in Fresh Water Sediments of Sitka Stream from Czech Republic. Curr Microbiol 2014; 69:809-16. [DOI: 10.1007/s00284-014-0659-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Accepted: 05/26/2014] [Indexed: 11/25/2022]
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Jin W, Cheng YF, Mao SY, Zhu WY. Discovery of a novel rumen methanogen in the anaerobic fungal culture and its distribution in the rumen as revealed by real-time PCR. BMC Microbiol 2014; 14:104. [PMID: 24758319 PMCID: PMC4017770 DOI: 10.1186/1471-2180-14-104] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Accepted: 04/17/2014] [Indexed: 12/11/2022] Open
Abstract
Background The novel archaea belonging to Rumen Cluster C (RCC), which may play an important role in methane production in the rumen have received increased attention. However, the present information on RCC in the rumen is limited by the unsuccessful isolation of axenic pure RCC from the rumen. In the present study, RCC grown in anaerobic fungal subcultures was identified by the molecular and culture methods. Results A novel RCC species existing in the fungal subcultures was identified and demonstrated by the 16S rRNA gene clone library. Interestingly, the novel RCC species survived in the fungal cultures over all the subculture transferring, even in the 62nd subculture, in contrast to the other methanogens, which disappeared during subcultures. Further work showed that subculture transfer frequency significantly affected the relative abundance of the novel RCC species in the fungal subcultures. The five-day and seven-day transfer frequencies increased the relative abundance of the RCC species (P<0.05). In addition, quantitative real-time PCR revealed that high concentrate diets did not affect the abundance of archaea, but numerically reduced the abundance of the novel RCC species in the rumen. In addition, the relative abundance of the RCC species was numerically higher in the rumen liquid fraction than in the rumen epithelium and solid fractions. Finally, a purified fungal culture containing the RCC species was successfully obtained. PCR and sequencing analysis showed that the novel RCC species contained a mcrA gene, which is known to play a crucial role in methanogenesis, and thus could be identified as a methanogen. Conclusion In this study, a novel RCC species was identified as a methanogen and closely associated with anaerobic fungi. This novel approach by using co-culture with anaerobic fungi may provide a feasible way to culture and investigate not yet identified methanogens.
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Affiliation(s)
| | | | | | - Wei Yun Zhu
- Laboratory of Gastrointestinal Microbiology, College of Animal Science and Technology, Nanjing Agricultural University, 210095 Nanjing, China.
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The use of direct-fed microbials for mitigation of ruminant methane emissions: a review. Animal 2014; 8:250-61. [DOI: 10.1017/s1751731113002085] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
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28
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Evaluation of bacterial and archaeal diversity in the rumen of Xiangxi yellow cattle (Bos taurus) fed Miscanthus sinensis or common mixed feedstuff. ANN MICROBIOL 2013. [DOI: 10.1007/s13213-013-0783-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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Li ZP, Liu HL, Jin CA, Cui XZ, Jing Y, Yang FH, Li GY, Wright ADG. Differences in the methanogen population exist in sika deer (Cervus nippon) fed different diets in China. MICROBIAL ECOLOGY 2013; 66:879-888. [PMID: 24061342 DOI: 10.1007/s00248-013-0282-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Accepted: 08/21/2013] [Indexed: 06/02/2023]
Abstract
Understanding the methanogen structure from sika deer (Cervus nippon) in China may be beneficial to methane mitigation. In the present preliminary study, we investigated the methanogen community in the rumen of domesticated sika deer fed either tannin-rich plants (oak leaf, OL group) or corn stalk (CS group) using 16S rRNA gene clone libraries. Overall, we obtained 197 clone sequences, revealing 146 unique phylotypes, which were assigned to 36 operational taxonomic units at the species level (98 % identity). Methanogens related to the genus Methanobrevibacter were the predominant phylotypes representing 83.9 % (OL library) and 85.9 % (CS library) of the clones. Methanobrevibacter millerae was the most abundant species in both libraries, but the proportion of M. millerae-related clones in the CS library was higher than in the OL library (69.5 and 51.4 %, respectively). Moreover, Methanobrevibacter wolinii-related clones (32.5 %) were predominant in the OL library. Methanobrevibacter smithii-related clones and Methanobrevibacter ruminantium-related clones accounted for 6.5 and 6.6 % in the CS library, respectively. However, these clones were absent from the OL library. The concentrations of butyrate and total short-chain fatty acids (SCFAs) were significantly higher in the OL group, but the concentrations of acetate, propionate, and valerate and the acetate to propionate ratio in the OL group were not significantly different between the two groups. Tannin-rich plants may have affected the distribution of genus Methanobrevibacter phylotypes at the species level and the concentration and composition of SCFAs.
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Affiliation(s)
- Zhi Peng Li
- Department of Economical Animal Nutrition and Feed Science, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Jilin, China
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Sirohi SK, Chaudhary PP, Singh N, Singh D, Puniya AK. The 16S rRNA and mcrA gene based comparative diversity of methanogens in cattle fed on high fibre based diet. Gene 2013; 523:161-6. [DOI: 10.1016/j.gene.2013.04.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2012] [Revised: 03/12/2013] [Accepted: 04/02/2013] [Indexed: 01/12/2023]
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Mao S, Huo W, Zhu W. Use of Pyrosequencing to Characterize the Microbiota in the Ileum of Goats Fed with Increasing Proportion of Dietary Grain. Curr Microbiol 2013; 67:341-50. [DOI: 10.1007/s00284-013-0371-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2012] [Accepted: 03/11/2013] [Indexed: 11/28/2022]
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Zhou M, Hünerberg M, Beauchemin KA, McAllister TA, Okine EK, Guan LL. Individuality of ruminal methanogen/protozoa populations in beef cattle fed diets containing dried distillers' grain with solubles. ACTA AGR SCAND A-AN 2012. [DOI: 10.1080/09064702.2013.788206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Sirohi SK, Singh N, Dagar SS, Puniya AK. Molecular tools for deciphering the microbial community structure and diversity in rumen ecosystem. Appl Microbiol Biotechnol 2012; 95:1135-54. [PMID: 22782251 DOI: 10.1007/s00253-012-4262-2] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2012] [Revised: 06/20/2012] [Accepted: 06/22/2012] [Indexed: 12/30/2022]
Abstract
Rumen microbial community comprising of bacteria, archaea, fungi, and protozoa is characterized not only by the high population density but also by the remarkable diversity and the most complex microecological interactions existing in the biological world. This unprecedented biodiversity is quite far from full elucidation as only about 15-20 % of the rumen microbes are identified and characterized till date using conventional culturing and microscopy. However, the last two decades have witnessed a paradigm shift from cumbersome and time-consuming classical methods to nucleic acid-based molecular approaches for deciphering the rumen microbial community. These techniques are rapid, reproducible and allow both the qualitative and quantitative assessment of microbial diversity. This review describes the different molecular methods and their applications in elucidating the rumen microbial community.
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Affiliation(s)
- Sunil Kumar Sirohi
- Nutrition Biotechnology Laboratory, Dairy Cattle Nutrition Division, National Dairy Research Institute, Karnal, 132001, Haryana, India.
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