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Salmanizadeh H, Beheshti-Maal K, Nayeri H, Torabi LR. Optimization of xylanase production by Pichia kudriavzevii and Candida tropicalis isolated from the wood product workshop. Braz J Microbiol 2024; 55:155-168. [PMID: 37957443 DOI: 10.1007/s42770-023-01171-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 10/27/2023] [Indexed: 11/15/2023] Open
Abstract
Enzymatic compounds can be found abundantly and provide numerous advantages in microbial organisms. Xylanases are used in various pharmaceutical, food, livestock, poultry, and paper industries. This study aimed to investigate xylanase-producing yeasts, xylose concentration curve and their enzymatic activity under various factors including carbon and nitrogen sources, temperature, and pH. Enzyme activity was evaluated under different conditions before, during, and after purification. The yeast strains were obtained from the wood product workshop and were subsequently cultivated on YPD (yeast extract peptone dextrose) medium. Additionally, the growth curve of the yeast and its molecular identification were conducted. The optimization and design process of xylan isolated from corn wood involved the use of Taguchi software to test different parameters like carbon and nitrogen sources, temperature, and pH, with the goal of determining the most optimal conditions for enzyme production. In addition, the Taguchi method was utilized to conduct a multifactorial optimization of xylanase enzyme activity. The isolated species were partially purified using ammonium sulfate precipitation and dialysis bag techniques. The results indicated that 3 species (8S, 18S, and 16W) after molecular identification based on 18S rRNA gene sequencing were identified as Candida tropicalis SBN-IAUF-1, Candida tropicalis SBN-IAUF-3, and Pichia kudriavzevii SBN-IAUF-2, respectively. The optimal parameters for wheat carbon source and peptone nitrogen source were found at 50 °C and pH 9.0 through single-factor optimization. By using the Taguchi approach, the best combination for highest activity was rice-derived carbon source and peptone nitrogen source at 50 °C and pH 6.0. The best conditions for xylanase enzyme production in single-factor optimization of wheat bran were 2135.6 U/mL, peptone 4475.25 U/mL, temperature 50 °C 1868 U/mL, and pH 9.0 2002.4 U/mL. Among the tested yeast, Candida tropicalis strain SBN-IAUF-1 to the access number MZ816946.1 in NCBI was found to be the best xylanase product. The highest ratio of enzyme production at the end of the delayed phase and the beginning of the logarithmic phase was concluded by comparing the growth ratio of 8S, 16W, and 18S yeasts with the level of enzymatic activity. This is the first report on the production of xylan polymer with a relative purity of 80% in Iran. The extracellular xylanases purified from the yeast species of C. tropicalis were introduced as a desirable biocatalyst due to their high enzymatic activity for the degradation of xylan polymers.
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Affiliation(s)
- Hoda Salmanizadeh
- Department of Microbiology, Falavarjan Branch, Islamic Azad University, Falavarjan, Isfahan, Iran
| | - Keivan Beheshti-Maal
- Department of Microbiology, Falavarjan Branch, Islamic Azad University, Falavarjan, Isfahan, Iran.
| | - Hashem Nayeri
- Department of Biochemistry, Falavarjan Branch, Islamic Azad University, Falavarjan, Isfahan, Iran
| | - Ladan Rahimzadeh Torabi
- Department of Microbiology, Falavarjan Branch, Islamic Azad University, Falavarjan, Isfahan, Iran
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2
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Rabee AE, Mohamed M Ghandour M, Sallam A, Elwakeel EA, Mohammed RS, Sabra EA, Abdel-Wahed AM, Mourad DM, Hamed AA, Hafez OR. Rumen fermentation and microbiota in Shami goats fed on condensed tannins or herbal mixture. BMC Vet Res 2024; 20:35. [PMID: 38297287 PMCID: PMC10829277 DOI: 10.1186/s12917-024-03887-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 01/17/2024] [Indexed: 02/02/2024] Open
Abstract
BACKGROUND Phytochemical compounds can modify the rumen microbiome and improve rumen fermentation. This study evaluated the impact of supplementation with tannin and an herbal mixture containing ginger (Zingiber officinale), garlic (Allium sativum), Artemisia (Artemisia vulgaris), and turmeric (Curcuma longa) on the rumen fermentation and microbiota, and histology of rumen tissue of goats. Eighteen Shami male goats were divided into three groups (n = 6): non-supplemented animals fed the basal diet (C, control); animals fed basal diet and supplemented with condensed tannin (T); and animals fed basal diet and supplemented with herbal mixture (HM). Each animal received a basal diet composed of Alfalfa hay and a concentrate feed mixture. RESULTS Group HM revealed higher (P < 0.05) rumen pH, total volatile fatty acids (VFA), acetic, propionic, isobutyric, butyric, isovaleric, and valeric. Principal Co-ordinate analysis (PCoA) showed that rumen microbial communities in the control group and supplemented groups were distinct. The supplementation increased (P < 0.05) the relative abundances of phylum Bacteroidota and Proteobacteria and declined (P < 0.05) Firmicutes and Fibrobacterota. Additionally, the dominant genus Prevotella and Rikenellaceae RC9 gut group were increased (P < 0.05) and the family Ruminococcaceae was declined (P < 0.05) due to the supplementation. The supplementation decreased (P < 0.05) the archaeal genus Methanobrevibacter and increased (P < 0.05) Candidatus Methanomethylophilus. Tannin supplementation in T group shortened the rumen papillae. CONCLUSIONS The results revealed that the herbal mixture might be used to alter the rumen microbiota to improve rumen fermentation.
