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Cammack KM, Austin KJ, Lamberson WR, Conant GC, Cunningham HC. RUMINANT NUTRITION SYMPOSIUM: Tiny but mighty: the role of the rumen microbes in livestock production. J Anim Sci 2018; 96:752-770. [PMID: 29385535 PMCID: PMC6140983 DOI: 10.1093/jas/skx053] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 12/07/2017] [Indexed: 12/14/2022] Open
Abstract
The microbes inhabiting the rumen convert low-quality, fibrous, plant material into useable energy for the host ruminant. Consisting of bacteria, protozoa, fungi, archaea, and viruses, the rumen microbiome composes a sophisticated network of symbiosis essential to maintenance, immune function, and overall production efficiency of the host ruminant. Robert Hungate laid the foundation for rumen microbiome research. This area of research has expanded immensely with advances in methodology and technology that have not only improved the ability to describe microbes in taxonomic and density terms but also characterize populations of microbes, their functions, and their interactions with each other and the host. The interplay between the rumen microbiome and the host contributes to variation in many phenotypic traits expressed by the host animal. A better understanding of how the rumen microbiome influences host health and performance may lead to novel strategies and treatments for trait improvement. Furthermore, elucidation of maternal, genetic, and environmental factors that influence rumen microbiome establishment and development may provide novel insights into possible mechanisms for manipulating the rumen microbial composition to enhance long-term host health and performance. The potential for these tiny but mighty rumen microbes to play a role in improving livestock production is appreciated despite being relatively obscure.
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Affiliation(s)
- Kristi M Cammack
- Department of Animal Science and West River Ag Center, South Dakota State University, Rapid City, SD
| | | | | | - Gavin C Conant
- Department of Biological Sciences, North Carolina State University, Raleigh, NC
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Witzig M, Zeder M, Rodehutscord M. Effect of the ionophore monensin and tannin extracts supplemented to grass silage on populations of ruminal cellulolytics and methanogens in vitro. Anaerobe 2018; 50:44-54. [PMID: 29408017 DOI: 10.1016/j.anaerobe.2018.01.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 01/26/2018] [Accepted: 01/29/2018] [Indexed: 10/18/2022]
Abstract
This study examined whether the methane-decreasing effect of monensin (∼21%) and different hydrolysable tannins (24%-65%) during in vitro fermentation of grass silage was accompanied by changes in abundances of cellulolytics and methanogens. Samples of liquid (LAM) and solid (SAM) associated microbes were obtained from two rumen simulation technique experiments in which grass silage was either tested in combination with monensin (0, 2 or 4 mg d-1) or with different tannin extracts from chestnut, valonea, sumac and grape seed (0 or 1.5 g d-1). Total prokaryotes were quantified by 4',6-diamidino-2-phenylindol (DAPI) staining of paraformaldehyde-ethanol-fixed cells and relative abundances of ruminal cellulolytic and methanogenic species were assessed by real time quantitative PCR. Results revealed no change in absolute numbers of prokaryotic cells with monensin treatment, neither in LAM nor in SAM. By contrast, supplementation of chestnut and grape seed tannins decreased total prokaryotic counts compared to control. However, relative abundances of total methanogens did not differ between tannin treatments. Thus, the decreased methane production by 65% and 24% observed for chestnut and grape seed tannins, respectively, may have been caused by a lower total number of methanogens, but methane production seemed to be also dependent on changes in the microbial community composition. While the relative abundance of F. succinogenes decreased with monensin addition, chestnut and valonea tannins inhibited R. albus. Moreover, a decline in relative abundances of Methanobrevibacter sp., especially M. ruminantium, and Methanosphaera stadtmanae was shown with supplementation of monensin or chestnut tannins. Proportions of Methanomicrobium mobile were decreased by monensin in LAM while chestnut and valonea had an increasing effect on this methanogenic species. Our results demonstrate a different impact of monensin and tannins on ruminal cellulolytics and gave indication that methane decrease by monensin and chestnut tannins was associated with decreased abundances of M. ruminantium and M. stadtmanae.
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Affiliation(s)
- M Witzig
- Universität Hohenheim, Institut für Nutztierwissenschaften, 70593 Stuttgart, Germany.
| | - M Zeder
- Technobiology GmbH, 6033 Buchrain, Switzerland
| | - M Rodehutscord
- Universität Hohenheim, Institut für Nutztierwissenschaften, 70593 Stuttgart, Germany
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Neumann AP, Weimer PJ, Suen G. A global analysis of gene expression in Fibrobacter succinogenes S85 grown on cellulose and soluble sugars at different growth rates. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:295. [PMID: 30386432 PMCID: PMC6204037 DOI: 10.1186/s13068-018-1290-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 10/15/2018] [Indexed: 05/04/2023]
Abstract
BACKGROUND Cellulose is the most abundant biological polymer on earth, making it an attractive substrate for the production of next-generation biofuels and commodity chemicals. However, the economics of cellulose utilization are currently unfavorable due to a lack of efficient methods for its hydrolysis. Fibrobacter succinogenes strain S85, originally isolated from the bovine rumen, is among the most actively cellulolytic mesophilic bacteria known, producing succinate as its major fermentation product. In this study, we examined the transcriptome of F. succinogenes S85 grown in continuous culture at several dilution rates on cellulose, cellobiose, or glucose to gain a system-level understanding of cellulose degradation by this bacterium. RESULTS Several patterns of gene expression were observed for the major cellulases produced by F. succinogenes S85. A large proportion of cellulase genes were constitutively expressed, including the gene encoding for Cel51A, the major cellulose-binding endoglucanase produced by this bacterium. Moreover, other cellulase genes displayed elevated expression during growth on cellulose relative to growth on soluble sugars. Growth rate had a strong effect on global gene expression, particularly with regard to genes predicted to encode carbohydrate-binding modules and glycoside hydrolases implicated in hemicellulose degradation. Expression of hemicellulase genes was tightly regulated, with these genes displaying elevated expression only during slow growth on soluble sugars. Clear differences in gene expression were also observed between adherent and planktonic populations within continuous cultures growing on cellulose. CONCLUSIONS This work emphasizes the complexity of the fiber-degrading system utilized by F. succinogenes S85, and reinforces the complementary role of hemicellulases for accessing cellulose by these bacteria. We report for the first time evidence of global differences in gene expression between adherent and planktonic populations of an anaerobic bacterium growing on cellulose at steady state during continuous cultivation. Finally, our results also highlight the importance of controlling for growth rate in investigations of gene expression.
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Affiliation(s)
- Anthony P. Neumann
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI USA
| | - Paul J. Weimer
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI USA
- Agricultural Research Service, United States Department of Agriculture, Madison, WI USA
| | - Garret Suen
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI USA
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Sari WN, Safika, Darmawi, Fahrimal Y. Isolation and identification of a cellulolytic Enterobacter from rumen of Aceh cattle. Vet World 2017; 10:1515-1520. [PMID: 29391695 PMCID: PMC5771179 DOI: 10.14202/vetworld.2017.1515-1520] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 11/24/2017] [Indexed: 11/16/2022] Open
Abstract
Aims: The aim of this study was to isolate and identify a cellulolytic bacterium from the rumen fluid of Aceh’s cattle. Biodegradation by cellulolytic rumen bacteria can be used as a source of cellulolytic bacteria that act to degrade feed fibrous material so as to improve the quality of nutrients and digestibility of feed ingredients at a cheaper price than the use of commercial cellulase enzymes. Materials and Methods: Samples were collected from rumen fluid of Aceh’s cattle in Abattoirs (RPH) of Banda Aceh city, Indonesia, isolation, and screening of cellulolytic bacteria were done in Microbiology Laboratory, Faculty of Veterinary Medicine, Syiah Kuala University, Banda Aceh, Indonesia. Results: The S1 isolates showed ±2.5 cm of clear zone diameter. Microscopically, this strain was found to be a Gram-negative, Bacillus. Homology and phylogenetic tree analysis of 16S rRNA showed that S1 isolate has 91% of sequence similarity with that of Enterobacter cloacae. 91% sequence homology shown in this study proved that the S1 isolate is probably either a new species or another genus of Enterobacteriaceae. Conclusion: Current study suggests that cellulose hydrolytic bacteria isolated from rumen fluid of Aceh cattle on Bushnell Haas medium-carboxymethylcellulose agar, and some potent cellulose degrading bacteria have been identified.
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Affiliation(s)
- Wenny Novita Sari
- Postgraduate student of Mathematics and Applied Sciences, Syiah Kuala University, Darussalam, Banda Aceh 23111, Indonesia
| | - Safika
- Department of Veterinary Infectious Diseases and Veterinary Public Health, Faculty of Veterinary Medicine, Bogor Agricultural University, Jalan Agatis IPB, Darmaga, Bogor, Indonesia
| | - Darmawi
- Microbiology Laboratory, Faculty of Veterinary Medicine, Syiah Kuala University, Darussalam, Banda Aceh 23111, Indonesia
| | - Yudha Fahrimal
- Parasitology Laboratory, Faculty of Veterinary, Syiah Kuala University, Darussalam, Banda Aceh 23111, Indonesia
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Jose VL, Appoothy T, More RP, Arun AS. Metagenomic insights into the rumen microbial fibrolytic enzymes in Indian crossbred cattle fed finger millet straw. AMB Express 2017; 7:13. [PMID: 28050853 PMCID: PMC5209320 DOI: 10.1186/s13568-016-0310-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 12/19/2016] [Indexed: 11/24/2022] Open
Abstract
The rumen is a unique natural habitat, exhibiting an unparalleled genetic resource of fibrolytic enzymes of microbial origin that degrade plant polysaccharides. The objectives of this study were to identify the principal plant cell wall-degrading enzymes and the taxonomic profile of rumen microbial communities that are associated with it. The cattle rumen microflora and the carbohydrate-active enzymes were functionally classified through a whole metagenomic sequencing approach. Analysis of the assembled sequences by the Carbohydrate-active enzyme analysis Toolkit identified the candidate genes encoding fibrolytic enzymes belonging to different classes of glycoside hydrolases(11,010 contigs), glycosyltransferases (6366 contigs), carbohydrate esterases (4945 contigs), carbohydrate-binding modules (1975 contigs), polysaccharide lyases (480 contigs), and auxiliary activities (115 contigs). Phylogenetic analysis of CAZyme encoding contigs revealed that a significant proportion of CAZymes were contributed by bacteria belonging to genera Prevotella, Bacteroides, Fibrobacter, Clostridium, and Ruminococcus. The results indicated that the cattle rumen microbiome and the CAZymes are highly complex, structurally similar but compositionally distinct from other ruminants. The unique characteristics of rumen microbiota and the enzymes produced by resident microbes provide opportunities to improve the feed conversion efficiency in ruminants and serve as a reservoir of industrially important enzymes for cellulosic biofuel production.
