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Beecher M, Buckley F, Waters SM, Boland TM, Enriquez-Hidalgo D, Deighton MH, O'Donovan M, Lewis E. Gastrointestinal tract size, total-tract digestibility, and rumen microflora in different dairy cow genotypes. J Dairy Sci 2014; 97:3906-17. [PMID: 24704226 DOI: 10.3168/jds.2013-7708] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Accepted: 02/11/2014] [Indexed: 11/19/2022]
Abstract
The superior milk production efficiency of Jersey (JE) and Jersey × Holstein-Friesian (JE × HF) cows compared with Holstein-Friesian (HF) has been widely published. The biological differences among dairy cow genotypes, which could contribute to the milk production efficiency differences, have not been as widely studied however. A series of component studies were conducted using cows sourced from a longer-term genotype comparison study (JE, JE × HF, and HF). The objectives were to (1) determine if differences exist among genotypes regarding gastrointestinal tract (GIT) weight, (2) assess and quantify whether the genotypes tested differ in their ability to digest perennial ryegrass, and (3) examine the relative abundance of specific rumen microbial populations potentially relating to feed digestibility. Over 3 yr, the GIT weight was obtained from 33 HF, 35 JE, and 27 JE × HF nonlactating cows postslaughter. During the dry period the cows were offered a perennial ryegrass silage diet at maintenance level. The unadjusted GIT weight was heavier for the HF than for JE and JE × HF. When expressed as a proportion of body weight (BW), JE and JE × HF had a heavier GIT weight than HF. In vivo digestibility was evaluated on 16 each of JE, JE × HF, and HF lactating dairy cows. Cows were individually stalled, allowing for the total collection of feces and were offered freshly cut grass twice daily. During this time, daily milk yield, BW, and dry matter intake (DMI) were greater for HF and JE × HF than for JE; milk fat and protein concentration ranked oppositely. Daily milk solids yield did not differ among the 3 genotypes. Intake capacity, expressed as DMI per BW, tended to be different among treatments, with JE having the greatest DMI per BW, HF the lowest, and JE × HF being intermediate. Production efficiency, expressed as milk solids per DMI, was higher for JE than HF and JE × HF. Digestive efficiency, expressed as digestibility of dry matter, organic matter, N, neutral detergent fiber, and acid detergent fiber, was higher for JE than HF. In grazing cows (n=15 per genotype) samples of rumen fluid, collected using a transesophageal sampling device, were analyzed to determine the relative abundance of rumen microbial populations of cellulolytic bacteria, protozoa, and fungi. These are critically important for fermentation of feed into short-chain fatty acids. A decrease was observed in the relative abundance of Ruminococcus flavefaciens in the JE rumen compared with HF and JE × HF. We can deduce from this study that the JE genotype has greater digestibility and a different rumen microbial population than HF. Jersey and JE × HF cows had a proportionally greater GIT weight than HF. These differences are likely to contribute to the production efficiency differences among genotypes previously reported.
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Affiliation(s)
- M Beecher
- Teagasc, Animal & Grassland Research and Innovation Centre, Moorepark, Fermoy, Co. Cork, Ireland; School of Agriculture and Food Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - F Buckley
- Teagasc, Animal & Grassland Research and Innovation Centre, Moorepark, Fermoy, Co. Cork, Ireland
| | - S M Waters
- Teagasc, Animal & Grassland Research and Innovation Centre, Grange, Dunsany, Co. Meath, Ireland
| | - T M Boland
- School of Agriculture and Food Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - D Enriquez-Hidalgo
- Teagasc, Animal & Grassland Research and Innovation Centre, Moorepark, Fermoy, Co. Cork, Ireland; Queen's University Belfast, Belfast, BT7 1NN, Northern Ireland
| | - M H Deighton
- Teagasc, Animal & Grassland Research and Innovation Centre, Moorepark, Fermoy, Co. Cork, Ireland
| | - M O'Donovan
- Teagasc, Animal & Grassland Research and Innovation Centre, Moorepark, Fermoy, Co. Cork, Ireland
| | - E Lewis
- Teagasc, Animal & Grassland Research and Innovation Centre, Moorepark, Fermoy, Co. Cork, Ireland.