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Affiliation(s)
- Alaa Emara Rabee
- Animal and Poultry Nutrition Department, Desert Research Center, Ministry of Agriculture and Land Reclamation, Cairo, Egypt.
| | - Moustafa Mohamed M Ghandour
- Animal and Poultry Nutrition Department, Desert Research Center, Ministry of Agriculture and Land Reclamation, Cairo, Egypt
| | - Ahmed Sallam
- Animal and Poultry Breeding Department, Desert Research Center, Cairo, Egypt
| | - Eman A Elwakeel
- Department of Animal and Fish production, Faculty of Agriculture, Alexandria University, Alexandria, Egypt
| | - Rasha S Mohammed
- Animal and Poultry Health Department, Desert Research Center, Ministry of Agriculture and Land Reclamation, Cairo, Egypt
| | - Ebrahim A Sabra
- Genetic Engineering and Biotechnology Research Institute, University of Sadat City, Sadat City, Egypt
| | - Adel M Abdel-Wahed
- Animal and Poultry Nutrition Department, Desert Research Center, Ministry of Agriculture and Land Reclamation, Cairo, Egypt
| | - Disouky Mohamed Mourad
- Animal and Poultry Health Department, Desert Research Center, Ministry of Agriculture and Land Reclamation, Cairo, Egypt
| | - Amal Amin Hamed
- Botany and Microbiology Department, Faculty of science, Cairo University, Cairo, Egypt
| | - Osama Raef Hafez
- Animal and Poultry Nutrition Department, Desert Research Center, Ministry of Agriculture and Land Reclamation, Cairo, Egypt
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Raghav D, Jyoti A, Siddiqui AJ, Saxena J. Plant associated endophytic fungi as potential bio-factories for extracellular enzymes: Progress, Challenges and Strain improvement with precision approaches. J Appl Microbiol 2022; 133:287-310. [PMID: 35396804 DOI: 10.1111/jam.15574] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 03/04/2022] [Accepted: 04/04/2022] [Indexed: 11/29/2022]
Abstract
There is an intricate network of relations between endophytic fungi and their hosts that affects the production of various bioactive compounds. Plant-associated endophytic contain industrially important enzymes and have the potential to fulfill their rapid demand in the international market to boost business in technology. Being safe and metabolically active, they have replaced the usage of toxic and harmful chemicals and hold a credible application in biotransformation, bioremediation, and industrial processes. Despite these, there are limited reports on fungal endophytes that can directly cater to the demand and supply of industrially stable enzymes. The underlying reasons include low endogenous production and secretion of enzymes from fungal endophytes which have raised concern for widely accepted applications. Hence it is imperative to augment the biosynthetic and secretory potential of fungal endophytes. Modern state-of-the-art biotechnological technologies aiming at strain improvement using cell factory engineering as well as precise gene editing like Clustered Regularly Interspaced Palindromic Repeats (CRISPR) and its Associated proteins (Cas) systems which can provide a boost in fungal endophyte enzyme production. Additionally, it is vital to characterize optimum conditions to grow one strain with multiple enzymes (OSME). The present review encompasses various plants-derived endophytic fungal enzymes and their applications in various sectors. Further, we postulate the feasibility of new precision approaches with an aim for strain improvement and enhanced enzyme production.
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Affiliation(s)
- Divyangi Raghav
- Faculty of Applied Sciences and Biotechnology, Shoolini University of Biotechnology and Management Sciences, Solan, Himachal Pradesh, India
| | - Anupam Jyoti
- Faculty of Applied Sciences and Biotechnology, Shoolini University of Biotechnology and Management Sciences, Solan, Himachal Pradesh, India.,Department of Biotechnology, University Institute of Biotechnology, Chandigarh University, SAS, Nagar, Punjab
| | - Arif Jamal Siddiqui
- Department of Biology, College of Science, University of Ha'il, Ha'il, P O Box, Saudi Arabia
| | - Juhi Saxena
- Faculty of Applied Sciences and Biotechnology, Shoolini University of Biotechnology and Management Sciences, Solan, Himachal Pradesh, India.,Department of Biotechnology, University Institute of Biotechnology, Chandigarh University, SAS, Nagar, Punjab
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Takizawa S, Asano R, Fukuda Y, Baba Y, Tada C, Nakai Y. Shifts in xylanases and the microbial community associated with xylan biodegradation during treatment with rumen fluid. Microb Biotechnol 2021; 15:1729-1743. [PMID: 34964273 PMCID: PMC9151333 DOI: 10.1111/1751-7915.13988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 11/03/2021] [Accepted: 11/24/2021] [Indexed: 11/29/2022] Open
Abstract
Treatment with rumen fluid improves methane production from non‐degradable lignocellulosic biomass during subsequent methane fermentation; however, the kinetics of xylanases during treatment with rumen fluid remain unclear. This study aimed to identify key xylanases contributing to xylan degradation and their individual activities during xylan treatment with bovine rumen microorganisms. Xylan was treated with bovine rumen fluid at 37°C for 48 h under anaerobic conditions. Total solids were degraded into volatile fatty acids and gases during the first 24 h. Zymography showed that xylanases of 24, 34, 85, 180, and 200 kDa were highly active during the first 24 h. Therefore, these xylanases are considered to be crucial for xylan degradation during treatment with rumen fluid. Metagenomic analysis revealed that the rumen microbial community’s structure and metabolic function temporally shifted during xylan biodegradation. Although statistical analyses did not reveal significantly positive correlations between xylanase activities and known xylanolytic bacterial genera, they positively correlated with protozoal (e.g., Entodinium, Diploplastron, and Eudiplodinium) and fungal (e.g., Neocallimastix, Orpinomyces, and Olpidium) genera and unclassified bacteria. Our findings suggest that rumen protozoa, fungi, and unclassified bacteria are associated with key xylanase activities, accelerating xylan biodegradation into volatile fatty acids and gases, during treatment of lignocellulosic biomass with rumen fluid.