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Jiang Y, Ogunade I, Arriola K, Qi M, Vyas D, Staples C, Adesogan A. Effects of the dose and viability of Saccharomyces cerevisiae. 2. Ruminal fermentation, performance of lactating dairy cows, and correlations between ruminal bacteria abundance and performance measures. J Dairy Sci 2017; 100:8102-8118. [DOI: 10.3168/jds.2016-12371] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 06/07/2017] [Indexed: 02/02/2023]
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The unusual cellulose utilization system of the aerobic soil bacterium Cytophaga hutchinsonii. Appl Microbiol Biotechnol 2017; 101:7113-7127. [PMID: 28849247 DOI: 10.1007/s00253-017-8467-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 08/05/2017] [Indexed: 10/19/2022]
Abstract
Cellulolytic microorganisms play important roles in global carbon cycling and have evolved diverse strategies to digest cellulose. Some are 'generous,' releasing soluble sugars from cellulose extracellularly to feed both themselves and their neighbors. The gliding soil bacterium Cytophaga hutchinsonii exhibits a more 'selfish' strategy. It digests crystalline cellulose using cell-associated cellulases and releases little soluble sugar outside of the cell. The mechanism of C. hutchinsonii cellulose utilization is still poorly understood. In this review, we discuss novel aspects of the C. hutchinsonii cellulolytic system. Recently developed genetic manipulation tools allowed the identification of proteins involved in C. hutchinsonii cellulose utilization. These include periplasmic and cell-surface endoglucanases and novel cellulose-binding proteins. The recently discovered type IX secretion system is needed for cellulose utilization and appears to deliver some of the cellulolytic enzymes and other proteins to the cell surface. The requirement for periplasmic endoglucanases for cellulose utilization is unusual and suggests that cello-oligomers must be imported across the outer membrane before being further digested. Cellobiohydrolases or other predicted processive cellulases that play important roles in many other cellulolytic bacteria appear to be absent in C. hutchinsonii. Cells of C. hutchinsonii attach to and glide along cellulose fibers, which may allow them to find sites most amenable to attack. A model of C. hutchinsonii cellulose utilization summarizing recent progress is proposed.
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Deusch S, Camarinha-Silva A, Conrad J, Beifuss U, Rodehutscord M, Seifert J. A Structural and Functional Elucidation of the Rumen Microbiome Influenced by Various Diets and Microenvironments. Front Microbiol 2017; 8:1605. [PMID: 28883813 PMCID: PMC5573736 DOI: 10.3389/fmicb.2017.01605] [Citation(s) in RCA: 139] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 08/07/2017] [Indexed: 12/11/2022] Open
Abstract
The structure and function of the microbiome inhabiting the rumen are, amongst other factors, mainly shaped by the animal's feed intake. Describing the influence of different diets on the inherent community arrangement and associated metabolic activities of the most active ruminal fractions (bacteria and archaea) is of great interest for animal nutrition, biotechnology, and climatology. Samples were obtained from three fistulated Jersey cows rotationally fed with corn silage, grass silage or grass hay, each supplemented with a concentrate mixture. Samples were fractionated into ruminal fluid, particle-associated rumen liquid, and solid matter. DNA, proteins and metabolites were analyzed subsequently. DNA extracts were used for Illumina sequencing of the 16S rRNA gene and the metabolomes of rumen fluids were determined by 500 MHz-NMR spectroscopy. Tryptic peptides derived from protein extracts were measured by LC-ESI-MS/MS and spectra were processed by a two-step database search for quantitative metaproteome characterization. Data are available via ProteomeXchange with the identifier PXD006070. Protein- and DNA-based datasets revealed significant differences between sample fractions and diets and affirmed similar trends concerning shifts in phylogenetic composition. Ribosomal genes and proteins belonging to the phylum of Proteobacteria, particularly Succinivibrionaceae, exhibited a higher abundance in corn silage-based samples while fiber-degraders of the Lachnospiraceae family emerged in great quantities throughout the solid phase fractions. The analysis of 8163 quantified bacterial proteins revealed the presence of 166 carbohydrate active enzymes in varying abundance. Cellulosome affiliated proteins were less expressed in the grass silage, glycoside hydrolases appeared in slightest numbers in the corn silage. Most expressed glycoside hydrolases belonged to families 57 and 2. Enzymes analogous to ABC transporters for amino acids and monosaccharides were more abundant in the corn silage whereas oligosaccharide transporters showed a higher abundance in the fiber-rich diets. Proteins involved in carbon metabolism were detected in high numbers and identification of metabolites like short-chain fatty acids, methylamines and phenylpropionate by NMR enabled linkage between producers and products. This study forms a solid basis to retrieve deeper insight into the complex network of microbial adaptation in the rumen.
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Affiliation(s)
- Simon Deusch
- Department of Feed-Gut Microbiota Interaction, Institute of Animal Science, University of HohenheimStuttgart, Germany
| | - Amélia Camarinha-Silva
- Department of Feed-Gut Microbiota Interaction, Institute of Animal Science, University of HohenheimStuttgart, Germany
| | - Jürgen Conrad
- Department of Bioorganic Chemistry, Institute of Chemistry, University of HohenheimStuttgart, Germany
| | - Uwe Beifuss
- Department of Bioorganic Chemistry, Institute of Chemistry, University of HohenheimStuttgart, Germany
| | - Markus Rodehutscord
- Department of Feed-Gut Microbiota Interaction, Institute of Animal Science, University of HohenheimStuttgart, Germany
| | - Jana Seifert
- Department of Feed-Gut Microbiota Interaction, Institute of Animal Science, University of HohenheimStuttgart, Germany
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Belanche A, Newbold CJ, Lin W, Rees Stevens P, Kingston-Smith AH. A Systems Biology Approach Reveals Differences in the Dynamics of Colonization and Degradation of Grass vs. Hay by Rumen Microbes with Minor Effects of Vitamin E Supplementation. Front Microbiol 2017; 8:1456. [PMID: 28824585 PMCID: PMC5541034 DOI: 10.3389/fmicb.2017.01456] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 07/18/2017] [Indexed: 11/29/2022] Open
Abstract
Increasing the efficiency of utilization of fresh and preserved forage is a key target for ruminant science. Vitamin E is often used as additive to improve product quality but its impact of the rumen function is unknown. This study investigated the successional microbial colonization of ryegrass (GRA) vs. ryegrass hay (HAY) in presence of zero or 50 IU/d supplementary vitamin E, using a rumen simulation technique. A holistic approach was used to link the dynamics of feed degradation with the structure of the liquid-associated (LAB) and solid-associated bacteria (SAB). Results showed that forage colonization by SAB was a tri-phasic process highly affected by the forage conservation method: Early colonization (0-2 h after feeding) by rumen microbes was 2× faster for GRA than HAY diets and dominated by Lactobacillus and Prevotella which promoted increased levels of lactate (+56%) and ammonia (+18%). HAY diets had lower DM degradation (-72%) during this interval being Streptococcus particularly abundant. During secondary colonization (4-8 h) the SAB community increased in size and decreased in diversity as the secondary colonizers took over (Pseudobutyrivibrio) promoting the biggest differences in the metabolomics profile between diets. Secondary colonization was 3× slower for HAY vs. GRA diets, but this delay was compensated by a greater bacterial diversity (+197 OTUs) and network complexity resulting in similar feed degradations. Tertiary colonization (>8 h) consisted of a slowdown in the colonization process and simplification of the bacterial network. This slowdown was less evident for HAY diets which had higher levels of tertiary colonizers (Butyrivibrio and Ruminococcus) and may explain the higher DM degradation (+52%) during this interval. The LAB community was particularly active during the early fermentation of GRA and during the late fermentation for HAY diets indicating that the availability of nutrients in the liquid phase reflects the dynamics of feed degradation. Vitamin E supplementation had minor effects but promoted a simplification of the LAB community and a slight acceleration in the SAB colonization sequence which could explain the higher DM degradation during the secondary colonization. Our findings suggest that when possible, grass should be fed instead of hay, in order to accelerate feed utilization by rumen microbes.
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Affiliation(s)
- Alejandro Belanche
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth UniversityAberystwyth, United Kingdom
- Estacion Experimental del Zaidín, Consejo Superior de Investigaciones CientíficasGranada, Spain
| | - Charles J. Newbold
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth UniversityAberystwyth, United Kingdom
| | - Wanchang Lin
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth UniversityAberystwyth, United Kingdom
| | - Pauline Rees Stevens
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth UniversityAberystwyth, United Kingdom
| | - Alison H. Kingston-Smith
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth UniversityAberystwyth, United Kingdom
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Effect of feeding long or short wheat hay v. wheat silage in the ration of lactating cows on intake, milk production and digestibility. Animal 2017; 11:2203-2210. [PMID: 28532526 DOI: 10.1017/s1751731117001100] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
The objective of this study was to evaluate in lactating cows the effect of either chopping or ensiling of wheat roughage on: intake, digestibility, lactation performance and animal behavior. Three groups of 14 lactating cows each, were fed total mixed rations (TMRs) based on either long wheat hay (HL), short wheat hay (HS) or wheat silage (SI), as the sole roughage source (30% of TMR dry matter (DM)). Parameters examined: sorting behavior, DM intake, milk yield and composition, rumination, recumbence, average daily rumen pH, digesta passage rate, and in-vivo digestibility. Performance data was summarized by day and analyzed using a proc-mixed model. The content of physically effective neutral detergent fiber (peNDF) was similar in the HL and SI and lower in the HS, resulting in similar differences among the three corresponding TMRs. In vitro DM digestibility of wheat silage was higher than that of the two hays (65.6% v. 62.8%) resulting in higher in vitro DM digestibility of the SI-TMR compared with the hay-based TMRs (79.3 v. 77.0%). HS-TMR was better than HL- or SI-TMRs at preventing feed sorting by cows after 12 or 24 h eating of the diets. Cows fed HS-TMR consumed more DM and NDF but less peNDF than the other two groups. Average daily rumen pH was similar in the three groups, but daily rumination time was highest in the cows fed HS-TMR. Rumen retention time was longest in cows fed HL-TMR. DM digestibility in cows fed SI-TMR was higher than that of HS and HL groups (65.2%, 61.8% and 62.4%, respectively), but NDF digestibility was similar in the three treatments. The highest intake of digestible DM was observed in cows fed SI-TMR, HS cows were intermediate and HL cows were the lowest. Consequently, cows fed SI-TMR had higher yields of milk, 4% fat corrected milk and energy-corrected milk (47.1, 42.9 and 43.2 kg/day, respectively) than cows fed HS-TMR (45.7, 41.0 and 41.0 kg/day, respectively) or HL-TMR (44.1, 40.3 and 40.3 kg/day, respectively). Net energy production (NEL+M+gain) per kg DM intake was highest in the SI-TMR, lowest in the HS-TMR and intermediate in the HL-TMR (1.52, 1.40 and 1.45, respectively). Animal welfare, as expressed in daily recumbence time and BW gain was similar in the SI and HS groups and higher than the HL cows.
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Huang J, Li Y, Luo Y. Bacterial community in the rumen of Tibetan sheep and Gansu alpine fine-wool sheep grazing on the Qinghai-Tibetan Plateau, China. J GEN APPL MICROBIOL 2017; 63:122-130. [PMID: 28239039 DOI: 10.2323/jgam.2016.08.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The rumen microbiome plays a vital role in ruminant nutrition and health, and its community is affected by environmental factors. However, little is known about the rumen bacterial community of ruminants living in the special ecological environment of the Qinghai-Tibetan Plateau (QTP) of China. The objectives of this study were to investigate the rumen bacterial community of the typical plateau sheep (Tibetan sheep, TS, and Gansu alpine fine-wool sheep, GS) grazing on the QTP, using 16S rRNA gene sequence analysis, and to evaluate the relationship between the rumen bacterial community and the QTP environment. A total of 116 sequences (201 clones) were examined and divided into 53 operational taxonomic units (OTUs) in the TS library and 46 OTUs in the GS library. Phylogenetic analysis showed that the sequences that belonged to the Firmicutes were the most predominant bacteria in both TS and GS libraries, representing 79.4% and 62.8% of the total clones, respectively. The remaining sequences belonged to Bacteroidetes, Proteobacteria, Actinobacteria, or were unclassified bacteria. Sequence analysis revealed that the TS and GS rumens harbored many novel sequences associated with uncultured bacteria that accounted for 63.6% and 46.8% of the total clones, respectively. Comparison of the composition and diversity of the TS and GS rumen bacteria revealed few overlapping known bacteria between the two breeds, and a higher diversity in TS. The rumen bacteria of the plateau sheep showed higher percentages of bacteria that belonged to Firmicutes and novel species compared with the low-elevation sheep. The unique bacterial community in the plateau sheep rumens is perhaps one of the major reasons that they can adapt to the harsh plateau environment. These results can help identify the rumen bacterial community of the ruminants in the QTP, and provide bacteria resources and basic data to improve ruminant productivity.