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Leng RA. Interactions between microbial consortia in biofilms: a paradigm shift in rumen microbial ecology and enteric methane mitigation. ANIMAL PRODUCTION SCIENCE 2014. [DOI: 10.1071/an13381] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Minimising enteric CH4 emissions from ruminants is a current research priority because CH4 contributes to global warming. The most effective mitigation strategy is to adjust the animal’s diet to complement locally available feed resources so that optimal production is gained from a minimum of animals. This essay concentrates on a second strategy – the use of feed additives that are toxic to methanogens or that redirect H2 (and electrons) to inhibit enteric CH4 emissions from individual animals. Much of the published research in this area is contradictory and may be explained when the microbial ecology of the rumen is considered. Rumen microbes mostly exist in organised consortia within biofilms composed of self-secreted extracellular polymeric substances attached to or within feed particles. In these biofilms, individual colonies are positioned to optimise their use of preferred intermediates from an overall process of organic matter fermentation that generates end-products the animal can utilise. Synthesis of CH4 within biofilms prevents a rise in the partial pressure of H2 (pH2) to levels that inhibit bacterial dehydrogenases, and so reduce fermentation rate, feed intake and digestibility. In this context, hypotheses are advanced to explain changes in hydrogen disposal from the biofilms in the rumen resulting from use of anti-methanogenic feed additives as follows. Nitrate acts as an alternative electron sink when it is reduced via NO2– to NH3 and CH4 synthesis is reduced. However, efficiency of CH4 mitigation is always lower than that predicted and decreases as NO3– ingestion increases. Suggested reasons include (1) variable levels of absorption of NO3–or NO2– from the rumen and (2) increases in H2 production. One suggestion is that NO3– reduction may lower pH2 at the surface of biofilms, thereby creating an ecological niche for growth of syntrophic bacteria that oxidise propionate and/or butyrate to acetate with release of H2. Chlorinated hydrocarbons also inhibit CH4 synthesis and increase H2 and formate production by some rumen methanogens. Formate diffuses from the biofilm and is converted to HCO3– and H2 in rumen fluid and is then excreted via the breath. Short-chain nitro-compounds inhibit both CH4 and formate synthesis when added to ruminal fluid but have little or no effect in redirecting H2 to other sinks, so the pH2 within biofilms may increase to levels that support reductive acetogenesis. Biochar or activated charcoal may also alter biofilm activity and reduce net CH4 synthesis; direct electron transfer between microbes within biofilms may also be involved. A final suggestion is that, during their sessile life stage, protozoa interact with biofilm communities and help maintain pH2 in the biofilm, supporting methanogenesis.
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Fiorentini G, Messana J, Dian P, Reis R, Canesin R, Pires A, Berchielli T. Digestibility, fermentation and rumen microbiota of crossbred heifers fed diets with different soybean oil availabilities in the rumen. Anim Feed Sci Technol 2013. [DOI: 10.1016/j.anifeedsci.2013.01.011] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Sirohi SK, Choudhury PK, Puniya AK, Singh D, Dagar SS, Singh N. Ribosomal ITS1 sequence-based diversity analysis of anaerobic rumen fungi in cattle fed on high fiber diet. ANN MICROBIOL 2013. [DOI: 10.1007/s13213-013-0620-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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Boots B, Lillis L, Clipson N, Petrie K, Kenny DA, Boland TM, Doyle E. Responses of anaerobic rumen fungal diversity (phylum Neocallimastigomycota) to changes in bovine diet. J Appl Microbiol 2012; 114:626-35. [PMID: 23163953 DOI: 10.1111/jam.12067] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2012] [Revised: 10/12/2012] [Accepted: 11/10/2012] [Indexed: 12/25/2022]
Abstract
AIMS Anaerobic rumen fungi (Neocallimastigales) play important roles in the breakdown of complex, cellulose-rich material. Subsequent decomposition products are utilized by other microbes, including methanogens. The aim of this study was to determine the effects of dietary changes on anaerobic rumen fungi diversity. METHODS AND RESULTS Altered diets through increasing concentrate/forage (50 : 50 vs 90 : 10) ratios and/or the addition of 6% soya oil were offered to steers and the Neocallimastigales community was assessed by PCR-based fingerprinting with specific primers within the barcode region. Both a decrease in fibre content and the addition of 6% soya oil affected Neocallimastigales diversity within solid and liquid rumen phases. The addition of 6% soya oil decreased species richness. Assemblages were strongly affected by the addition of 6% soya oil, whereas unexpectedly, the fibre decrease had less effect. Differences in volatile fatty acid contents (acetate, propionate and butyrate) were significantly associated with changes in Neocallimastigales assemblages between the treatments. CONCLUSIONS Diet clearly influences Neocallimastigales assemblages. The data are interpreted in terms of interactions with other microbial groups involved in fermentation processes within the rumen. SIGNIFICANCE AND IMPACT OF THE STUDY Knowledge on the influence of diet on anaerobic fungi is necessary to understand changes in microbial processes occurring within the rumen as this may impact on other rumen processes such as methane production.
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Affiliation(s)
- B Boots
- Environmental Microbiology Group, School of Biology and Environmental Science and Earth Science Institute, University College Dublin, Belfield, Ireland.