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Affiliation(s)
- Shuhei Takizawa
- Laboratory of Sustainable Animal Environment, Graduate School of Agricultural Science, Tohoku University, Osaki, Japan.,Japan Society for the Promotion of Science, Chiyoda-ku, Japan
| | - Ryoki Asano
- Department of Agro-Food Science, Faculty of Agro-Food Science, Niigata Agro-Food University, Tainai, Japan
| | - Yasuhiro Fukuda
- Laboratory of Sustainable Animal Environment, Graduate School of Agricultural Science, Tohoku University, Osaki, Japan
| | - Yasunori Baba
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Nonoichi, Japan
| | - Chika Tada
- Laboratory of Sustainable Animal Environment, Graduate School of Agricultural Science, Tohoku University, Osaki, Japan
| | - Yutaka Nakai
- Department of Agro-Food Science, Faculty of Agro-Food Science, Niigata Agro-Food University, Tainai, Japan
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Improvement of PersiXyn2 activity and stability in presence of Trehalose and proline as a natural osmolyte. Int J Biol Macromol 2020; 163:348-357. [DOI: 10.1016/j.ijbiomac.2020.06.288] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 06/29/2020] [Accepted: 06/30/2020] [Indexed: 01/04/2023]
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Rabee AE, Forster R, Elekwachi C, Sabra E, Lamara M. Comparative analysis of the metabolically active microbial communities in the rumen of dromedary camels under different feeding systems using total rRNA sequencing. PeerJ 2020; 8:e10184. [PMID: 33194403 PMCID: PMC7603790 DOI: 10.7717/peerj.10184] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 09/23/2020] [Indexed: 11/20/2022] Open
Abstract
Breakdown of plant biomass in rumen depends on interactions between bacteria, archaea, fungi, and protozoa; however, the majority of studies of the microbiome of ruminants, including the few studies of the rumen of camels, only studied one of these microbial groups. In this study, we applied total rRNA sequencing to identify active microbial communities in 22 solid and liquid rumen samples from 11 camels. These camels were reared at three stations that use different feeding systems: clover, hay and wheat straw (G1), fresh clover (G2), and wheat straw (G3). Bacteria dominated the libraries of sequence reads generated from all rumen samples, followed by protozoa, archaea, and fungi respectively. Firmicutes, Thermoplasmatales, Diplodinium, and Neocallimastix dominated bacterial, archaeal, protozoal and fungal communities, respectively in all samples. Libraries generated from camels reared at facility G2, where they were fed fresh clover, showed the highest alpha diversity. Principal co-ordinate analysis and linear discriminate analysis showed clusters associated with facility/feed and the relative abundance of microbes varied between liquid and solid fractions. This provides preliminary evidence that bacteria dominate the microbial communities of the camel rumen and these communities differ significantly between populations of domesticated camels.
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Affiliation(s)
- Alaa Emara Rabee
- Animal and Poultry Nutrition Department, Desert Research Center, Cairo, Cairo, Egypt
| | - Robert Forster
- Lethbridge Research and Development Centre, Agriculture and Agrifood Canada, Lethbridge, AB, Canada
| | - Chijioke Elekwachi
- Lethbridge Research and Development Centre, Agriculture and Agrifood Canada, Lethbridge, AB, Canada
| | - Ebrahim Sabra
- Genetic Engineering and Biotechnology Research Institute, University of Sadat City, Sadat City, Menoufia, Egypt
| | - Mebarek Lamara
- Institut de Recherche sur les Forêts, Université du Québec en Abitibi-Témiscamingue, Rouyn-Noranda, QC, Canada
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7
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Abstract
The rumen contains a great diversity of prokaryotic and eukaryotic microorganisms that allow the ruminant to utilize ligno-cellulose material and to convert non-protein nitrogen into microbial protein to obtain energy and amino acids. However, rumen fermentation also has potential deleterious consequences associated with the emissions of greenhouse gases, excessive nitrogen excreted in manure and may also adversely influence the nutritional value of ruminant products. While several strategies for optimizing the energy and nitrogen use by ruminants have been suggested, a better understanding of the key microorganisms involved and their activities is essential to manipulate rumen processes successfully. Diet is the most obvious factor influencing the rumen microbiome and fermentation. Among dietary interventions, the ban of antimicrobial growth promoters in animal production systems has led to an increasing interest in the use of plant extracts to manipulate the rumen. Plant extracts (e.g. saponins, polyphenol compounds, essential oils) have shown potential to decrease methane emissions and improve the efficiency of nitrogen utilization; however, there are limitations such as inconsistency, transient and adverse effects for their use as feed additives for ruminants. It has been proved that the host animal may also influence the rumen microbial population both as a heritable trait and through the effect of early-life nutrition on microbial population structure and function in adult ruminants. Recent developments have allowed phylogenetic information to be upscaled to metabolic information; however, research effort on cultivation of microorganisms for an in-depth study and characterization is needed. The introduction and integration of metagenomic, transcriptomic, proteomic and metabolomic techniques is offering the greatest potential of reaching a truly systems-level understanding of the rumen; studies have been focused on the prokaryotic population and a broader approach needs to be considered.
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Williams CL, Thomas BJ, McEwan NR, Rees Stevens P, Creevey CJ, Huws SA. Rumen Protozoa Play a Significant Role in Fungal Predation and Plant Carbohydrate Breakdown. Front Microbiol 2020; 11:720. [PMID: 32411103 PMCID: PMC7200989 DOI: 10.3389/fmicb.2020.00720] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 03/27/2020] [Indexed: 11/23/2022] Open
Abstract
The rumen protozoa, alongside fungi, comprise the eukaryotic portion of the rumen microbiome. Rumen protozoa may account for up to 50% of biomass, yet their role in this ecosystem remains unclear. Early experiments inferred a role in carbohydrate and protein metabolism, but due to their close association with bacteria, definitively attributing these functions to the protozoa was challenging. The advent of ‘omic technologies has created opportunities to broaden our understanding of the rumen protozoa. This study aimed to utilize these methods to further our understanding of the role that protozoa play in the rumen in terms of their metabolic capacities, and in doing so, contribute valuable sequence data to reduce the chance of mis or under-representation of the rumen protozoa in meta’omic datasets. Rumen protozoa were isolated and purified using glucose-based sedimentation and differential centrifugation, extracted RNA was Poly(A) fraction enriched and DNase treated before use in a phage-based, cDNA metatranscriptomic library. Biochemical activity testing of the phage library showed 6 putatively positive plaques in response to carboxymethyl cellulose agar (indicative of cellulose activity), and no positive results for tributyrin (indicative of esterase/lipase activity) or egg yolk agar (indicative of proteolysis). Direct sequencing of the cDNA was also conducted using the Illumina HiSeq 2500. The metatranscriptome identified a wealth of carbohydrate-active enzymes which accounted for 8% of total reads. The most highly expressed carbohydrate-active enzymes were glycosyl hydrolases 5 and 11, polysaccharide lyases and deacetylases, xylanases and enzymes active against pectin, mannan and chitin; the latter likely used to digest rumen fungi which contain a chitin-rich cell membrane. Codon usage analysis of expressed genes also showed evidence of horizontal gene transfer, suggesting that many of these enzymes were acquired from the rumen bacteria in an evolutionary response to the carbohydrate-rich environment of the rumen. This study provides evidence of the significant contribution that the protozoa make to carbohydrate breakdown in the rumen, potentially using horizontally acquired genes, and highlights their predatory capacity.