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Affiliation(s)
- Jinqiang Huang
- College of Animal Science and Technology, Gansu Agricultural University
| | - Yongjuan Li
- College of Science, Gansu Agricultural University
| | - Yuzhu Luo
- College of Animal Science and Technology, Gansu Agricultural University.,Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University
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Kala A, Kamra DN, Kumar A, Agarwal N, Chaudhary LC, Joshi CG. Impact of levels of total digestible nutrients on microbiome, enzyme profile and degradation of feeds in buffalo rumen. PLoS One 2017; 12:e0172051. [PMID: 28207851 PMCID: PMC5313230 DOI: 10.1371/journal.pone.0172051] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 01/30/2017] [Indexed: 11/19/2022] Open
Abstract
The present study was aimed at understanding a shift in rumen microbiome of buffaloes fed various levels of total digestible nutrients. To understand the process, the metagenomics of rumen microbes, in vivo and in vitro rumen fermentation studies were carried out. Three rumen fistulated adult male Murrah buffaloes were fed three isonitrogenous diets varying in total digestible nutrients (70, 85 and 100% of TDN requirement) in 3X3 switch over design. On dry matter basis, wheat straw/ roughage content were 81, 63 and 51% and that of maize grain was 8, 16 and 21% in three diets respectively. After 20 d of feeding, rumen liquor and rumen contents were sampled just before (0h) and 4h post feeding. Ruminococcus flavefaciens and R. albus (estimated with real time PCR) were higher in high roughage diets. The predominant phyla in all the three groups were Bacteroidetes, Firmicutes followed by Proteobacteria, Actinobacteria and Fibrobacteres. A core group of more than fifty rumen bacteria was present in all the animals with very little variations due to level of TDN. The most predominant bacterial genera reported in order of decreasing abundance were: Prevotella, Bacteroides, Clostridium, Ruminococcus, Eubacterium, Parabacteroides, Fibrobacter, Butyrivibrio etc. The higher diversity of the enyzmes families GH 23, GH 28, GH 39, GH 97, GH 106, and GH 127 (the enzymes active in fibre and starch degradation) were significantly higher on 100%TDN diet while CE 14 (required for the hydrolysis of bond between carbohydrate and lignin) was higher on low TDN (70%) diet, indicating ester bond cleavage was better in animals fed high roughage (wheat straw) diet.
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Affiliation(s)
- Anju Kala
- ICAR National Professorial Chair, Center of Advanced Faculty Training in Animal Nutrition, Indian Veterinary Research Institute, Izatnagar, India
- * E-mail:
| | - D. N. Kamra
- ICAR National Professorial Chair, Center of Advanced Faculty Training in Animal Nutrition, Indian Veterinary Research Institute, Izatnagar, India
| | - Avinash Kumar
- ICAR National Professorial Chair, Center of Advanced Faculty Training in Animal Nutrition, Indian Veterinary Research Institute, Izatnagar, India
| | - Neeta Agarwal
- ICAR National Professorial Chair, Center of Advanced Faculty Training in Animal Nutrition, Indian Veterinary Research Institute, Izatnagar, India
| | - L. C. Chaudhary
- ICAR National Professorial Chair, Center of Advanced Faculty Training in Animal Nutrition, Indian Veterinary Research Institute, Izatnagar, India
| | - C. G. Joshi
- Dept. of Biotechnology, College of Veterinary Science, Anand Agricultural University, Anand, Gujarat, India
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63
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Wang Z, Elekwachi C, Jiao J, Wang M, Tang S, Zhou C, Tan Z, Forster RJ. Changes in Metabolically Active Bacterial Community during Rumen Development, and Their Alteration by Rhubarb Root Powder Revealed by 16S rRNA Amplicon Sequencing. Front Microbiol 2017; 8:159. [PMID: 28223972 PMCID: PMC5293741 DOI: 10.3389/fmicb.2017.00159] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 01/20/2017] [Indexed: 01/12/2023] Open
Abstract
The objective of this present study was to explore the initial establishment of metabolically active bacteria and subsequent evolution in four fractions: rumen solid-phase (RS), liquid-phase (RL), protozoa-associated (RP), and epithelium-associated (RE) through early weaning and supplementing rhubarb root powder in 7 different age groups (1, 10, 20, 38, 41, 50, and 60 d) during rumen development. Results of the 16S rRNA sequencing based on RNA isolated from the four fractions revealed that the potentially active bacterial microbiota in four fractions were dominated by the phyla Proteobacteria, Firmicutes, and Bacteroidetes regardless of different ages. An age-dependent increment of Chao 1 richness was observed in the fractions of RL and RE. The principal coordinate analysis (PCoA) indicated that samples in four fractions all clustered based on different age groups, and the structure of the bacterial community in RE was distinct from those in other three fractions. The abundances of Proteobacteria decreased significantly (P < 0.05) with age, while increases in the abundances of Firmicutes and Bacteroidetes were noted. At the genus level, the abundance of the predominant genus Mannheimia in the Proteobacteria phylum decreased significantly (P < 0.05) after 1 d, while the genera Quinella, Prevotella, Fretibacterium, Ruminococcus, Lachnospiraceae NK3A20 group, and Atopobium underwent different manners of increases and dominated the bacterial microbiota across four fractions. Variations of the distributions of some specific bacterial genera across fractions were observed, and supplementation of rhubarb affected the relative abundance of various genera of bacteria.
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Affiliation(s)
- Zuo Wang
- Key Laboratory for Agro-Ecological Processes in Subtropical Region, Hunan Research Center of Livestock and Poultry Sciences, South-Central Experimental Station of Animal Nutrition and Feed Science in Ministry of Agriculture, Institute of Subtropical Agriculture, Chinese Academy of SciencesChangsha, China; University of Chinese Academy of SciencesBeijing, China; Lethbridge Research and Development Centre, Agriculture and Agri-Food CanadaLethbridge, AB, Canada
| | - Chijioke Elekwachi
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada Lethbridge, AB, Canada
| | - Jinzhen Jiao
- Key Laboratory for Agro-Ecological Processes in Subtropical Region, Hunan Research Center of Livestock and Poultry Sciences, South-Central Experimental Station of Animal Nutrition and Feed Science in Ministry of Agriculture, Institute of Subtropical Agriculture, Chinese Academy of Sciences Changsha, China
| | - Min Wang
- Key Laboratory for Agro-Ecological Processes in Subtropical Region, Hunan Research Center of Livestock and Poultry Sciences, South-Central Experimental Station of Animal Nutrition and Feed Science in Ministry of Agriculture, Institute of Subtropical Agriculture, Chinese Academy of Sciences Changsha, China
| | - Shaoxun Tang
- Key Laboratory for Agro-Ecological Processes in Subtropical Region, Hunan Research Center of Livestock and Poultry Sciences, South-Central Experimental Station of Animal Nutrition and Feed Science in Ministry of Agriculture, Institute of Subtropical Agriculture, Chinese Academy of Sciences Changsha, China
| | - Chuanshe Zhou
- Key Laboratory for Agro-Ecological Processes in Subtropical Region, Hunan Research Center of Livestock and Poultry Sciences, South-Central Experimental Station of Animal Nutrition and Feed Science in Ministry of Agriculture, Institute of Subtropical Agriculture, Chinese Academy of Sciences Changsha, China
| | - Zhiliang Tan
- Key Laboratory for Agro-Ecological Processes in Subtropical Region, Hunan Research Center of Livestock and Poultry Sciences, South-Central Experimental Station of Animal Nutrition and Feed Science in Ministry of Agriculture, Institute of Subtropical Agriculture, Chinese Academy of Sciences Changsha, China
| | - Robert J Forster
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada Lethbridge, AB, Canada
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64
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Leng RA. Biofilm compartmentalisation of the rumen microbiome: modification of fermentation and degradation of dietary toxins. ANIMAL PRODUCTION SCIENCE 2017. [DOI: 10.1071/an17382] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Many deleterious chemicals in plant materials ingested by ruminants produce clinical effects, varying from losses of production efficiency through to death. Many of the effects are insidious, often going unrecognised by animal managers. When secondary plant compounds enter the rumen, they may undergo modification by rumen microbes, which often removes the deleterious compounds, but in specific instances, the deleterious effect may be enhanced. Improved understanding of rumen ecology, particularly concerning the biofilm mode of microbial fermentation, has led to major advances in our understanding of fermentation. In the present review, the potential impact of the physical structuring of the rumen microbiome is discussed in relation to how several economically important secondary plant compounds and other toxins are metabolised by the rumen microbiome and how their toxic effects may be remedied by providing inert particles with a large surface area to weight ratio in the diet. These particles provide additional surfaces for attachment of rumen microorganisms that help alleviate toxicity problems associated with deleterious compounds, including fluoroacetate, mimosine, mycotoxins, cyanoglycosides and hydrogen cyanide. The review first summarises the basic science of biofilm formation and describes the properties of biofilms and their roles in the rumen. It then addresses how biofilms on inert solids and fermentable particulates may assist in detoxification of potentially toxic compounds. A hypothesis that explains how nitrate poisoning may occur as a result of compartmentalisation of nitrate and nitrite reduction in the rumen is included.
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65
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Liebetrau J, Sträuber H, Kretzschmar J, Denysenko V, Nelles M. Anaerobic Digestion. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2017; 166:281-299. [PMID: 28391363 DOI: 10.1007/10_2016_67] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The term anaerobic digestion usually refers to the microbial conversion of organic material to biogas, which mainly consists of methane and carbon dioxide. The technical application of the naturally-occurring process is used to provide a renewable energy carrier and - as the substrate is often waste material - to reduce the organic matter content of the substrate prior to disposal.Applications can be found in sewage sludge treatment, the treatment of industrial and municipal solid wastes and wastewaters (including landfill gas utilization), and the conversion of agricultural residues and energy crops.For biorefinery concepts, the anaerobic digestion (AD) process is, on the one hand, an option to treat organic residues from other production processes. Concomitant effects are the reduction of organic carbon within the treated substance, the conversion of nitrogen and sulfur components, and the production of an energy-rich gas - the biogas. On the other hand, the multistep conversion of complex organic material offers the possibility of interrupting the conversion chain and locking out intermediates for utilization as basic material within the chemical industry.