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Isolation, characterization and fibre degradation potential of anaerobic rumen fungi from cattle. ANN MICROBIOL 2012. [DOI: 10.1007/s13213-012-0577-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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57
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Marano AV, Gleason FH, Bärlocher F, Pires-Zottarelli CLA, Lilje O, Schmidt SK, Rasconi S, Kagami M, Barrera MD, Sime-Ngando T, Boussiba S, de Souza JI, Edwards JE. Quantitative methods for the analysis of zoosporic fungi. J Microbiol Methods 2012; 89:22-32. [PMID: 22360942 DOI: 10.1016/j.mimet.2012.02.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2011] [Revised: 02/08/2012] [Accepted: 02/10/2012] [Indexed: 12/27/2022]
Abstract
Quantitative estimations of zoosporic fungi in the environment have historically received little attention, primarily due to methodological challenges and their complex life cycles. Conventional methods for quantitative analysis of zoosporic fungi to date have mainly relied on direct observation and baiting techniques, with subsequent fungal identification in the laboratory using morphological characteristics. Although these methods are still fundamentally useful, there has been an increasing preference for quantitative microscopic methods based on staining with fluorescent dyes, as well as the use of hybridization probes. More recently however PCR based methods for profiling and quantification (semi- and absolute) have proven to be rapid and accurate diagnostic tools for assessing zoosporic fungal assemblages in environmental samples. Further application of next generation sequencing technologies will however not only advance our quantitative understanding of zoosporic fungal ecology, but also their function through the analysis of their genomes and gene expression as resources and databases expand in the future. Nevertheless, it is still necessary to complement these molecular-based approaches with cultivation-based methods in order to gain a fuller quantitative understanding of the ecological and physiological roles of zoosporic fungi.
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Affiliation(s)
- Agostina V Marano
- Instituto de Botánica Spegazzini, calle 53 N 477, La Plata, 1900, Buenos Aires, Argentina.
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Bootten TJ, Joblin KN, McArdle BH, Harris PJ. Degradation of lignified secondary cell walls of lucerne (Medicago sativa L.) by rumen fungi growing in methanogenic co-culture. J Appl Microbiol 2011; 111:1086-96. [PMID: 21848807 DOI: 10.1111/j.1365-2672.2011.05127.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AIMS To compare the abilities of the monocentric rumen fungi Neocallimastix frontalis, Piromyces communis and Caecomyces communis, growing in coculture with Methanobrevibacter smithii, to colonize and degrade lignified secondary cell walls of lucerne (alfalfa) hay. METHODS AND RESULTS The cell walls of xylem cylinders isolated from stems of lucerne contained mostly xylans, cellulose and lignin together with a small proportion of pectic polysaccharides. All of these major components were removed during incubation with the three fungi, and differing cell wall polysaccharides were degraded to different extents. The greatest dry weight loss was found with N. frontalis and least with C. communis, and scanning electron microscopy revealed that these extensively colonized different cell types. C. communis specifically colonized secondary xylem fibres and showed much less degradation than N. frontalis and P. communis. CONCLUSIONS Neocallimastix frontalis and P. communis were efficient degraders of the cell walls of lucerne xylem cylinders. Degradation occurred of pectic polysaccharides, xylan and cellulose. Loss of lignin from the xylem cylinders probably resulted from the cleavage of xylan releasing xylan-lignin complexes. SIGNIFICANCE AND IMPACT OF THE STUDY Unlike rumen bacteria, the rumen fungi N. frontalis, P. communis and C. communis are able to degrade lignified secondary walls in lucerne stems. These fungi could improve forage utilization by ruminants and may have potential in the degradation of lignocellulosic biomass in the production of biofuels.
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Affiliation(s)
- T J Bootten
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
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Jin W, Cheng YF, Mao SY, Zhu WY. Isolation of natural cultures of anaerobic fungi and indigenously associated methanogens from herbivores and their bioconversion of lignocellulosic materials to methane. BIORESOURCE TECHNOLOGY 2011; 102:7925-7931. [PMID: 21719276 DOI: 10.1016/j.biortech.2011.06.026] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2011] [Revised: 06/05/2011] [Accepted: 06/06/2011] [Indexed: 05/31/2023]
Abstract
This study aimed to obtain natural cultures of anaerobic fungi and their indigenously associated methanogens from herbivores and investigate their ability to degrade lignocelluloses to methane. Eight natural cultures were obtained by Hungate roll tube technique. The fungi were identified as belonging to Piromyces, Anaeromyces and Neocallimastix respectively by microscopy, and the methanogens as Methanobrevibacter spp. by 16S rRNA gene sequencing. In vitro studies with rice straw showed that these cultures degraded 33.5-48.3% substrate and produced 0.33-0.84 mmol/(100ml culture) methane. Two cultures were further selected for their ability to degrade different lignocellulosic materials and could produce 0.38-1.27 mmol/(100ml culture) methane. When methanogens were inhibited, the lignocellulose-degrading ability of cultures significantly reduced. In conclusion, natural cultures of anaerobic fungi with indigenously associated methanogens with high fiber degradation ability were obtained, and these cultures may have the potential in industrial use in lignocelluloses degradation and methane production.