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Affiliation(s)
- Cate L Williams
- Institute of Biological, Environmental and Rural Science, Aberystwyth University, Aberystwyth, United Kingdom
| | - Benjamin J Thomas
- School of Biological Sciences, Institute for Global Food Security, Queen's University Belfast, Belfast, United Kingdom
| | - Neil R McEwan
- School of Pharmacy and Life Sciences, Robert Gordon University, Aberdeen, United Kingdom
| | - Pauline Rees Stevens
- Institute of Biological, Environmental and Rural Science, Aberystwyth University, Aberystwyth, United Kingdom
| | - Christopher J Creevey
- School of Biological Sciences, Institute for Global Food Security, Queen's University Belfast, Belfast, United Kingdom
| | - Sharon A Huws
- School of Biological Sciences, Institute for Global Food Security, Queen's University Belfast, Belfast, United Kingdom
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Feng JM, Jiang CQ, Sun ZY, Hua CJ, Wen JF, Miao W, Xiong J. Single-cell transcriptome sequencing of rumen ciliates provides insight into their molecular adaptations to the anaerobic and carbohydrate-rich rumen microenvironment. Mol Phylogenet Evol 2019; 143:106687. [PMID: 31740334 DOI: 10.1016/j.ympev.2019.106687] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 11/11/2019] [Accepted: 11/13/2019] [Indexed: 01/26/2023]
Abstract
Rumen ciliates are a specialized group of ciliates exclusively found in the anaerobic, carbohydrate-rich rumen microenvironment. However, the molecular and mechanistic basis of the physiological and behavioral adaptation of ciliates to the rumen microenvironment is undefined. We used single-cell transcriptome sequencing to explore the adaptive evolution of three rumen ciliates: two entodiniomorphids, Entodinium furca and Diplodinium dentatum; and one vestibuliferid, Isotricha intestinalis. We found that all three species are members of monophyletic orders within the class Litostomatea, with E. furca and D. dentatum in Entodiniomorphida and I. intestinalis in Vestibuliferida. The two entodiniomorphids might use H2-producing mitochondria and the vestibuliferid might use anaerobic mitochondria to survive under strictly anaerobic conditions. Moreover, carbohydrate-active enzyme (CAZyme) genes were identified in all three species, including cellulases, hemicellulases, and pectinases. The evidence that all three species have acquired prokaryote-derived genes by horizontal gene transfer (HGT) to digest plant biomass includes a significant enrichment of gene ontology categories such as cell wall macromolecule catabolic process and carbohydrate catabolic process and the identification of genes in common between CAZyme and HGT groups. These findings suggest that HGT might be an important mechanism in the adaptive evolution of ciliates to the rumen microenvironment.
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Affiliation(s)
- Jin-Mei Feng
- Department of Pathogenic Biology, School of Medicine, Jianghan University, Wuhan 430056, China
| | - Chuan-Qi Jiang
- Shenzhen Institute of Guangdong Ocean University, Shenzhen 518120, China; Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, Shenzhen 518120, China; Shenzhen Dapeng New District Science and Technology Innovation Service Center, Shenzhen 518119, China; Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Zong-Yi Sun
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Cong-Jie Hua
- Department of Pathogenic Biology, School of Medicine, Jianghan University, Wuhan 430056, China
| | - Jian-Fan Wen
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Wei Miao
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; State Key Laboratory of Freshwater Ecology and Biotechnology of China, Wuhan 430072, China; CAS Center for Excellence in Animal Evolution and Genetics, Kunming 650223, China.
| | - Jie Xiong
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
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Moraïs S, Mizrahi I. Islands in the stream: from individual to communal fiber degradation in the rumen ecosystem. FEMS Microbiol Rev 2019; 43:362-379. [PMID: 31050730 PMCID: PMC6606855 DOI: 10.1093/femsre/fuz007] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Accepted: 04/05/2019] [Indexed: 12/20/2022] Open
Abstract
The herbivore rumen ecosystem constitutes an extremely efficient degradation machinery for the intricate chemical structure of fiber biomass, thus, enabling the hosting animal to digest its feed. The challenging task of deconstructing and metabolizing fiber is performed by microorganisms inhabiting the rumen. Since most of the ingested feed is comprised of plant fiber, these fiber-degrading microorganisms are of cardinal importance to the ecology of the rumen microbial community and to the hosting animal, and have a great impact on our environment and food sustainability. We summarize herein the enzymological fundamentals of fiber degradation, how the genes encoding these enzymes are spread across fiber-degrading microbes, and these microbes' interactions with other members of the rumen microbial community and potential effect on community structure. An understanding of these concepts has applied value for agriculture and our environment, and will also contribute to a better understanding of microbial ecology and evolution in anaerobic ecosystems.
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Affiliation(s)
- Sarah Moraïs
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Sderot Ben Gurion 1, Beer-Sheva 8499000, Israel
| | - Itzhak Mizrahi
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Sderot Ben Gurion 1, Beer-Sheva 8499000, Israel
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Wu H, Li H, Xue Y, Luo G, Gan L, Liu J, Mao L, Long M. High efficiency co-production of ferulic acid and xylooligosaccharides from wheat bran by recombinant xylanase and feruloyl esterase. Biochem Eng J 2017. [DOI: 10.1016/j.bej.2017.01.001] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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12
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Optimization of fermentation media and growth conditions for microbial xylanase production. 3 Biotech 2016; 6:122. [PMID: 28330199 PMCID: PMC4909030 DOI: 10.1007/s13205-016-0445-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 05/25/2016] [Indexed: 11/23/2022] Open
Abstract
Efficiency of cellulase-free xylanases is one of the determining factors in paper and pulp industries. Use of microbes which can produce cellulase-free xylanases may help to overcome the current challenges in kraft pulp processing. Isolation and screening of microorganisms from local samples offers a possibility for obtaining the potential microbes for this purpose. This research was therefore aimed to collect, screen, characterize and identify potential cellulase-free xylanase producers. A total of 313 microbial isolates were collected while using selective media (EBAM and XAM) to determine the xylanolytic potential of microbes. Qualitative and quantitative analyses were performed and finally 11 bacterial and 6 fungal strains were selected for characterization and identification. The potential isolates were identified as Bacillus pumilus (388.82 U/mg), Bacillus safensis (385.26 U/mg), Aspergillus flavus (493.33 U/mg) and Aspergillus niger (419.33 U/mg). Optimization of the microbial strains while using agro-industrial waste is suggested.