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Affiliation(s)
- Jan Liebetrau
- Deutsches Biomasseforschungszentrum DBFZ, Leipzig, Germany.
| | - Heike Sträuber
- Helmholtz-Zentrum für Umweltforschung - UFZ, Leipzig, Germany
| | | | | | - Michael Nelles
- Deutsches Biomasseforschungszentrum DBFZ, Leipzig, Germany.,Universität Rostock, Rostock, Germany
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66
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Coletti Zabala TL, Zerbatto ME, Perotti EBR, Smacchia AM, Ombrella A, Pidello AR. Effect of metronidazole supplemented with hydroquinone on the adhesion of Lactobacillus acidophilus in ovine vaginal cells. Rev Argent Microbiol 2016; 48:313-319. [PMID: 27919512 DOI: 10.1016/j.ram.2016.08.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Revised: 06/09/2016] [Accepted: 08/22/2016] [Indexed: 11/26/2022] Open
Abstract
This work demonstrates that the addition of metronidazole together with a ubiquitous quinone compound reduces adherence of Lactobacillus acidophilus to ovine vaginal cells. Spectrophotometric and voltammetric studies have shown that neoformed compounds were observed in these systems; there were also changes in their electroactive composition, and the oxidant status had a significantly higher value compared to the control (p<0.05). Based on reduction potential (E; mV), the distribution of electroactive compound concentrations suggests that the compounds with low reduction potential induce this behavior, which would indicate that the addition of metronidazole with a ubiquitous quinone compound to the vaginal system might increase the reductive capacity of these systems. This work shows that the study of behavior and fluctuations of the redox compounds that compose the vaginal environment, in terms of concentration and species of redox molecules, must be hierarchized in order to better understand the early stages of colonization by microorganisms.
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Affiliation(s)
- Tamara L Coletti Zabala
- Laboratorio de Química Biológica I, Facultad de Ciencias Veterinarias, Consejo de Investigaciones, Universidad Nacional de Rosario, Santa Fe, Argentina.
| | - María E Zerbatto
- Laboratorio de Química Biológica I, Facultad de Ciencias Veterinarias, Consejo de Investigaciones, Universidad Nacional de Rosario, Santa Fe, Argentina; Cátedra de Microbiología, Facultad de Ciencias Médicas, Universidad Nacional de Rosario, Santa Fe, Argentina
| | - Elda B R Perotti
- Laboratorio de Química Biológica I, Facultad de Ciencias Veterinarias, Consejo de Investigaciones, Universidad Nacional de Rosario, Santa Fe, Argentina
| | - Ana M Smacchia
- Laboratorio de Química Biológica I, Facultad de Ciencias Veterinarias, Consejo de Investigaciones, Universidad Nacional de Rosario, Santa Fe, Argentina
| | - Adriana Ombrella
- Cátedra de Microbiología, Facultad de Ciencias Médicas, Universidad Nacional de Rosario, Santa Fe, Argentina
| | - Alejandro R Pidello
- Laboratorio de Química Biológica I, Facultad de Ciencias Veterinarias, Consejo de Investigaciones, Universidad Nacional de Rosario, Santa Fe, Argentina
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Medjekal S, Ghadbane M, Bodas R, Bousseboua H, López S. Volatile fatty acids and methane production from browse species of Algerian arid and semi-arid areas. JOURNAL OF APPLIED ANIMAL RESEARCH 2016. [DOI: 10.1080/09712119.2016.1257432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Samir Medjekal
- Department of Applied Microbiology, University Mentouri of Constantine, Constantine, Algeria
- Department of Microbiology and Biochemistry, Faculty of Science, University Mohamed Boudiaf of M’sila, M’sila, Algeria
| | - Mouloud Ghadbane
- Department of Microbiology and Biochemistry, Faculty of Science, University Mohamed Boudiaf of M’sila, M’sila, Algeria
| | - Raúl Bodas
- Instituto Tecnológico Agrario de Castilla y León, Subdirección de Investigación y Tecnología, Valladolid, Spain
| | - Hacène Bousseboua
- Ecole Nationale Supérieure de Biotechnologie, Ville universitaire Ali Mendjeli, Ali Mendjeli/Constantine, Algérie
| | - Secundino López
- Instituto de Ganadería de Montaña (IGM) CSIC-Universidad de León, Departamento de Producción Animal, Universidad de León, León, Spain
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68
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Mayorga OL, Kingston-Smith AH, Kim EJ, Allison GG, Wilkinson TJ, Hegarty MJ, Theodorou MK, Newbold CJ, Huws SA. Temporal Metagenomic and Metabolomic Characterization of Fresh Perennial Ryegrass Degradation by Rumen Bacteria. Front Microbiol 2016; 7:1854. [PMID: 27917166 PMCID: PMC5114307 DOI: 10.3389/fmicb.2016.01854] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 11/03/2016] [Indexed: 11/24/2022] Open
Abstract
Understanding the relationship between ingested plant material and the attached microbiome is essential for developing methodologies to improve ruminant nutrient use efficiency. We have previously shown that perennial ryegrass (PRG) rumen bacterial colonization events follow a primary (up to 4 h) and secondary (after 4 h) pattern based on the differences in diversity of the attached bacteria. In this study, we investigated temporal niche specialization of primary and secondary populations of attached rumen microbiota using metagenomic shotgun sequencing as well as monitoring changes in the plant chemistry using mid-infrared spectroscopy (FT-IR). Metagenomic Rapid Annotation using Subsystem Technology (MG-RAST) taxonomical analysis of shotgun metagenomic sequences showed that the genera Butyrivibrio, Clostridium, Eubacterium, Prevotella, and Selenomonas dominated the attached microbiome irrespective of time. MG-RAST also showed that Acidaminococcus, Bacillus, Butyrivibrio, and Prevotella rDNA increased in read abundance during secondary colonization, whilst Blautia decreased in read abundance. MG-RAST Clusters of Orthologous Groups (COG) functional analysis also showed that the primary function of the attached microbiome was categorized broadly within “metabolism;” predominantly amino acid, carbohydrate, and lipid metabolism and transport. Most sequence read abundances (51.6, 43.8, and 50.0% of COG families pertaining to amino acid, carbohydrate and lipid metabolism, respectively) within these categories were higher in abundance during secondary colonization. Kyoto encyclopedia of genes and genomes (KEGG) pathways analysis confirmed that the PRG-attached microbiota present at 1 and 4 h of rumen incubation possess a similar functional capacity, with only a few pathways being uniquely found in only one incubation time point only. FT-IR data for the plant residues also showed that the main changes in plant chemistry between primary and secondary colonization was due to increased carbohydrate, amino acid, and lipid metabolism. This study confirmed primary and secondary colonization events and supported the hypothesis that functional changes occurred as a consequence of taxonomical changes. Sequences within the carbohydrate metabolism COG families contained only 3.2% of cellulose activities, on average across both incubation times (1 and 4 h), suggesting that degradation of the plant cell walls may be a key rate-limiting factor in ensuring the bioavailability of intra-plant nutrients in a timely manner to the microbes and ultimately the animal. This suggests that a future focus for improving ruminant nutrient use efficiency should be altering the recalcitrant plant cell wall components and/or improving the cellulolytic capacity of the rumen microbiota.
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Affiliation(s)
- Olga L Mayorga
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University Aberystwyth, UK
| | - Alison H Kingston-Smith
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University Aberystwyth, UK
| | - Eun J Kim
- Department of Animal Science, Kyungpook National University Sangju, Korea
| | - Gordon G Allison
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University Aberystwyth, UK
| | - Toby J Wilkinson
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University Aberystwyth, UK
| | - Matthew J Hegarty
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University Aberystwyth, UK
| | - Michael K Theodorou
- Department of Animal Production, Welfare and Veterinary Sciences, Harper Adams University Newport, UK
| | - Charles J Newbold
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University Aberystwyth, UK
| | - Sharon A Huws
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University Aberystwyth, UK
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69
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Wang C, Liu Q, Guo G, Huo W, Ma L, Zhang Y, Pei C, Zhang S, Wang H. Effects of rumen-protected folic acid on ruminal fermentation, microbial enzyme activity, cellulolytic bacteria and urinary excretion of purine derivatives in growing beef steers. Anim Feed Sci Technol 2016. [DOI: 10.1016/j.anifeedsci.2016.09.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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70
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Effect of wheat hay particle size and replacement of wheat hay with wheat silage on rumen pH, rumination and digestibility in ruminally cannulated non-lactating cows. Animal 2016; 11:426-435. [PMID: 27609699 DOI: 10.1017/s1751731116001865] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
This study examined the effects on intake, diurnal rumen pH changes, rumination and digestibility of feeding ruminally cannulated non-lactating cows in a Latin square design (four cows×four periods) with four total mixed rations (TMRs) typical for lactating cows. TMRs were based on: long wheat hay or short wheat hay, wheat silage or wheat silage+1.5% NaHCO3 buffer, as the sole roughage source (30% of TMR dry matter (DM)). The level of physically effective NDF remaining above the 8 mm screen (peNDF) was similar in the long hay and silage-based TMRs (9.45% to 9.64% of DM) and lower in the short hay TMR (7.47% of DM). The four TMRs were offered individually at 95% of ad libitum intake to avoid orts within 24 h. Cows fed long hay consumed less DM than the short hay and silage groups (9.6 v. 10.5 and 10.8 kg/day, respectively) and sorted against large hay particles at 12 h post-feeding. Under the limitations of this study (non-lactating cows fed at restricted intake) short hay TMR prevented sorting within 12 h post-feeding, encouraged rumination per kg peNDF ingested, and had higher average rumen pH (6.24), whereas preventing sub acute ruminal acidosis (SARA, defined as pH<5.8 for at least 5 h/day). In contrast, the long hay and silage-based groups were under SARA. In vitro methane production of rumen fluid was higher in the hay-fed cows than in their silage-fed counterparts, and in all treatments lower at 1 h pre-feeding than at 6 h post-feeding. In vivo DM and NDF digestibility were similar for the short hay and silage TMRs, and higher than those of the long hay TMR. Under the conditions of this study, addition of 1.5% buffer to the wheat silage TMR had no effect on intake, rumen pH, creation of SARA and digestibility.
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71
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Franche N, Tardif C, Ravachol J, Harchouni S, Ferdinand PH, Borne R, Fierobe HP, Perret S. Cel5I, a SLH-Containing Glycoside Hydrolase: Characterization and Investigation on Its Role in Ruminiclostridium cellulolyticum. PLoS One 2016; 11:e0160812. [PMID: 27501457 PMCID: PMC4976890 DOI: 10.1371/journal.pone.0160812] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 07/25/2016] [Indexed: 11/19/2022] Open
Abstract
Ruminiclostridium cellulolyticum (Clostridium cellulolyticum) is a mesophilic cellulolytic anaerobic bacterium that produces a multi-enzymatic system composed of cellulosomes and non-cellulosomal enzymes to degrade plant cell wall polysaccharides. We characterized one of the non-cellulosomal enzymes, Cel5I, composed of a Family-5 Glycoside Hydrolase catalytic module (GH5), a tandem of Family-17 and -28 Carbohydrate Binding Modules (CBM), and three S-layer homologous (SLH) modules, where the latter are expected to anchor the protein on the cell surface. Cel5I is the only putative endoglucanase targeting the cell surface as well as the only putative protein in R. cellulolyticum containing CBM17 and/or CBM28 modules. We characterized different recombinant structural variants from Cel5I. We showed that Cel5I has an affinity for insoluble cellulosic substrates through its CBMs, that it is the most active endoglucanase on crystalline cellulose of R. cellulolyticum characterized to date and mostly localized in the cell envelope of R. cellulolyticum. Its role in vivo was analyzed using a R. cellulolyticum cel5I mutant strain. Absence of Cel5I in the cell envelope did not lead to a significant variation of the phenotype compared to the wild type strain. Neither in terms of cell binding to cellulose, nor for its growth on crystalline cellulose, thus indicating that the protein has a rather subtle role in tested conditions. Cel5I might be more important in a natural environment, at low concentration of degradable glucose polymers, where its role might be to generate higher concentration of short cellodextrins close to the cell surface, facilitating their uptake or for signalization purpose.