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Affiliation(s)
- Wei Jin
- Laboratory of Gastrointestinal Microbiology, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
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60
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Urubschurov V, Janczyk P, Souffrant WB, Freyer G, Zeyner A. Establishment of intestinal microbiota with focus on yeasts of unweaned and weaned piglets kept under different farm conditions. FEMS Microbiol Ecol 2011; 77:493-502. [DOI: 10.1111/j.1574-6941.2011.01129.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Kissin I, Szallasi A. Therapeutic targeting of TRPV1 by resiniferatoxin, from preclinical studies to clinical trials. Curr Top Med Chem 2011. [PMID: 21671878 DOI: 10.1101/128884] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
In primary sensory neurons, the capsaicin receptor TRPV1 functions as a molecular integrator for a broad range of seemingly unrelated chemical and physical noxious stimuli, including heat and altered pH. Indeed, TRPV1 is thought to be a major transducer of the thermal hyperalgesia that follows inflammation and tissue injury as this response is impaired in TRPV1-deficient mice. Following the molecular cloning of TRPV1 in 1997, over a dozen companies embarked on efforts to find clinically useful TRPV1 antagonists, but side-effects and limited efficacy have thus far prevented any compounds from progressing beyond phase II. This has rekindled interest in desensitization of nociceptive neurons to TRPV1 agonists (e.g. capsaicin and its ultrapotent analog resiniferatoxin) as an alternative pharmacological approach to block pain in the periphery where it is generated. The clinical value of capsaicin is, however, limited by its unfavorable irritancy to desensitization ratio. In animal experiments, resiniferatoxin treatment is a powerful approach to achieve long-lasting analgesia. In patients with overactive bladder, intravesical resiniferatoxin improves bladder function (or even restores continence) without significant irritancy and/or toxicity. In this review, we argue that resiniferatoxin is an attractive alternative to capsaicin in that it achieves lasting desensitization without the side effects that complicate capsaicin therapy.
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Affiliation(s)
- Igor Kissin
- Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.
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Paul SS, Deb SM, Punia BS, Singh D, Kumar R. Fibrolytic potential of anaerobic fungi (Piromyces sp.) isolated from wild cattle and blue bulls in pure culture and effect of their addition on in vitro fermentation of wheat straw and methane emission by rumen fluid of buffaloes. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2010; 90:1218-1226. [PMID: 20394004 DOI: 10.1002/jsfa.3952] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
BACKGROUND Ten isolates of anaerobic fungi of Piromyces genus from wild cattle and blue bulls (five isolates from each host species) were evaluated for their fibrolytic ability in pure culture, their suitability for use as a microbial additive in buffaloes and their effect on methane emission. RESULTS In pure culture, only two out of five isolates from wild cattle degraded wheat straw efficiently, whereas all five isolates from wild blue bulls did. Isolate CF1 (from cattle) showed the highest apparent digestibility (53.4%), true digestibility (70.8%) and neutral detergent fibre digestibility (75.0%) of wheat straw after 5 days of incubation. When added to buffalo rumen fluid, all five isolates from cattle increased (P < 0.05) in vitro apparent digestibility of wheat straw compared with the control (received autoclaved culture), but all five isolates from blue bulls failed to influence in vitro digestibility of wheat straw. Isolate CF1 showed the highest stimulating effect on straw digestion by buffalo rumen fluid microbes and increased apparent digestibility (51.9 vs 29.4%, P < 0.05), true digestibility (57.9 vs 36.5%, P < 0.05) and neutral detergent fibre digestibility (51.5 vs 26.9%, P < 0.05) of wheat straw compared with the control after 24 h of fermentation. There were also significant increases in fungal count and enzyme activities of carboxymethylcellulase and xylanase in the CF1-added group compared with the control group. Gas and methane production g(-1) truly digested dry matter of straw were comparable among all groups including the control. CONCLUSION Wild cattle and blue bulls harbour some anaerobic fungal strains with strong capability to hydrolyse fibre. The fungal isolate CF1 has high potential for use as a microbial feed additive in buffaloes to improve digestibility of fibrous feeds without increasing methane emission per unit of digested feed.
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Affiliation(s)
- Shyam S Paul
- Central Institute for Research on Buffaloes, Sub Campus, Bir Dosanjh, Nabha 147201, Punjab, India.
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63
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Messana J, Berchielli T, Arcuri P, Reis R, Malheiros E, Rivera A, Queiroz M. Effects of dry sugar cane yeast on the diet intake, digestibility and bovine rumen microbial populations. Livest Sci 2010. [DOI: 10.1016/j.livsci.2010.02.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Srinivasan N. Telling apart friend from foe: discriminating between commensals and pathogens at mucosal sites. Innate Immun 2010; 16:391-404. [PMID: 20083498 DOI: 10.1177/1753425909357577] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
From the moment we are born, we are exposed to a vast variety of microbes. The intestine in particular is perhaps inhabited by the largest number of microbes, consisting of both established commensals as well as sporadic pathogens. Mucosal surfaces form an important barrier against microbial invasion. Together with the physical barrier that they provide, mucosal surfaces also rely on innate immune functions to sense luminal microbes and signal accordingly to generate protective immune responses. However, since innate immune recognition is microbial specific and antigen-independent, the contact with both beneficial commensals and harmful pathogens creates the need for discrimination between the two. The mechanisms governing the ability of the mucosal immune system to discriminate between commensals and pathogens have long been unclear; however, recent discoveries have shed some light on this distinction. This review will summarize the current theories put forth to explain how the mucosal immune system maintains tolerance towards commensals while retaining the ability to mount inflammatory responses against pathogens.