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Goux X, Calusinska M, Fossépré M, Benizri E, Delfosse P. Start-up phase of an anaerobic full-scale farm reactor - Appearance of mesophilic anaerobic conditions and establishment of the methanogenic microbial community. BIORESOURCE TECHNOLOGY 2016; 212:217-226. [PMID: 27099947 DOI: 10.1016/j.biortech.2016.04.040] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Revised: 04/08/2016] [Accepted: 04/10/2016] [Indexed: 05/07/2023]
Abstract
The goal of this study was to investigate how the microbial community structure establishes during the start-up phase of a full-scale farm anaerobic reactor inoculated with stale and cold cattle slurry. The 16S/18S high-throughput amplicon sequencing results showed an increase of the bacterial, archaeal and eukaryotic diversity, evenness and richness during the settlement of the mesophilic anaerobic conditions. When a steady performing digestion process was reached, the microbial diversity, evenness and richness decreased, indicating the establishment of a few dominant microbial populations, best adapted to biogas production. Interestingly, among the environmental parameters, the temperature, alkalinity, free-NH3, total solids and O2 content were found to be the main drivers of microbial dynamics. Interactions between eukaryotes, characterized by a high number of unknown organisms, and the bacterial and archaeal communities were also evidenced, suggesting that eukaryotes might play important roles in the anaerobic digestion process.
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Affiliation(s)
- Xavier Goux
- Environmental Research and Innovation Department, Luxembourg Institute of Science and Technology, 41 rue du Brill, L-4422 Belvaux, Luxembourg; Laboratoire Sols et Environnement, Université de Lorraine, UMR 1120, 2 avenue de la Forêt de Haye, TSA 40602, F-54518 Vandœuvre-lès-Nancy, France; INRA, Laboratoire Sols et Environnement, UMR 1120, 2 avenue de la Forêt de Haye, TSA 40602, F-54518 Vandœuvre-lès-Nancy, France
| | - Magdalena Calusinska
- Environmental Research and Innovation Department, Luxembourg Institute of Science and Technology, 41 rue du Brill, L-4422 Belvaux, Luxembourg
| | - Marie Fossépré
- Environmental Research and Innovation Department, Luxembourg Institute of Science and Technology, 41 rue du Brill, L-4422 Belvaux, Luxembourg
| | - Emile Benizri
- Laboratoire Sols et Environnement, Université de Lorraine, UMR 1120, 2 avenue de la Forêt de Haye, TSA 40602, F-54518 Vandœuvre-lès-Nancy, France; INRA, Laboratoire Sols et Environnement, UMR 1120, 2 avenue de la Forêt de Haye, TSA 40602, F-54518 Vandœuvre-lès-Nancy, France
| | - Philippe Delfosse
- Environmental Research and Innovation Department, Luxembourg Institute of Science and Technology, 41 rue du Brill, L-4422 Belvaux, Luxembourg.
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14
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Newbold CJ, de la Fuente G, Belanche A, Ramos-Morales E, McEwan NR. The Role of Ciliate Protozoa in the Rumen. Front Microbiol 2015; 6:1313. [PMID: 26635774 PMCID: PMC4659874 DOI: 10.3389/fmicb.2015.01313] [Citation(s) in RCA: 301] [Impact Index Per Article: 33.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 11/09/2015] [Indexed: 01/17/2023] Open
Abstract
First described in 1843, Rumen protozoa with their striking appearance were assumed to be important for the welfare of their host. However, despite contributing up to 50% of the bio-mass in the rumen, the role of protozoa in rumen microbial ecosystem remains unclear. Phylogenetic analysis of 18S rDNA libraries generated from the rumen of cattle, sheep, and goats has revealed an unexpected diversity of ciliated protozoa although variation in gene copy number between species makes it difficult to obtain absolute quantification. Despite repeated attempts it has proven impossible to maintain rumen protozoa in axenic culture. Thus it has been difficult to establish conclusively a role of ciliate protozoa in rumen fiber degradation. The development of techniques to clone and express ciliate genes in λ phage, together with bioinformatic indices to confirm the ciliate origin of the genes has allowed the isolation and characterization of fibrolytic genes from rumen protozoa. Elimination of the ciliate protozoa increases microbial protein supply by up to 30% and reduces methane production by up to 11%. Our recent findings suggest that holotrich protozoa play a disproportionate role in supporting methanogenesis whilst the small Entodinium are responsible for much of the bacterial protein turnover. As yet no method to control protozoa in the rumen that is safe and practically applicable has been developed, however a range of plant extract capable of controlling if not completely eliminating rumen protozoa have been described.