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Affiliation(s)
| | | | | | | | | | - Romain Borne
- Aix Marseille Univ, CNRS, LCB, Marseille, France
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72
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Yáñez-Ruiz D, Bannink A, Dijkstra J, Kebreab E, Morgavi D, O’Kiely P, Reynolds C, Schwarm A, Shingfield K, Yu Z, Hristov A. Design, implementation and interpretation of in vitro batch culture experiments to assess enteric methane mitigation in ruminants—a review. Anim Feed Sci Technol 2016. [DOI: 10.1016/j.anifeedsci.2016.03.016] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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73
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Khan RU, Naz S, Dhama K, Karthik K, Tiwari R, Abdelrahma MM, Alhidary IA, Zahoor A. Direct-Fed Microbial: Beneficial Applications, Modes of Action and
Prospects as a Safe Tool for Enhancing Ruminant Production and
Safeguarding Health. INT J PHARMACOL 2016. [DOI: 10.3923/ijp.2016.220.231] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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74
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Cobellis G, Trabalza-Marinucci M, Yu Z. Critical evaluation of essential oils as rumen modifiers in ruminant nutrition: A review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2016; 545-546:556-68. [PMID: 26760275 DOI: 10.1016/j.scitotenv.2015.12.103] [Citation(s) in RCA: 124] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Revised: 12/21/2015] [Accepted: 12/21/2015] [Indexed: 05/22/2023]
Abstract
Ruminant livestock systems contribute significantly to emission of methane, a potent greenhouse gas as they waste a portion of the ingested energy (2-15%) as methane and a large proportion (75-95%) of the ingested nitrogen as ammonia. Recently, numerous researches have been conducted to evaluate plant secondary metabolites, including essential oils (EO), as natural feed additives in ruminant nutrition and to exploit their potential to improve rumen fermentation efficiency. Essential oils appeared to be very promising compounds as they selectively reduced methane production and protein breakdown in both in vitro and in vivo studies. However, in some studies, the use of EO as feed additives was accompanied with decreased feed degradability and lowered volatile fatty acid. These adverse effects could be attributed to their broad and often non-specific antimicrobial activities within the rumen. Future research should be directed to identification of the active and useful EO compounds, optimization of EO doses, and use of a whole-farm approach with a focus on animal welfare, performance and economic benefits.
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Affiliation(s)
- Gabriella Cobellis
- Dipartimento di Medicina Veterinaria, Università degli Studi di Perugia, Perugia, Italy; Department of Animal Sciences, The Ohio State University, Columbus, OH 43210, USA.
| | | | - Zhongtang Yu
- Department of Animal Sciences, The Ohio State University, Columbus, OH 43210, USA
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75
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Shinkai T, Mitsumori M, Sofyan A, Kanamori H, Sasaki H, Katayose Y, Takenaka A. Comprehensive detection of bacterial carbohydrate-active enzyme coding genes expressed in cow rumen. Anim Sci J 2016; 87:1363-1370. [PMID: 26875748 DOI: 10.1111/asj.12585] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 10/27/2015] [Accepted: 11/17/2015] [Indexed: 11/29/2022]
Abstract
To find the abundant and characteristic fibrolytic enzyme-coding gene expressed in fiber-associating microbiota, a metatranscriptomic data set was obtained from fiber-associating microbiota, and it was compared with that of rumen fluid-floating microbiota and two metagenomic data sets. Fibrolytic rumen bacteria associate with plant polysaccharide and hydrolyze it in the rumen. We obtained a metatranscriptomic assembly from fiber-associating microbiota in three ruminally fistulated Holstein cows fed timothy (Phleum pratense) hay. Each metatranscriptomic data set involved over a thousand of the glycoside hydrolase (GH) gene transcripts that accounted for about 1% of total protein coding gene transcripts. Three-quarters of the total GH gene transcripts were dominated by non-structural oligosaccharide-acting hydrolase gene transcripts. In the fiber-associating microbiota, endo-cellulase coding gene families, especially GHs 9 and 5, were abundantly detected, and GHs 9, 11, 30 and 43, carbohydrate esterase 8 and carbohydrate-binding module 6 were characteristically detected. Most fibrolytic gene transcripts assigned to Fibrobacter succinogenes were detected in fiber-associating sections, and GHs 45, 44, 74, 11, 30 and 16 were Fibrobacter-characteristically detected. The metatranscriptomic assembly highlighted the characteristic fibrolytic enzymes expressed in the fiber-associated rumen microbiota and offered access to the fibrolytic activities in each fibrolytic bacteria.
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Affiliation(s)
| | - Makoto Mitsumori
- NARO Institute of Livestock and Grassland Science.,Graduate School of Life and Environmental Sciences, University of Tsukuba
| | - Ahmad Sofyan
- Graduate School of Life and Environmental Sciences, University of Tsukuba
| | - Hiroyuki Kanamori
- National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan
| | - Harumi Sasaki
- National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan
| | - Yuichi Katayose
- National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan
| | - Akio Takenaka
- NARO Institute of Livestock and Grassland Science.,National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan
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76
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Abdul Rahman N, Parks DH, Vanwonterghem I, Morrison M, Tyson GW, Hugenholtz P. A Phylogenomic Analysis of the Bacterial Phylum Fibrobacteres. Front Microbiol 2016; 6:1469. [PMID: 26779135 PMCID: PMC4704652 DOI: 10.3389/fmicb.2015.01469] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 12/07/2015] [Indexed: 12/13/2022] Open
Abstract
The Fibrobacteres has been recognized as a bacterial phylum for over a decade, but little is known about the group beyond its environmental distribution, and characterization of its sole cultured representative genus, Fibrobacter, after which the phylum was named. Based on these incomplete data, it is thought that cellulose hydrolysis, anaerobic metabolism, and lack of motility are unifying features of the phylum. There are also contradicting views as to whether an uncultured sister lineage, candidate phylum TG3, should be included in the Fibrobacteres. Recently, chitin-degrading cultured representatives of TG3 were isolated from a hypersaline soda lake, and the genome of one species, Chitinivibrio alkaliphilus, sequenced and described in detail. Here, we performed a comparative analysis of Fibrobacter succinogenes, C. alkaliphilus and eight near or substantially complete Fibrobacteres/TG3 genomes of environmental populations recovered from termite gut, anaerobic digester, and sheep rumen metagenomes. We propose that TG3 should be amalgamated with the Fibrobacteres phylum based on robust monophyly of the two lineages and shared character traits. Polymer hydrolysis, using a distinctive set of glycoside hydrolases and binding domains, appears to be a prominent feature of members of the Fibrobacteres. Not all members of this phylum are strictly anaerobic as some termite gut Fibrobacteres have respiratory chains adapted to the microaerophilic conditions found in this habitat. Contrary to expectations, flagella-based motility is predicted to be an ancestral and common trait in this phylum and has only recently been lost in F. succinogenes and its relatives based on phylogenetic distribution of flagellar genes. Our findings extend current understanding of the Fibrobacteres and provide an improved basis for further investigation of this phylum.
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Affiliation(s)
- Nurdyana Abdul Rahman
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland Brisbane, QLD, Australia
| | - Donovan H Parks
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland Brisbane, QLD, Australia
| | - Inka Vanwonterghem
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of QueenslandBrisbane, QLD, Australia; Advanced Water Management Center, The University of QueenslandBrisbane, QLD, Australia
| | - Mark Morrison
- Microbial Biology and Metagenomics, The University of Queensland Diamantina Institute, Translational Research Institute Brisbane, QLD, Australia
| | - Gene W Tyson
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland Brisbane, QLD, Australia
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of QueenslandBrisbane, QLD, Australia; Genomics and Computational Biology, Institute for Molecular Bioscience, The University of QueenslandBrisbane, QLD, Australia
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Erdem F, Cetinkaya N. Digestibility of Juncus acutusand its effects on ruminal cellulolytic bacteria. ITALIAN JOURNAL OF ANIMAL SCIENCE 2016. [DOI: 10.1080/1828051x.2016.1139327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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78
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Huws SA, Edwards JE, Creevey CJ, Rees Stevens P, Lin W, Girdwood SE, Pachebat JA, Kingston-Smith AH. Temporal dynamics of the metabolically active rumen bacteria colonizing fresh perennial ryegrass. FEMS Microbiol Ecol 2015; 92:fiv137. [PMID: 26542074 DOI: 10.1093/femsec/fiv137] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/03/2015] [Indexed: 01/21/2023] Open
Abstract
This study investigated successional colonization of fresh perennial ryegrass (PRG) by the rumen microbiota over time. Fresh PRG was incubated in sacco in the rumens of three Holstein × Friesian cows over a period of 8 h, with samples recovered at various times. The diversity of attached bacteria was assessed using 454 pyrosequencing of 16S rRNA (cDNA). Results showed that plant epiphytic communities either decreased to low relative abundances or disappeared following rumen incubation, and that temporal colonization of the PRG by the rumen bacteria was biphasic with primary (1 and 2 h) and secondary (4-8 h) events evident with the transition period being with 2-4 h. A decrease in sequence reads pertaining to Succinivibrio spp. and increases in Pseudobutyrivibrio, Roseburia and Ruminococcus spp. (the latter all order Clostridiales) were evident during secondary colonization. Irrespective of temporal changes, the continually high abundances of Butyrivibrio, Fibrobacter, Olsenella and Prevotella suggest that they play a major role in the degradation of the plant. It is clear that a temporal understanding of the functional roles of these microbiota within the rumen is now required to unravel the role of these bacteria in the ruminal degradation of fresh PRG.