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Affiliation(s)
- Naren Srinivasan
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.
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Yang H, Yue Q, Cao Y, Zhang D, Wang J. Effects of crude feruloyl and acetyl esterase solutions of Neocallimastix sp. YQ1 and Anaeromyces sp. YQ3 isolated from Holstein steers on hydrolysis of Chinese wildrye grass hay, wheat bran, maize bran, wheat straw and corn stalks. Anim Feed Sci Technol 2009. [DOI: 10.1016/j.anifeedsci.2009.09.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Affiliation(s)
- Jason E. Stajich
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720-3102 USA
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA 92521 USA
| | - Mary L. Berbee
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Meredith Blackwell
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803 USA
| | | | - Timothy Y. James
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Joseph W. Spatafora
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331 USA
| | - John W. Taylor
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720-3102 USA
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Potential of biofilm-based biofuel production. Appl Microbiol Biotechnol 2009; 83:1-18. [PMID: 19300995 DOI: 10.1007/s00253-009-1940-9] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2008] [Revised: 03/02/2009] [Accepted: 03/02/2009] [Indexed: 01/09/2023]
Abstract
Biofilm technology has been extensively applied to wastewater treatment, but its potential application in biofuel production has not been explored. Current technologies of converting lignocellulose materials to biofuel are hampered by costly processing steps in pretreatment, saccharification, and product recovery. Biofilms may have a potential to improve efficiency of these processes. Advantages of biofilms include concentration of cell-associated hydrolytic enzymes at the biofilm-substrate interface to increase reaction rates, a layered microbial structure in which multiple species may sequentially convert complex substrates and coferment hexose and pentose as hydrolysates diffuse outward, and the possibility of fungal-bacterial symbioses that allow simultaneous delignification and saccharification. More importantly, the confined microenvironment within a biofilm selectively rewards cells with better phenotypes conferred from intercellular gene or signal exchange, a process which is absent in suspended cultures. The immobilized property of biofilm, especially when affixed to a membrane, simplifies the separation of biofuel from its producer and promotes retention of biomass for continued reaction in the fermenter. Highly consolidated bioprocessing, including delignification, saccharification, fermentation, and separation in a single reactor, may be possible through the application of biofilm technology. To date, solid-state fermentation is the only biofuel process to which the advantages of biofilms have been applied, even though it has received limited attention and improvements. The transfer of biofilm technology from environmental engineering has the potential to spur great innovations in the optimization of biofuel production.
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Dijkstra J, Mills JAN, France J. The role of dynamic modelling in understanding the microbial contribution to rumen function. Nutr Res Rev 2009; 15:67-90. [DOI: 10.1079/nrr200237] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Denman SE, Nicholson MJ, Brookman JL, Theodorou MK, McSweeney CS. Detection and monitoring of anaerobic rumen fungi using an ARISA method. Lett Appl Microbiol 2009; 47:492-9. [PMID: 19120916 DOI: 10.1111/j.1472-765x.2008.02449.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
AIM To develop an automated ribosomal intergenic spacer region analysis (ARISA) method for the detection of anaerobic rumen fungi and also to demonstrate utility of the technique to monitor colonization and persistence of fungi, and diet-induced changes in community structure. METHODS AND RESULTS The method could discriminate between three genera of anaerobic rumen fungal isolates, representing Orpinomyces, Piromyces and Neocallimastix species. Changes in anaerobic fungal composition were observed between animals fed a high-fibre diet compared with a grain-based diet. ARISA analysis of rumen samples from animals on grain showed a decrease in fungal diversity with a dominance of Orpinomyces and Piromyces spp. Clustering analysis of ARISA profile patterns grouped animals based on diet. A single strain of Orpinomyces was dosed into a cow and was detectable within the rumen fungal population for several weeks afterwards. CONCLUSIONS The ARISA technique was capable of discriminating between pure cultures at the genus level. Diet composition has a significant influence on the diversity of anaerobic fungi in the rumen and the method can be used to monitor introduced strains. SIGNIFICANCE AND IMPACT OF THE STUDY Through the use of ARISA analysis, a better understanding of the effect of diets on rumen anaerobic fungi populations is provided.