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Affiliation(s)
- Charles J. Newbold
- Institute of Biological Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - Gabriel de la Fuente
- Departament de Producció Animal, Escola Tècnica Superior d’Enginyeria Agrària, Universitat de Lleida, Lleida, Spain
| | - Alejandro Belanche
- Institute of Biological Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - Eva Ramos-Morales
- Institute of Biological Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - Neil R. McEwan
- Institute of Biological Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
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15
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de Aguiar SC, Zeoula LM, do Prado OPP, Arcuri PB, Forano E. Characterization of rumen bacterial strains isolated from enrichments of rumen content in the presence of propolis. World J Microbiol Biotechnol 2014; 30:2917-26. [PMID: 25172217 DOI: 10.1007/s11274-014-1719-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Accepted: 08/07/2014] [Indexed: 01/20/2023]
Abstract
Propolis presents many biological properties, including antibacterial activities, and has been proposed as an additive in ruminant nutrition. Twenty bacterial strains, previously isolated from enrichments of Brazilian cow rumen contents in the presence of different propolis extracts (LLOS), were characterized using phenotyping and 16S rRNA identification. Seven strains were assigned to Streptococcus sp., most likely S. bovis, and were all degrading starch. One amylolytic lactate-utilizing strain of Selenomonas ruminantium was also found. Two strains of Clostridium bifermentans were identified and showed proteolytic activity. Two strains were assigned to Mitsuokella jalaludinii and were saccharolytic. One strain belonged to a Bacillus species and seven strains were affiliated with Escherichia coli. All of the 20 strains were able to use many sugars, but none of them were able to degrade the polysaccharides carboxymethylcellulose and xylans. The effect of three propolis extracts (LLOS B1, C1 and C3) was tested on the in vitro growth of four representative isolates of S. bovis, E. coli, M. jalaludinii and C. bifermentans. The growth of S. bovis, E. coli and M. jalaludinii was not affected by the three propolis extracts at 1 mg ml(-1). C. bifermentans growth was completely inhibited at this LLOS concentration, but this bacterium was partially resistant at lower concentrations. LLOS C3, with the lower concentration of phenolic compounds, was a little less inhibitory than B1 and C1 on this strain.
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Affiliation(s)
- Sílvia Cristina de Aguiar
- Departamento de Zootecnia, Universidade Estadual de Maringá, Avenida Colombo 5790, Maringá, PR, 87020-900, Brazil
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16
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Pauchet Y, Heckel DG. The genome of the mustard leaf beetle encodes two active xylanases originally acquired from bacteria through horizontal gene transfer. Proc Biol Sci 2013; 280:20131021. [PMID: 23698014 DOI: 10.1098/rspb.2013.1021] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The primary plant cell wall comprises the most abundant polysaccharides on the Earth and represents a rich source of energy for organisms which have evolved the ability to digest them. Enzymes able to degrade plant cell wall polysaccharides are widely distributed in micro-organisms but are generally absent in animals, although their presence in insects, especially phytophagous beetles from the superfamilies Chrysomeloidea and Curculionoidea, has recently begun to be appreciated. The observed patchy distribution of endogenous genes encoding these enzymes in animals has raised questions about their evolutionary origins. Recent evidence suggests that endogenous plant cell wall degrading enzymes-encoding genes have been acquired by animals through a mechanism known as horizontal gene transfer (HGT). HGT describes how genetic material is moved by means other than vertical inheritance from a parent to an offspring. Here, we provide evidence that the mustard leaf beetle, Phaedon cochleariae, possesses in its genome genes encoding active xylanases from the glycoside hydrolase family 11 (GH11). We also provide evidence that these genes were originally acquired by P. cochleariae from a species of gammaproteobacteria through HGT. This represents the first example of the presence of genes from the GH11 family in animals.
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Affiliation(s)
- Yannick Pauchet
- Department of Entomology, Max Planck institute for Chemical Ecology, Hans-Knoell-Strasse 8, 07745 Jena, Germany.
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17
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Lamrabet O, Merhej V, Pontarotti P, Raoult D, Drancourt M. The genealogic tree of mycobacteria reveals a long-standing sympatric life into free-living protozoa. PLoS One 2012; 7:e34754. [PMID: 22511965 PMCID: PMC3325273 DOI: 10.1371/journal.pone.0034754] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2011] [Accepted: 03/08/2012] [Indexed: 02/07/2023] Open
Abstract
Free-living protozoa allow horizontal gene transfer with and between the microorganisms that they host. They host mycobacteria for which the sources of transferred genes remain unknown. Using BLASTp, we searched within the genomes of 15 mycobacteria for homologous genes with 34 amoeba-resistant bacteria and the free-living protozoa Dictyostelium discoideum. Subsequent phylogenetic analysis of these sequences revealed that eight mycobacterial open-reading frames (ORFs) were probably acquired via horizontal transfer from beta- and gamma-Proteobacteria and from Firmicutes, but the transfer histories could not be reliably established in details. One further ORF encoding a pyridine nucleotide disulfide oxidoreductase (pyr-redox) placed non-tuberculous mycobacteria in a clade with Legionella spp., Francisella spp., Coxiella burnetii, the ciliate Tetrahymena thermophila and D. discoideum with a high reliability. Co-culturing Mycobacterium avium and Legionella pneumophila with the amoeba Acanthamoeba polyphaga demonstrated that these two bacteria could live together in amoebae for five days, indicating the biological relevance of intra-amoebal transfer of the pyr-redox gene. In conclusion, the results of this study support the hypothesis that protists can serve as a source and a place for gene transfer in mycobacteria.
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Affiliation(s)
- Otmane Lamrabet
- URMITE CNRS-IRD UMR 6236, IFR48, Méditerranée Infection, Aix-Marseille Université, Marseille, France
| | - Vicky Merhej
- URMITE CNRS-IRD UMR 6236, IFR48, Méditerranée Infection, Aix-Marseille Université, Marseille, France
| | - Pierre Pontarotti
- Equipe Evolution Biologique et Modélisation UMR 6632, IRF48, Aix-Marseille Université/CNRS, Marseille, France
| | - Didier Raoult
- URMITE CNRS-IRD UMR 6236, IFR48, Méditerranée Infection, Aix-Marseille Université, Marseille, France
| | - Michel Drancourt
- URMITE CNRS-IRD UMR 6236, IFR48, Méditerranée Infection, Aix-Marseille Université, Marseille, France
- * E-mail:
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Paës G, Berrin JG, Beaugrand J. GH11 xylanases: Structure/function/properties relationships and applications. Biotechnol Adv 2011; 30:564-92. [PMID: 22067746 DOI: 10.1016/j.biotechadv.2011.10.003] [Citation(s) in RCA: 275] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2011] [Revised: 10/06/2011] [Accepted: 10/13/2011] [Indexed: 01/02/2023]
Abstract
For technical, environmental and economical reasons, industrial demands for process-fitted enzymes have evolved drastically in the last decade. Therefore, continuous efforts are made in order to get insights into enzyme structure/function relationships to create improved biocatalysts. Xylanases are hemicellulolytic enzymes, which are responsible for the degradation of the heteroxylans constituting the lignocellulosic plant cell wall. Due to their variety, xylanases have been classified in glycoside hydrolase families GH5, GH8, GH10, GH11, GH30 and GH43 in the CAZy database. In this review, we focus on GH11 family, which is one of the best characterized GH families with bacterial and fungal members considered as true xylanases compared to the other families because of their high substrate specificity. Based on an exhaustive analysis of the sequences and 3D structures available so far, in relation with biochemical properties, we assess biochemical aspects of GH11 xylanases: structure, catalytic machinery, focus on their "thumb" loop of major importance in catalytic efficiency and substrate selectivity, inhibition, stability to pH and temperature. GH11 xylanases have for a long time been used as biotechnological tools in various industrial applications and represent in addition promising candidates for future other uses.