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Affiliation(s)
- Sharon A Huws
- Animal and Microbial Sciences, Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth SY23 3FG, UK
| | - Joan E Edwards
- Animal and Microbial Sciences, Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth SY23 3FG, UK
| | - Christopher J Creevey
- Animal and Microbial Sciences, Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth SY23 3FG, UK
| | - Pauline Rees Stevens
- Animal and Microbial Sciences, Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth SY23 3FG, UK
| | - Wanchang Lin
- Animal and Microbial Sciences, Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth SY23 3FG, UK
| | - Susan E Girdwood
- Animal and Microbial Sciences, Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth SY23 3FG, UK
| | - Justin A Pachebat
- Animal and Microbial Sciences, Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth SY23 3FG, UK
| | - Alison H Kingston-Smith
- Animal and Microbial Sciences, Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth SY23 3FG, UK
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79
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Tap J, Furet J, Bensaada M, Philippe C, Roth H, Rabot S, Lakhdari O, Lombard V, Henrissat B, Corthier G, Fontaine E, Doré J, Leclerc M. Gut microbiota richness promotes its stability upon increased dietary fibre intake in healthy adults. Environ Microbiol 2015; 17:4954-64. [DOI: 10.1111/1462-2920.13006] [Citation(s) in RCA: 228] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2015] [Accepted: 07/27/2015] [Indexed: 12/13/2022]
Affiliation(s)
- Julien Tap
- INRA Micalis Institute UMR1319 Jouy‐en‐Josas 78350 France
| | | | | | | | - Hubert Roth
- CHU Grenoble Bioénergétique‐INSERM U1055 Université J. Fourier Grenoble 38000 France
- CRNH Rhône‐Alpes Pierre Benite 69310 France
| | - Sylvie Rabot
- INRA Micalis Institute UMR1319 Jouy‐en‐Josas 78350 France
| | - Omar Lakhdari
- INRA Micalis Institute UMR1319 Jouy‐en‐Josas 78350 France
| | - Vincent Lombard
- Architecture et Fonction des Macromolécules Biologiques Aix‐Marseille Université CNRS UMR 7257, 163 Avenue de Luminy Marseille F‐13288 France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques Aix‐Marseille Université CNRS UMR 7257, 163 Avenue de Luminy Marseille F‐13288 France
| | | | - Eric Fontaine
- CHU Grenoble Bioénergétique‐INSERM U1055 Université J. Fourier Grenoble 38000 France
- CRNH Rhône‐Alpes Pierre Benite 69310 France
| | - Joël Doré
- INRA Micalis Institute UMR1319 Jouy‐en‐Josas 78350 France
| | - Marion Leclerc
- INRA Micalis Institute UMR1319 Jouy‐en‐Josas 78350 France
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80
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Eliyahu D, Yosef E, Weinberg Z, Hen Y, Nikbachat M, Solomon R, Mabjeesh S, Miron J. Composition, preservation and digestibility by sheep of wet by-products from the food industry. Anim Feed Sci Technol 2015. [DOI: 10.1016/j.anifeedsci.2015.05.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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81
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The camel faecal metagenome under different systems of management: Phylogenetic and gene-centric approach. Livest Sci 2015. [DOI: 10.1016/j.livsci.2015.05.024] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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82
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Morrell-Falvey JL, Elkins JG, Wang ZW. Determination of the cellulase activity distribution in Clostridium thermocellum and Caldicellulosiruptor obsidiansis cultures using a fluorescent substrate. J Environ Sci (China) 2015; 34:212-218. [PMID: 26257364 DOI: 10.1016/j.jes.2015.03.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2014] [Revised: 03/13/2015] [Accepted: 03/16/2015] [Indexed: 06/04/2023]
Abstract
This study took advantage of resorufin cellobioside as a fluorescent substrate to determine the distribution of cellulase activity in cellulosic biomass fermentation systems. Cellulolytic biofilms were found to express nearly four orders greater cellulase activity compared to planktonic cultures of Clostridium thermocellum and Caldicellulosiruptor obsidiansis, which can be primarily attributed to the high cell concentration and surface attachment. The formation of biofilms results in cellulases being secreted close to their substrates, which appears to be an energetically favorable stategy for insoluble substrate utilization. For the same reason, cellulases should be closely associated with the surfaces of suspended cell in soluble substrate-fed culture, which has been verified with cellobiose-fed cultures of C. thermocellum and C. obsidiansis. This study addressed the importance of cellulase activity distribution in cellulosic biomass fermentation, and provided theoretical foundation for the leading role of biofilm in cellulose degradation. System optimization and reactor designs that promote biofilm formation in cellulosic biomass hydrolysis may promise an improved cellulosic biofuel process.
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Affiliation(s)
- Jennifer L Morrell-Falvey
- BioEnergy Science Center, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - James G Elkins
- BioEnergy Science Center, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Zhi-Wu Wang
- BioEnergy Science Center, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; The Ohio State University ATI, 1328 Dover Rd, Wooster, OH 44691, USA.
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83
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Deusch S, Seifert J. Catching the tip of the iceberg - Evaluation of sample preparation protocols for metaproteomic studies of the rumen microbiota. Proteomics 2015; 15:3590-5. [DOI: 10.1002/pmic.201400556] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Revised: 01/29/2015] [Accepted: 03/10/2015] [Indexed: 11/11/2022]
Affiliation(s)
- Simon Deusch
- Institute of Animal Science; University of Hohenheim; Stuttgart Germany
| | - Jana Seifert
- Institute of Animal Science; University of Hohenheim; Stuttgart Germany
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84
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Abstract
Endodontic disease is a biofilm-mediated infection, and primary aim in the management of endodontic disease is the elimination of bacterial biofilm from the root canal system. The most common endodontic infection is caused by the surface-associated growth of microorganisms. It is important to apply the biofilm concept to endodontic microbiology to understand the pathogenic potential of the root canal microbiota as well as to form the basis for new approaches for disinfection. It is foremost to understand how the biofilm formed by root canal bacteria resists endodontic treatment measures. Bacterial etiology has been confirmed for common oral diseases such as caries and periodontal and endodontic infections. Bacteria causing these diseases are organized in biofilm structures, which are complex microbial communities composed of a great variety of bacteria with different ecological requirements and pathogenic potential. The biofilm community not only gives bacteria effective protection against the host's defense system but also makes them more resistant to a variety of disinfecting agents used as oral hygiene products or in the treatment of infections. Successful treatment of these diseases depends on biofilm removal as well as effective killing of biofilm bacteria. So, the fundamental to maintain oral health and prevent dental caries, gingivitis, and periodontitis is to control the oral biofilms. From these aspects, the formation of biofilms carries particular clinical significance because not only host defense mechanisms but also therapeutic efforts including chemical and mechanical antimicrobial treatment measures have the most difficult task of dealing with organisms that are gathered in a biofilm. The aim of this article was to review the mechanisms of biofilms’ formation, their roles in pulpal and periapical pathosis, the different types of biofilms, the factors influencing biofilm formation, the mechanisms of their antimicrobial resistance, techniques to identify biofilms.
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Affiliation(s)
- Kapil Jhajharia
- Department of Conservative Dentistry and Endodontics, Faculty of Dentistry, Melaka Manipal Medical College, Melaka, Malaysia
| | - Abhishek Parolia
- Department of Restorative Dentistry, Faculty of Dentistry, International Medical University, Kuala Lumpur, Malaysia
| | - K Vikram Shetty
- Department of Conservative Dentistry and Endodontics, Faculty of Dentistry, Melaka Manipal Medical College, Melaka, Malaysia
| | - Lata Kiran Mehta
- Department of Pedodontics and Preventive Dentistry, P. D. M. Dental College and Research Institute, Jhajjar, Haryana, India
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85
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Singh KM, Patel AK, Shah RK, Reddy B, Joshi CG. Potential functional gene diversity involved in methanogenesis and methanogenic community structure in Indian buffalo (Bubalus bubalis) rumen. J Appl Genet 2015; 56:411-26. [PMID: 25663664 DOI: 10.1007/s13353-015-0270-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Revised: 12/26/2014] [Accepted: 01/06/2015] [Indexed: 11/26/2022]
Abstract
Understanding the methanogen community structure and methanogenesis from Bubalus bubalis in India may be beneficial to methane mitigation. Our current understanding of the microbial processes leading to methane production is incomplete, and further advancement in the knowledge of methanogenesis pathways would provide means to manipulate its emission in the future. In the present study, we evaluated the methanogenic community structure in the rumen as well as their potential genes involved in methanogenesis. The taxonomic and metabolic profiles of methanogens were assessed by shotgun sequencing of rumen metagenome by Ion Torrent semiconductor sequencing. The buffalo rumen contained representative genera of all the families of methanogens. Members of Methanobacteriaceae were found to be dominant, followed by Methanosarcinaceae, Methanococcaceae, Methanocorpusculaceae, and Thermococcaceae. A total of 60 methanogenic genera were detected in buffalo rumen. Methanogens related to the genera Methanobrevibacter, Methanosarcina, Methanococcus, Methanocorpusculum, Methanothermobacter, and Methanosphaera were predominant, representing >70 % of total archaeal sequences. The metagenomic dataset indicated the presence of genes involved in the methanogenesis and acetogenesis pathways, and the main functional genes were those of key enzymes in the methanogenesis. Sequences related to CoB--CoM heterodisulfide reductase, methyl coenzyme M reductase, f420-dependent methylenetetrahydromethanopterin reductase, and formylmethanofuran dehydrogenase were predominant in rumen. In addition, methenyltetrahydrofolate cyclohydrolase, methylenetetrahydrofolate dehydrogenase, 5,10-methylenetetrahydrofolate reductase, and acetyl-coenzyme A synthetase were also recovered.
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Affiliation(s)
- Krishna M Singh
- Department of Animal Biotechnology, Anand Agricultural University, Anand, India,
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86
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Tsuji R, Koizumi H, Aoki D, Watanabe Y, Sugihara Y, Matsushita Y, Fukushima K, Fujiwara D. Lignin-rich enzyme lignin (LREL), a cellulase-treated lignin-carbohydrate derived from plants, activates myeloid dendritic cells via Toll-like receptor 4 (TLR4). J Biol Chem 2014; 290:4410-21. [PMID: 25548274 DOI: 10.1074/jbc.m114.593673] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Lignin-carbohydrates, one of the major cell wall components, are believed to be the structures that form chemical linkage between lignin and cell wall polysaccharides. Due to the molecular complexity of lignin-containing substances, their isolation and the assignment of their biological activities have so far remained a difficult task. Here, we extracted two lignin-containing carbohydrates, lignin-rich enzyme lignin (LREL) and pure enzyme lignin (PEL), from barley husk and demonstrated that they act as immune stimulators of dendritic cells (DCs), which are particularly important in linking innate and adaptive immunity. Thioacidolysis, acid hydrolysis, and mild alkali hydrolysis of both LREL and PEL revealed that their immunostimulatory activities depended on the lignin structure and/or content, neutral sugar content (especially the characteristic distribution of galactose and mannose), and presence of an ester bond. Furthermore, we showed that the immunostimulatory potency of the lignin-carbohydrate depended on its molecular weight and degree of polymerization. We also demonstrated that the LREL-induced activation of DCs was mediated via TLR4. Thus, LREL-induced increases in the expression levels of several cell surface marker proteins, production of inflammatory cytokines IL-12p40 and TNF-α, and activation and nuclear translocation of transcription factors, as was observed in the WT DCs, were completely abrogated in DCs derived from the TLR4(-/-) mice but not in DCs derived from the TLR2(-/-), TLR7(-/-), and TLR9(-/-) mice. We further demonstrated that LRELs isolated from other plant tissues also activated DCs. These immunostimulatory activities of lignin-carbohydrates, extracted from edible plant tissues, could have potential relevance in anti-infectious immunity and vaccine adjuvants.