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Affiliation(s)
- S E Denman
- CSIRO Livestock Industries, Queensland Bioscience Precinct, Brisbane, Queensland, Australia
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Suchodolski JS, Morris EK, Allenspach K, Jergens AE, Harmoinen JA, Westermarck E, Steiner JM. Prevalence and identification of fungal DNA in the small intestine of healthy dogs and dogs with chronic enteropathies. Vet Microbiol 2008; 132:379-88. [PMID: 18586415 DOI: 10.1016/j.vetmic.2008.05.017] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2008] [Revised: 05/11/2008] [Accepted: 05/20/2008] [Indexed: 02/06/2023]
Abstract
Limited information is available about the prevalence and phylogenetic classification of fungal organisms in the gastrointestinal tract of dogs. Also, the impact of fungal organisms on gastrointestinal health and disease is not well understood. The aim of this study was to evaluate the prevalence of fungal DNA in the small intestine of healthy dogs and dogs with chronic enteropathies. Small intestinal content was analyzed from 64 healthy and 71 diseased dogs from five different geographic locations in Europe and the USA. Fungal DNA was amplified with panfungal primers targeting the internal transcriber spacer (ITS) region. PCR amplicons were subjected to phylogenetic analysis. Fungal DNA was detected in 60.9% of healthy dogs and in 76.1% of dogs with chronic enteropathies. This prevalence was not significantly different between the two groups (p=0.065). Fungal DNA was significantly more prevalent in mucosal brush samples (82.8%) than in luminal samples (42.9%; p=0.002). Sequencing results revealed a total of 51 different phylotypes. All sequences belonged to two phyla and were classified as either Ascomycota (32 phylotypes) or Basidiomycota (19 phylotypes). Three major classes were identified: Saccharomycetes, Dothideomycetes, and Hymenomycetes. The most commonly observed sequences were classified as Pichia spp., Cryptococcus spp., Candida spp., and Trichosporon spp. Species believed to be clinically more important were more commonly observed in diseased dogs. These results indicate a high prevalence and diversity of fungal DNA in the small intestine of both healthy dogs and dogs with chronic enteropathies. The canine gastrointestinal tract of diseased dogs may harbor opportunistic fungal pathogens.
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Affiliation(s)
- Jan S Suchodolski
- Gastrointestinal Laboratory, Texas A&M University, College Station, TX 77843-4474, United States.
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71
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Moricca S, Ragazzi A. Fungal endophytes in Mediterranean oak forests: a lesson from Discula quercina. PHYTOPATHOLOGY 2008; 98:380-6. [PMID: 18944185 DOI: 10.1094/phyto-98-4-0380] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Fungal endophytes that colonize forest trees are widespread, but they are less well known than endophytes infecting grasses. The few studies on endophytes in trees mainly concern the tropical areas and the northernmost latitudes, while similar investigations in the Mediterranean region have so far been scarce and incidental. Endophytes are studied mostly in economically important forests suffering from diseases, such as oak forests. One common endophyte that has received some study on oak is the mitosporic Discula quercina. This paper, after first addressing some basic problems on tree endophytes, examines the ecology of D. quercina in Mediterranean oak stands. D. quercina is usually viewed as a symptomless colonizer of healthy Quercus cerris, infecting new leaves early in the growing season, in an unstable equilibrium between transient mutualism/neutralism and latent pathogenesis. It is postulated here that climatic factors can change the endophytic nature of D. quercina, turning it into a weak pathogen or an opportunistic invader of senescing and indeed healthy trees. It is argued more generally that stochastic events can cause the lifestyle of an endophyte to switch from beneficial/neutral to pathogenic, transforming the tree-endophyte interaction, an interaction that depends in part on the matching genomes of the tree and endophyte, and on the environmental context.
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Affiliation(s)
- S Moricca
- Dipartimento di Biotecnologie agrarie, Sezione di Patologia vegetale, Universita di Firenze, Firenze, Italy.
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72
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Steenbakkers PJM, Irving JA, Harhangi HR, Swinkels WJC, Akhmanova A, Dijkerman R, Jetten MSM, van der Drift C, Whisstock JC, Op den Camp HJM. A serpin in the cellulosome of the anaerobic fungus Piromyces sp. strain E2. ACTA ACUST UNITED AC 2008; 112:999-1006. [PMID: 18539447 DOI: 10.1016/j.mycres.2008.01.021] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2007] [Revised: 01/08/2008] [Accepted: 01/24/2008] [Indexed: 11/17/2022]
Abstract
A gene encoding a novel component of the cellulolytic complex (cellulosome) of the anaerobic fungus Piromyces sp. strain E2 was identified. The encoded 538 amino acid protein, named celpin, consists of a signal peptide, a positively charged domain of unknown function followed by two fungal dockerins, typical for components of the extracellular fungal cellulosome. The C-terminal end consists of a 380 amino acid serine proteinase inhibitor (or serpin) domain homologue, sharing 30% identity and 50% similarity to vertebrate and bacterial serpins. Detailed protein sequence analysis of the serpin domain revealed that it contained all features of a functional serpin. It possesses the conserved amino acids present in more than 70% of known serpins, and it contained the consensus of inhibiting serpins. Because of the confined space of the fungal cellulosome inside plant tissue and the auto-proteolysis of plant material in the rumen, the fungal serpin is presumably involved in protection of the cellulosome against plant proteinases. The celpin protein of Piromyces sp. strain E2 is the first non-structural, non-hydrolytic fungal cellulosome component. Furthermore, the celpin protein of Piromyces sp. strain E2 is the first representative of a serine proteinase inhibitor of the fungal kingdom.