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Affiliation(s)
- Gabriel Paës
- INRA, UMR614 FARE, 2 esplanade Roland-Garros, F-51686 Reims, France.
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19
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Activity-based metagenomic screening and biochemical characterization of bovine ruminal protozoan glycoside hydrolases. Appl Environ Microbiol 2011; 77:8106-13. [PMID: 21948825 DOI: 10.1128/aem.05925-11] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The rumen, the foregut of herbivorous ruminant animals such as cattle, functions as a bioreactor to process complex plant material. Among the numerous and diverse microbes involved in ruminal digestion are the ruminal protozoans, which are single-celled, ciliated eukaryotic organisms. An activity-based screen was executed to identify genes encoding fibrolytic enzymes present in the metatranscriptome of a bovine ruminal protozoan-enriched cDNA expression library. Of the four novel genes identified, two were characterized in biochemical assays. Our results provide evidence for the effective use of functional metagenomics to retrieve novel enzymes from microbial populations that cannot be maintained in axenic cultures.
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20
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Two Types of Phytases (Histidine Acid Phytase and β-Propeller Phytase) in Serratia sp. TN49 from the Gut of Batocera horsfieldi (Coleoptera) Larvae. Curr Microbiol 2011; 63:408-15. [DOI: 10.1007/s00284-011-9995-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2011] [Accepted: 08/07/2011] [Indexed: 11/26/2022]
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21
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Qi M, Wang P, O'Toole N, Barboza PS, Ungerfeld E, Leigh MB, Selinger LB, Butler G, Tsang A, McAllister TA, Forster RJ. Snapshot of the eukaryotic gene expression in muskoxen rumen--a metatranscriptomic approach. PLoS One 2011; 6:e20521. [PMID: 21655220 PMCID: PMC3105075 DOI: 10.1371/journal.pone.0020521] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2011] [Accepted: 05/01/2011] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Herbivores rely on digestive tract lignocellulolytic microorganisms, including bacteria, fungi and protozoa, to derive energy and carbon from plant cell wall polysaccharides. Culture independent metagenomic studies have been used to reveal the genetic content of the bacterial species within gut microbiomes. However, the nature of the genes encoded by eukaryotic protozoa and fungi within these environments has not been explored using metagenomic or metatranscriptomic approaches. METHODOLOGY/PRINCIPAL FINDINGS In this study, a metatranscriptomic approach was used to investigate the functional diversity of the eukaryotic microorganisms within the rumen of muskoxen (Ovibos moschatus), with a focus on plant cell wall degrading enzymes. Polyadenylated RNA (mRNA) was sequenced on the Illumina Genome Analyzer II system and 2.8 gigabases of sequences were obtained and 59129 contigs assembled. Plant cell wall degrading enzyme modules including glycoside hydrolases, carbohydrate esterases and polysaccharide lyases were identified from over 2500 contigs. These included a number of glycoside hydrolase family 6 (GH6), GH48 and swollenin modules, which have rarely been described in previous gut metagenomic studies. CONCLUSIONS/SIGNIFICANCE The muskoxen rumen metatranscriptome demonstrates a much higher percentage of cellulase enzyme discovery and an 8.7x higher rate of total carbohydrate active enzyme discovery per gigabase of sequence than previous rumen metagenomes. This study provides a snapshot of eukaryotic gene expression in the muskoxen rumen, and identifies a number of candidate genes coding for potentially valuable lignocellulolytic enzymes.
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Affiliation(s)
- Meng Qi
- Lethbridge Research Centre, Agriculture and Agri-Food Canada, Lethbridge, Alberta, Canada
| | - Pan Wang
- Lethbridge Research Centre, Agriculture and Agri-Food Canada, Lethbridge, Alberta, Canada
- Department of Biological Sciences, University of Lethbridge, Lethbridge, Alberta, Canada
| | - Nicholas O'Toole
- Centre for Structural and Functional Genomics, Concordia University, Montreal, Quebec, Canada
| | - Perry S. Barboza
- Department of Biology and Wildlife, Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, Alaska, United States of America
| | - Emilio Ungerfeld
- Lethbridge Research Centre, Agriculture and Agri-Food Canada, Lethbridge, Alberta, Canada
| | - Mary Beth Leigh
- Department of Biology and Wildlife, Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, Alaska, United States of America
| | - L. Brent Selinger
- Department of Biological Sciences, University of Lethbridge, Lethbridge, Alberta, Canada
| | - Greg Butler
- Centre for Structural and Functional Genomics, Concordia University, Montreal, Quebec, Canada
| | - Adrian Tsang
- Centre for Structural and Functional Genomics, Concordia University, Montreal, Quebec, Canada
| | - Tim A. McAllister
- Lethbridge Research Centre, Agriculture and Agri-Food Canada, Lethbridge, Alberta, Canada
| | - Robert J. Forster
- Lethbridge Research Centre, Agriculture and Agri-Food Canada, Lethbridge, Alberta, Canada
- * E-mail:
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22
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Chassard C, Delmas E, Robert C, Lawson PA, Bernalier-Donadille A. Ruminococcus champanellensis sp. nov., a cellulose-degrading bacterium from human gut microbiota. Int J Syst Evol Microbiol 2011; 62:138-143. [PMID: 21357460 DOI: 10.1099/ijs.0.027375-0] [Citation(s) in RCA: 109] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
A strictly anaerobic, cellulolytic strain, designated 18P13(T), was isolated from a human faecal sample. Cells were Gram-positive non-motile cocci. Strain 18P13(T) was able to degrade microcrystalline cellulose but the utilization of soluble sugars was restricted to cellobiose. Acetate and succinate were the major end products of cellulose and cellobiose fermentation. 16S rRNA gene sequence analysis revealed that the isolate belonged to the genus Ruminococcus of the family Ruminococcaceae. The closest phylogenetic relative was the ruminal cellulolytic strain Ruminococcus flavefaciens ATCC 19208(T) (<95% 16S rRNA gene sequence similarity). The DNA G+C content of strain 18P13(T) was 53.05±0.7 mol%. On the basis of phylogenetic analysis, and morphological and physiological data, strain 18P13(T) can be differentiated from other members of the genus Ruminococcus with validly published names. The name Ruminococcus champanellensis sp. nov. is proposed, with 18P13(T) (=DSM 18848(T)=JCM 17042(T)) as the type strain.