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Affiliation(s)
- Ryohei Tsuji
- From the Central Laboratories for Key Technologies, Kirin Co, Ltd., 1-13-5 Fukuura, Kanazawa, Yokohama 236-0004, Japan and
| | - Hideki Koizumi
- From the Central Laboratories for Key Technologies, Kirin Co, Ltd., 1-13-5 Fukuura, Kanazawa, Yokohama 236-0004, Japan and
| | - Dan Aoki
- the Division of Biological Material Sciences, Department of Biosphere Resources Science, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Yuta Watanabe
- From the Central Laboratories for Key Technologies, Kirin Co, Ltd., 1-13-5 Fukuura, Kanazawa, Yokohama 236-0004, Japan and
| | - Yoshihiko Sugihara
- From the Central Laboratories for Key Technologies, Kirin Co, Ltd., 1-13-5 Fukuura, Kanazawa, Yokohama 236-0004, Japan and
| | - Yasuyuki Matsushita
- the Division of Biological Material Sciences, Department of Biosphere Resources Science, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Kazuhiko Fukushima
- the Division of Biological Material Sciences, Department of Biosphere Resources Science, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Daisuke Fujiwara
- From the Central Laboratories for Key Technologies, Kirin Co, Ltd., 1-13-5 Fukuura, Kanazawa, Yokohama 236-0004, Japan and
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87
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Silva T, Santos E, Macedo C, Lima M, Azevedo J, Pinho R, Perazzo A, Oliveira J. Cinética de fermentação ruminal in vitro de silagens de híbridos de sorgo. ARQ BRAS MED VET ZOO 2014. [DOI: 10.1590/1678-6221] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Objetivou-se com esta pesquisa avaliar as silagens de 23 híbridos de sorgo por meio da técnica in vitro semiautomática de produção de gases. Foi utilizado o delineamento inteiramente ao acaso, com 23 tratamentos e três repetições, sendo os tratamentos as silagens de híbridos de sorgo. Os híbridos foram cultivados na estação experimental do Instituto Nacional do Semiárido (INSA), no município de Campina Grande - PB. A produção de gases foi estimada por intermédio do modelo logístico bicompartimental, ajustado às curvas de produção cumulativa de gases. Com relação ao volume final de carboidratos fibrosos (VfCF), houve efeito de híbrido (P<0,05), com resultados variando de 105,99 a 144,53mL/g de MS. Os valores de taxa de degradação dos carboidratos fibrosos (KdCF) variaram (P<0,05), e o híbrido 866041 apresentou o maior resultado 0,015h-1. Os valores de volume final total (VfT) variaram (P<0,05), e os híbridos 870085, Volumax e XBS 60329 apresentaram maiores (P<0,05) valores de VfT em relação aos demais. Pela análise multivariada, foram formados seis grupos distintos. O grupo 2, composto pelos híbridos 22 (Volumax) e 23 (XBS60329), apresentou os maiores valores médios para os volumes de gás, tanto para os carboidratos fibrosos quanto para os não fibrosos. O grupo 4, composto pelo híbrido 1 (866005), apresentou as menores médias para volume de gás produzido e o maior lag time (3,15 horas). Todos os híbridos estudados apresentam potencial para ensilagem, de acordo com a cinética de fermentação ruminal.
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88
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Hydrogen formation and its regulation in Ruminococcus albus: involvement of an electron-bifurcating [FeFe]-hydrogenase, of a non-electron-bifurcating [FeFe]-hydrogenase, and of a putative hydrogen-sensing [FeFe]-hydrogenase. J Bacteriol 2014; 196:3840-52. [PMID: 25157086 DOI: 10.1128/jb.02070-14] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Ruminococcus albus 7 has played a key role in the development of the concept of interspecies hydrogen transfer. The rumen bacterium ferments glucose to 1.3 acetate, 0.7 ethanol, 2 CO2, and 2.6 H2 when growing in batch culture and to 2 acetate, 2 CO2, and 4 H2 when growing in continuous culture in syntrophic association with H2-consuming microorganisms that keep the H2 partial pressure low. The organism uses NAD(+) and ferredoxin for glucose oxidation to acetyl coenzyme A (acetyl-CoA) and CO2, NADH for the reduction of acetyl-CoA to ethanol, and NADH and reduced ferredoxin for the reduction of protons to H2. Of all the enzymes involved, only the enzyme catalyzing the formation of H2 from NADH remained unknown. Here, we report that R. albus 7 grown in batch culture on glucose contained, besides a ferredoxin-dependent [FeFe]-hydrogenase (HydA2), a ferredoxin- and NAD-dependent electron-bifurcating [FeFe]-hydrogenase (HydABC) that couples the endergonic formation of H2 from NADH to the exergonic formation of H2 from reduced ferredoxin. Interestingly, hydA2 is adjacent to the hydS gene, which is predicted to encode an [FeFe]-hydrogenase with a C-terminal PAS domain. We showed that hydS and hydA2 are part of a larger transcriptional unit also harboring putative genes for a bifunctional acetaldehyde/ethanol dehydrogenase (Aad), serine/threonine protein kinase, serine/threonine protein phosphatase, and a redox-sensing transcriptional repressor. Since HydA2 and Aad are required only when R. albus grows at high H2 partial pressures, HydS could be a H2-sensing [FeFe]-hydrogenase involved in the regulation of their biosynthesis.
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89
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Kang S, Wanapat M. Using Plant Source as a Buffering Agent to Manipulating Rumen Fermentation in an In vitro Gas Production System. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2014; 26:1424-36. [PMID: 25049726 PMCID: PMC4093070 DOI: 10.5713/ajas.2013.13153] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Revised: 06/13/2013] [Accepted: 05/19/2013] [Indexed: 11/27/2022]
Abstract
The objective of this study was to investigate the effect of banana flower powder (BAFLOP) supplementation on gas production kinetics and rumen fermentation efficiency in in vitro incubation with different ratios of roughage to concentrate in swamp buffalo and cattle rumen fluid. Two male, rumen fistulated dairy steers and swamp buffaloes were used as rumen fluid donors. The treatments were arranged according to a 2×2×3 factorial arrangement in a Completely randomized design by using two ratios of roughage to concentrate (R:C; 75:25 and 25:75) and 3 levels of BAFLOP supplementation (0, 2 and 4% of dietary substrate) into two different kinds of rumen fluid (beef cattle and swamp buffalo). Under this investigation, the results revealed that the rumen ecology was affected by R:C ratio. The pH declined as a result of using high concentrate ratio; however, supplementation of BAFLOP could buffer the pH which led to an improvement of ruminal efficiency. BAFLOP supplementation affected acetic acid (C2) when the proportion of concentrate was increased. However, there were no effect on total volatile fatty acid (TVFA) and butyric acid (C4) by BAFLOP supplementation. The microbial community was affected by BAFLOP supplementation, especially the bacterial population. As revealed by real-time PCR, the populations of F. succinogenes and R. albus were reduced by the high concentrate treatments while that of R. flavafaciens were increased. The populations of three dominant cellulolytic bacteria were enhanced by BAFLOP supplementation, especially on high concentrate diet. BAFLOP supplementation did not influence the ammonia nitrogen (NH3-N) concentration, while R:C did. In addition, the in vitro digestibility was improved by either R:C or BAFLOP supplementation. The BAFLOP supplementation showed an effect on gas production kinetics, except for the gas production rate constant for the insoluble fraction (c), while treatments with high concentrate ratio resulted in the highest values. In addition, BAFLOP tended to increase gas production. Based on this study, it could be concluded that R:C had an effect on rumen ecology both in buffalo and cattle rumen fluid and hence, BAFLOP could be used as a rumen buffering agent for enhancing rumen ecology fed on high concentrate diet. It is recommended that level of BAFLOP supplementation should be at 2 to 4% of total dry matter of substrate. However, in vivo trials should be subsequently conducted to investigate the effect of BAFLOP in high concentrate diets on rumen ecology as well as ruminant production.
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Affiliation(s)
- S Kang
- Tropical Feed Resources Research and Development Center (TROFREC), Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002, Thailand
| | - M Wanapat
- Tropical Feed Resources Research and Development Center (TROFREC), Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002, Thailand
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90
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Kim MJ, Sung HG, Upadhaya SD, Ha JK, Lee SS. Effects of Methylcellulose on Fibrolytic Bacterial Detachment and In vitro Degradation of Rice Straw. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2014; 26:1459-65. [PMID: 25049729 PMCID: PMC4093079 DOI: 10.5713/ajas.2013.13220] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Revised: 06/24/2013] [Accepted: 06/04/2013] [Indexed: 11/27/2022]
Abstract
Two in vitro experiments were conducted to evaluate the effect of methylcellulose (MC) on i) bacterial detachment from rice straw as well as ii) inhibition of bacterial attachment and fiber digestibility. To evaluate the effect of MC on fibrolytic bacterial detachment (Exp 1), in vitro bacterial cultures with 0.1% (w/v) MC solution were compared with cultures without MC after 8 h incubation. The effect of MC on inhibition of bacterial attachment was determined by comparing with real-time PCR the populations of F. succinogenes, R. flavefaciens and R. albus established on rice straw pre-treated with 0.1% MC with those on untreated straw after incubation for 0, 6 and 12 h (Exp 2). The major fibrolytic bacterial attachment on rice straw showed significantly lower populations with either the addition of MC to the culture or pre-treated rice straw compared to controls (p<0.05). Also, the digestibility of rice straw with MC was significantly lower compared with control (p<0.05). The F. succinogenes population did not show detachment from rice straw, but showed an inhibition of attachment and proliferation on rice straw in accordance with a decrease of fiber digestion. The detachments of Ruminococcus species co-existed preventing the proliferations with subsequent reduction of fiber degradation by MC during the incubation. Their detachments were induced from stable colonization as well as the initial adhesion on rice straw by MC in in vitro ruminal fermentation. Furthermore, the detachment of R. albus was more sensitive to MC than was R. flavefaciens. These results showed the certain evidence that attachment of major fibrolytic bacteria had an effect on fiber digestion in the rumen, and each of fibrolytic bacteria, F. succinogenes, R. flavefaciens and R. albus had a specific mechanism of attachment and detachment to fiber.
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Affiliation(s)
- Min Ji Kim
- Department of Animal Science and Technology, Sangji University, Wonju, 220-702, Korea
| | - Ha Guyn Sung
- Department of Animal Science and Technology, Sangji University, Wonju, 220-702, Korea
| | - Santi Devi Upadhaya
- Department of Animal Science and Technology, Sangji University, Wonju, 220-702, Korea
| | - Jong K Ha
- Department of Animal Science and Technology, Sangji University, Wonju, 220-702, Korea
| | - Sung Sill Lee
- Division of Applied Life Science and IALS, Gyeongsang National University, Jinju 660-701, Korea
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91
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Anantasook N, Wanapat M. Influence of Rain Tree Pod Meal Supplementation on Rice Straw Based Diets Using In vitro Gas Fermentation Technique. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2014; 25:325-34. [PMID: 25049570 PMCID: PMC4092966 DOI: 10.5713/ajas.2011.11131] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2011] [Revised: 07/26/2011] [Accepted: 07/22/2011] [Indexed: 11/27/2022]
Abstract
The objective of this study was to determine the roughage to concentrate (R:C) ratio with rain tree pod meal (RPM) supplementation on in vitro fermentation using gas production technique. The experiment design was a 6×4 factorial arrangement in a CRD. Factor A was 6 levels of R:C ratio (100:0, 80:20, 60:40, 40:60, 20:80 and 0:100) and factor B was 4 levels of RPM (0, 4, 8 and 12 mg). It was found that gas kinetic, extent rate (c) was linearly increased (p<0.01) with an increasing level of concentrate while cumulative gas production (96 h) was higher in R:C of 40:60. In addition, interaction of R:C ratio and RPM level affected NH3-N and IVDMD and were highest in R:C of 0:100 with 0, 4 mg of RPM and 40:60 with 8 mg of RPM, respectively. Moreover, interaction of R:C ratio and RPM level significantly increased total volatile fatty acids and propionate concentration whereas lower acetate, acetate to propionate ratios and CH4 production in R:C of 20:80 with 8 mg of RPM. Moreover, the two factors, R:C ratio and RPM level influenced the protozoal population and the percentage of methanogens in the total bacteria population. In addition, the use of real-time PCR found that a high level of concentrate in the diet remarkably decreased three cellulolytic bacteria numbers (F. succinogenes, R. flavefaciens and R. albus). Based on this study, it is suggested that the ratio of R:C at 40:60 and RPM level at 12 mg could improve ruminal fluid fermentation in terms of reducing fermentation losses, thus improving VFA profiles and ruminal ecology.