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Affiliation(s)
- Peter J M Steenbakkers
- Department of Microbiology, IWWR, Radboud University Nijmegen, Toernooiveld 1, NL-6525ED Nijmegen, The Netherlands
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73
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Advances in microbial ecosystem concepts and their consequences for ruminant agriculture. Animal 2008; 2:653-60. [PMID: 22443590 DOI: 10.1017/s1751731108002164] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
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74
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Tripathi VK, Sehgal JP, Puniya AK, Singh K. Effect of administration of anaerobic fungi isolated from cattle and wild blue bull (Boselaphus tragocamelus) on growth rate and fibre utilization in buffalo calves. Arch Anim Nutr 2007; 61:416-23. [PMID: 18030922 DOI: 10.1080/17450390701556759] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Fifteen Murrah buffalo calves (age about 10 months, 163-176 kg BW) were divided into three groups. Group I (Control) was fed a complete feed mixture consisted of 50% wheat straw and 50% concentrate mixture (contained per kg: maize 330 g, groundnut cake 210 g, mustard cake 120 g, wheat bran 200 g, de-oiled rice bran 110 g, mineral mixture 20 g and common salt 10 g) along with 2 kg green oats per animal and day to meet the vitamin A requirements. Calves of Groups II and III were fed with the Control diet supplemented with Orpinomyces sp. C-14 and Piromyces sp. WNG-12 cultures, respectively. The digestibility of DM was significantly highest with Piromyces sp. WNG-12 in Group III (62.2%) followed by Orpinomyces sp. C-14 in Group II (60.3%), and Control (53.5%). A similar pattern of increase in digestibility of crude protein and cell-wall contents was observed in treatment groups. The digestible energy in terms of percent total digestible nutrients was also significantly enhanced in Groups II (56.6%) and III (59.9%) when compared to Control (49.2%). The rumen fermentation parameters such as pH and NH3-N were found to be lower, whereas total nitrogen, tricarboxylic acid precipitable-, nitrogen, total volatile fatty acids and zoospore counts per millilitre of rumen liquor were significantly higher in fungal administered groups. After administration of fungal cultures, improvements of animal growth rate (i.e. body weight gain) and feed efficiency were also observed.
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Affiliation(s)
- Vimal K Tripathi
- Dairy Cattle Nutrition Division, National Dairy Research Institute, Karnal, India
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75
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Annison EF, Bryden WL. Perspectives on ruminant nutrition and metabolism I. Metabolism in the Rumen. Nutr Res Rev 2007; 11:173-98. [DOI: 10.1079/nrr19980014] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
AbstractAdvances in knowledge of ruminant nutrition and metabolism during the second half of the twentieth century have been reviewed. Part I is concerned with metabolism in the rumen: Part II discusses utilization of nutrients absorbed from the rumen and lower tract to support growth and reproduction. The time frame was prompted by the crucial advances in ruminant physiology which arose from the work of Sir Jospeh Barcroft and his colleagues at Cambridge in the 1940s and 50s, and by the brilliant studies of Robert Hungate on rumen microbiology at much the same time.In reviewing the growth of knowledge of the role of bacteria, protozoa, fungi and bacteriophages in the rumen, outstanding developments have included the identification and characterization of fungi and the recognition that the utilization of polysaccharides in the rumen is accomplished by the sequential activities of consortia of rumen microorganisms. The role of protozoa is discussed in relation to the long standing debate on whether or not the removal of protozoa (defaunation) improves the efficiency of ruminant production. In relation to nitrogen (N) metabolism, the predation of bacteria by protozoa increases protein turnover in the rumen and reduces the efficiency of microbial protein production. This may account for the beneficial effects of defaunation where dietary N intakes are low and possibly rate limiting for growth and production.Current approaches to the measurement of rates of production of short chain fatty acids (SCFA) in the rumen based on the mathematical modelling of isotope dilution data are outlined. The absorption of SCFA from the rumen and hindgut is primarily a passive permeation process.The role of microorganisms in N metabolism in the rumen has been discussed in relation to ammonia and urea interrelationships and to current inadequacies in the measurement of both protein degradation in the rumen and microbial protein synthesis. The growth of knowledge of digestion and absorption of dietary lipids has been reviewed with emphasis on the antimicrobial activity of lipids and the biohydrogenation of unsaturated fatty acids. The protection of unsaturated dietary fats from ruminal biohydrogenation is an approach to the manipulation of the fatty acid composition of meat and dairy products.Discussion of the production of toxins in the rumen and the role of microorganisms in detoxification has focused on the metabolism of oxalate, nitrate, mycotoxins, saponins and the amino acid mimosine. Mimosine occurs in the tropical shrub leucaena, which is toxic to cattle in Australia but not in Hawaii. Tolerance to leucaena stems from the presence of a bacterium found in the rumen of Hawaiian cattle, which when transferred to Australian cattle survives and confers protection from mimosine. The genetic modification of rumen microorganisms to improve their capacity to ultilize nutrients or to detoxify antinutritive factors is an attractive strategy which has been pursued with outstanding success in the case of fluoroacetate. A common rumen bacterium has been genetically modified to express the enzyme fluoroacetate dehalogenase. The modified organism has been shown to survive in the rumen at metabolically significant levels and to confer substantial protection from fluoroacetate poisoning.