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92
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High potential source for biomass degradation enzyme discovery and environmental aspects revealed through metagenomics of Indian buffalo rumen. BIOMED RESEARCH INTERNATIONAL 2014; 2014:267189. [PMID: 25136572 PMCID: PMC4124647 DOI: 10.1155/2014/267189] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Revised: 06/04/2014] [Accepted: 06/05/2014] [Indexed: 11/17/2022]
Abstract
The complex microbiomes of the rumen functions as an effective system for plant cell wall degradation, and biomass utilization provide genetic resource for degrading microbial enzymes that could be used in the production of biofuel. Therefore the buffalo rumen microbiota was surveyed using shot gun sequencing. This metagenomic sequencing generated 3.9 GB of sequences and data were assembled into 137270 contiguous sequences (contigs). We identified potential 2614 contigs encoding biomass degrading enzymes including glycoside hydrolases (GH: 1943 contigs), carbohydrate binding module (CBM: 23 contigs), glycosyl transferase (GT: 373 contigs), carbohydrate esterases (CE: 259 contigs), and polysaccharide lyases (PE: 16 contigs). The hierarchical clustering of buffalo metagenomes demonstrated the similarities and dissimilarity in microbial community structures and functional capacity. This demonstrates that buffalo rumen microbiome was considerably enriched in functional genes involved in polysaccharide degradation with great prospects to obtain new molecules that may be applied in the biofuel industry.
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93
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Seasonal effect on rumen function in sheep on range in the Accra Plains of Ghana. Trop Anim Health Prod 2014; 46:1223-8. [PMID: 24996816 DOI: 10.1007/s11250-014-0629-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/24/2014] [Indexed: 10/25/2022]
Abstract
This study aimed at investigating the effect of the seasonal decline in quality and availability of feed on rumen function in sheep grazing without supplementation. Effects of season on rumen pH, ammonia nitrogen concentration and rumen degradation of urea-treated rice straw in grazing sheep were determined. Four fistulated Djallonké sheep were added to a group of grazing sheep and used for this study. Rumen contents were sampled for pH and ammonia in the rainy season and in the dry season. Ammoniated rice straw was incubated in the rumen to determine its degradation characteristics. Rumen pH was higher (p < 0.1) in the dry season than in the rainy season. Rumen ammonia nitrogen concentrations on the other hand were similar (p > 0.05) in the two seasons. In sacco dry matter degradation parameters of urea-ammoniated rice straw showed seasonal differences in the soluble (a) and the insoluble but degradable (b) fractions as well as lag time before the start of degradation. It was concluded that despite higher pH in the dry season and similar ammonia nitrogen concentration in the two seasons, rumen degradability of dry matter of urea-treated rice straw in sheep was higher in the rainy season than that in the dry season.
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94
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The effect of fibre source on the numbers of some fibre-degrading bacteria of Arabian camel's (Camelus dromedarius) foregut origin. Trop Anim Health Prod 2014; 46:1161-6. [PMID: 24898095 DOI: 10.1007/s11250-014-0621-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/23/2014] [Indexed: 10/25/2022]
Abstract
The total bacterial community of Fibrobacter succinogenes and Ruminococcus flavefaciens in fibre-enriched culture of the foregut contents of 12 adult feral camels (Camelus dromedaries) fed on native vegetation in Australia was investigated using quantitative PCR. Foregut contents were collected postmortem, pooled and filtered before divided into two fractions. One fraction was used for extraction of DNA, while the other fraction was inoculated straight away into BM 10 contained filter paper (FP), cotton thread (CT) or neutral detergent fibre (NDF) as the sole carbohydrate sources in Hungate tubes. The tubes were incubated anaerobically at 39 °C for 1 week. After a near complete degradation of the FP and CT and extensive turbidity in the NDF, media subculturing was carried out into fresh media tubes. This was repeated twice before genomic DNA was extracted and used for quantification of bacteria. Using an absolute quantification method, the numbers of cells in 1 ml of each sample ranged from 4.07 × 10(6) to 2.73 × 10(9) for total bacteria, 1.34 × 10(3) to 2.17 × 10(5) for F. succinogenes and 5.78 × 10(1) to 3.53 × 10(4) for R. flavefaciens. The mean cell number of F. succinogenes was highest in the FP enrichment medium at approximately 107-fold, whereas for the R. flavefaciens targeted primer, the NDF enrichment media had the highest mean cell number at approximately 4-fold when compared to the rumen content. The data presented here provide evidence of fibre type preference by the two main fibre-degrading bacteria and would help us understand the interaction between fibre type and fibre-degrading microorganisms, which has ramification on camel nutrition at different seasons and environments.
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95
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Mikaelyan A, Strassert JFH, Tokuda G, Brune A. The fibre-associated cellulolytic bacterial community in the hindgut of wood-feeding higher termites (Nasutitermesspp.). Environ Microbiol 2014. [DOI: 10.1111/1462-2920.12425] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Aram Mikaelyan
- Department of Biogeochemistry; Max Planck Institute for Terrestrial Microbiology; Marburg Germany
| | - Jürgen F. H. Strassert
- Department of Biogeochemistry; Max Planck Institute for Terrestrial Microbiology; Marburg Germany
| | - Gaku Tokuda
- Tropical Biosphere Research Center; COMB; University of the Ryukyus; Nishihara Okinawa Japan
| | - Andreas Brune
- Department of Biogeochemistry; Max Planck Institute for Terrestrial Microbiology; Marburg Germany
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96
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Singh KM, Pandya PR, Tripathi AK, Patel GR, Parnerkar S, Kothari RK, Joshi CG. Study of rumen metagenome community using qPCR under different diets. Meta Gene 2014; 2:191-9. [PMID: 25606402 PMCID: PMC4287863 DOI: 10.1016/j.mgene.2014.01.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2013] [Revised: 12/23/2013] [Accepted: 01/06/2014] [Indexed: 01/06/2023] Open
Abstract
The aim of this study was to detect the major bacteria present in rumen microbiota. Here, we performed qPCR based absolute quantitation of selected rumen microbes in rumen fluid of river buffalo adapted to varying proportion of concentrate to roughage diets. Animals were adapted to roughage-to-concentrate ratio in the proportion of 100:00 (T1), 75:25 (T2), 50:50 (T3) and 25:75 (T4) respectively for 30 days. At the end of each treatment, rumen fluid was collected at 0 h and 2 h after feeding. It was found that among fibrolytic bacteria Ruminococcus flavefaciens (2.22 × 10(8) copies/ml) were highest in T2 group and followed by 1.11 × 10(8) copies/ml for Fibrobacter succinogenes (T2), 2.56 × 10(7) copies/ml for Prevotella ruminicola (T1) and 1.25 × 10(7) copies/ml for Ruminococcus albus (T4). In non-fibrolytic bacteria, the Selenomonas ruminantium (2.62 × 10(7) copies/ml) was predominant in group T3 and followed by Treponema bryantii (2.52 × 10(7)copies/ml) in group T1, Ruminobacter amylophilus (1.31 × 10(7)copies/ml) in group T1 and Anaerovibrio lipolytica (2.58 × 10(6) copies/ml) in group T4. It is most notable that R. flavefaciens were the highest in population in the rumen of Surti buffalo fed wheat straw as roughage source.
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Affiliation(s)
- K M Singh
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand 388 001, Gujarat, India
| | - P R Pandya
- Animal Nutrition Research Station, AAU, Anand, Gujarat, India
| | - A K Tripathi
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand 388 001, Gujarat, India
| | - G R Patel
- Animal Nutrition Research Station, AAU, Anand, Gujarat, India
| | - S Parnerkar
- Animal Nutrition Research Station, AAU, Anand, Gujarat, India
| | - R K Kothari
- Department of Microbiology, Christ College, Rajkot, Gujarat, India
| | - C 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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97
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Mirón L, Mira A, Rocha-Ramírez V, Belda-Ferre P, Cabrera-Rubio R, Folch-Mallol J, Cardénas-Vázquez R, DeLuna A, Hernández AL, Maya-Elizarrarás E, Schondube JE. Gut Bacterial Diversity of the House Sparrow (Passer domesticus) Inferred by 16S rRNA Sequence Analysis. ACTA ACUST UNITED AC 2014. [DOI: 10.4303/mg/235853] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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98
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Wang ZW, Li Y. A theoretical derivation of the Contois equation for kinetic modeling of the microbial degradation of insoluble substrates. Biochem Eng J 2014. [DOI: 10.1016/j.bej.2013.11.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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99
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Chapleur O, Bize A, Serain T, Mazéas L, Bouchez T. Co-inoculating ruminal content neither provides active hydrolytic microbes nor improves methanization of13C-cellulose in batch digesters. FEMS Microbiol Ecol 2013; 87:616-29. [DOI: 10.1111/1574-6941.12249] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Revised: 10/25/2013] [Accepted: 11/08/2013] [Indexed: 11/29/2022] Open
Affiliation(s)
- Olivier Chapleur
- Hydrosystems and Bioprocesses Research Unit; Irstea; Antony Cedex France
| | - Ariane Bize
- Hydrosystems and Bioprocesses Research Unit; Irstea; Antony Cedex France
| | - Thibaut Serain
- Hydrosystems and Bioprocesses Research Unit; Irstea; Antony Cedex France
| | - Laurent Mazéas
- Hydrosystems and Bioprocesses Research Unit; Irstea; Antony Cedex France
| | - Théodore Bouchez
- Hydrosystems and Bioprocesses Research Unit; Irstea; Antony Cedex France
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100
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Gomes G, Vasconcelos A, Egito A, Lima A, Carneiro J, Landim A, Fonteles N, Salles H. Degradabilidade in situ do bagaço de cana-de-açúcar para pequenos ruminantes de raças naturalizadas do Nordeste brasileiro. ARQ BRAS MED VET ZOO 2013. [DOI: 10.1590/s0102-09352013000600029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Com o crescimento da indústria sucroalcooleira, buscam-se alternativas de uso dos resíduos gerados por ela. Os pequenos ruminantes de raças naturalizadas do Nordeste brasileiro mostram-se como grupos potenciais para que seja utilizado o bagaço de cana-de-açúcar (BCA) nas dietas. Nesse contexto, objetivou-se determinar a degradabilidade ruminal in situ da matéria seca (MS) e da fibra em detergente neutro (FDN) do BCA e os parâmetros ruminais em caprinos Moxotó e ovinos Morada Nova, fistulados no rúmen. Contidos em sacos de náilon, 3g de BCA foram incubados no rúmen nos tempos seis, 24 e 96 horas, determinando-se o conteúdo de MS e FDN nos resíduos obtidos. Nos tempos zero, seis e 12 horas após a primeira refeição, mediram-se no líquido ruminal pH e nitrogênio amoniacal (N-NH3) ruminal. O CMS não diferiu entre caprinos e ovinos. O potencial de máxima degradação da MS foi semelhante entre espécies, e da FDN foi superior em caprinos. Ovinos apresentaram maiores tempo de colonização, taxa de degradação e degradabilidade efetiva da MS e FDN. O pH não diferiu entre as espécies. Observou-se maior concentração de N-NH3 ruminal em caprinos, no tempo zero. Diante da maior velocidade de degradação da MS do BCA pelos ovinos, essa espécie se mostra detentora de uma microbiota ruminal com crescimento mais eficiente sobre o BCA.
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