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76
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Tripathi VK, Sehgal JP, Puniya AK, Singh K. Hydrolytic activities of anaerobic fungi from wild blue bull (Boselaphus tragocamelus). Anaerobe 2007; 13:36-9. [PMID: 17218123 DOI: 10.1016/j.anaerobe.2006.11.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2006] [Revised: 11/07/2006] [Accepted: 11/09/2006] [Indexed: 11/25/2022]
Abstract
The anaerobic fungi play an active role in the plant fibre degradation by producing a wide array of potential hydrolytic enzymes in the rumen. In present study, 12 anaerobic fungal strains were isolated from the faecal samples of wild blue bull, and identified as species of Piromyces, Anaeromyces, Orpinomyces and Neocallimastix based on their morphological characteristics. Isolate WNG-12 (Piromyces sp.), showed maximum filter paper cellulase (23 mIU ml(-1)) and xylanase (127 mIU ml(-1)) activity, while WNG-5 (Piromyces sp.) showed maximum carboxymethyl cellulase activity (231 mIU ml(-1)). Based on the results obtained, it can be stated that Piromyces sp. WNG-12 may be a promising isolate in utilizing fibre rich diets in the rumen as evidenced by the production of hydrolytic enzymes in vitro.
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Affiliation(s)
- Vimal Kumar Tripathi
- Dairy Cattle Nutrition Division, National Dairy Research Institute, Karnal 132001, Haryana, India
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77
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Barboza PS, Peltier TC, Forster RJ. Ruminal fermentation and fill change with season in an arctic grazer: responses to hyperphagia and hypophagia in muskoxen (Ovibos moschatus). Physiol Biochem Zool 2006; 79:497-513. [PMID: 16691516 DOI: 10.1086/501058] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/17/2005] [Indexed: 11/03/2022]
Abstract
We studied castrated adult muskoxen fed a standard diet of grass hay and supplement throughout the year to determine seasonal changes in digesta passage, fill, and fermentation without the confounding effects of reproductive demands or changes in food quality. Although food intake increased by 74% between spring and autumn, mean retention times of fluid and particulate digesta markers were maintained between seasons in both the rumen (9-13 h) and the intestines (27-37 h). The rumen contained 84.5% of digesta and accounted for 79% of dry matter digestion in the whole digestive tract. Ruminal fluid space and whole-gut digesta fill increased by 31%-34%, while ruminal rates of in situ degradation increased by more than 100% between spring and autumn for cellulose and hemicellulose. Hyperphagia in autumn was accompanied by increased bacterial counts in ruminal fluid (30%), declines in ruminal pH, and increases in the concentration of fermentation acids (16%) when compared with spring hypophagia. Consumption of fresh hay and supplement increased the concentrations of acids most markedly during winter and spring when bacterial counts were low. Low food intakes in winter and spring may limit the microbial population, whereas hyperphagia in autumn may foster a much more active microflora that requires consistent supplies of substrate. Plasticity of fill and fermentation in muskoxen minimizes winter costs and maximizes nutrients and energy gained from coarse forages in small home ranges throughout the year.
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Affiliation(s)
- Perry S Barboza
- Institute of Arctic Biology, Department of Biology and Wildlife, University of Alaska, Fairbanks, 99775-7000, USA.
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79
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Reith F, Drake HL, Küsel K. Anaerobic activities of bacteria and fungi in moderately acidic conifer and deciduous leaf litter. FEMS Microbiol Ecol 2002; 41:27-35. [DOI: 10.1111/j.1574-6941.2002.tb00963.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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80
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McCabe BK, Kuek C, Gordon GL, Phillips MW. Immobilization of monocentric and polycentric types of anaerobic chytrid fungi in Ca-alginate. Enzyme Microb Technol 2001. [DOI: 10.1016/s0141-0229(01)00367-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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81
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Microscopic Studies of Structure and Ruminal Fungal Colonization in Sheep of Wheat Straw Treated with Different Alkalis. Anaerobe 2000. [DOI: 10.1006/anae.2000.0335] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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82
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Abstract
By combining analyses of G + C content and patterns of codon usage and constructing phylogenetic trees, we describe the gene transfer of an endoglucanase (celA) from the rumen bacteria Fibrobacter succinogenes to the rumen fungi Orpinomyces joyonii. The strong similarity between different glycosyl hydrolases of rumen fungi and bacteria suggests that most, if not all, of the glycosyl hydrolases of rumen fungi that play an important role in the degradation of cellulose and other plant polysaccharides were acquired by horizontal gene transfer events. This acquisition allows fungi to establish a habitat within a new environmental niche: the rumen of the herbivorous mammals for which cellulose and plant hemicellulose constitute the main raw nutritive substrate.
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Affiliation(s)
- S Garcia-Vallvé
- Department of Biochemistry and Biotechnology, Rovira i Virgili University, Catalonia, Spain
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83
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McGranaghan P, Davies J, Griffith G, Davies D, Theodorou M. The survival of anaerobic fungi in cattle faeces. FEMS Microbiol Ecol 1999. [DOI: 10.1111/j.1574-6941.1999.tb00620.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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