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Affiliation(s)
- Christophe Chassard
- Unité de Microbiologie, INRA, Centre de Recherches de Clermont Ferrand - Theix, 63 122 Saint Genès-Champanelle, France
| | - Eve Delmas
- Unité de Microbiologie, INRA, Centre de Recherches de Clermont Ferrand - Theix, 63 122 Saint Genès-Champanelle, France
| | - Céline Robert
- Unité de Microbiologie, INRA, Centre de Recherches de Clermont Ferrand - Theix, 63 122 Saint Genès-Champanelle, France
| | - Paul A Lawson
- Department of Botany and Microbiology, University of Oklahoma, Norman, OK 73019, USA
| | - Annick Bernalier-Donadille
- Unité de Microbiologie, INRA, Centre de Recherches de Clermont Ferrand - Theix, 63 122 Saint Genès-Champanelle, France
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23
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Bacterial infections associated with cancer: possible implication in etiology with special reference to lateral gene transfer. Cancer Metastasis Rev 2010; 29:331-7. [DOI: 10.1007/s10555-010-9217-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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24
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Mirande C, Kadlecikova E, Matulova M, Capek P, Bernalier-Donadille A, Forano E, Béra-Maillet C. Dietary fibre degradation and fermentation by two xylanolytic bacteria Bacteroides xylanisolvens XB1A and Roseburia intestinalis XB6B4 from the human intestine. J Appl Microbiol 2010; 109:451-460. [PMID: 20105245 DOI: 10.1111/j.1365-2672.2010.04671.x] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
AIMS To characterize fibre degradation, colonization and fermentation, and xylanase activity of two xylanolytic bacteria Bacteroides xylanisolvens XB1A(T) and Roseburia intestinalis XB6B4 from the human colon. METHODS AND RESULTS The bacteria grew well on all the substrates chosen to represent dietary fibres: wheat and corn bran, pea, cabbage and leek fibres, and also on purified xylans. Roseburia intestinalis colonized the substrates more efficiently than Bact. xylanisolvens. For the two bacteria, 80-99% of the total xylanase activity was associated with the cells whatever the substrate and time of growth. Optimal specific activities of cells were obtained on oat spelt xylan; they were higher than those previously measured for xylanolytic bacteria from the human gut. Roseburia intestinalis produced high molecular mass xylanases (100-70 kDa), while Bact. xylanisolvens produced lower molecular mass enzymes, including a cell-associated xylanase of 37 kDa. CONCLUSIONS The two bacteria display very high xylanolytic activity on the different substrates. Differences were observed on substrate attachment and enzyme systems, suggesting that the two species occupy different niches within the gut microbiota. SIGNIFICANCE AND IMPACT OF THE STUDY This study characterizes xylan degradation by two major species of the human intestine.
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Affiliation(s)
- C Mirande
- INRA, UR454 Unité de Microbiologie, Centre de Recherches de Clermont-Ferrand/Theix, Saint-Genès-Champanelle, France
| | - E Kadlecikova
- INRA, UR454 Unité de Microbiologie, Centre de Recherches de Clermont-Ferrand/Theix, Saint-Genès-Champanelle, France
| | - M Matulova
- Institute of Chemistry, Centre for Glycomics, Slovak Academy of Sciences, Bratislava, Slovak Republic
| | - P Capek
- Institute of Chemistry, Centre for Glycomics, Slovak Academy of Sciences, Bratislava, Slovak Republic
| | - A Bernalier-Donadille
- INRA, UR454 Unité de Microbiologie, Centre de Recherches de Clermont-Ferrand/Theix, Saint-Genès-Champanelle, France
| | - E Forano
- INRA, UR454 Unité de Microbiologie, Centre de Recherches de Clermont-Ferrand/Theix, Saint-Genès-Champanelle, France
| | - C Béra-Maillet
- INRA, UR454 Unité de Microbiologie, Centre de Recherches de Clermont-Ferrand/Theix, Saint-Genès-Champanelle, France
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25
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Flint HJ, Bayer EA. Plant cell wall breakdown by anaerobic microorganisms from the Mammalian digestive tract. Ann N Y Acad Sci 2008; 1125:280-8. [PMID: 18378598 DOI: 10.1196/annals.1419.022] [Citation(s) in RCA: 147] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Degradation of lignocellulosic plant material in the mammalian digestive tract is accomplished by communities of anaerobic microorganisms that exist in symbiotic association with the host. Catalytic domains and substrate-binding modules concerned with plant polysaccharide degradation are found in a variety of anaerobic bacteria, fungi, and protozoa from the mammalian gut. The organization of plant cell wall-degrading enzymes, however, varies widely. The cellulolytic gram-positive bacterium Ruminococcus flavefaciens produces an elaborate cellulosomal enzyme complex that is anchored to the bacterial cell wall; assembly of the complex involves at least five different dockerin:cohesin specificities, and the R. flavefaciens genome encodes at least 180 dockerin-containing proteins that encompass a wide array of catalytic and binding activities. On the other hand, in the cellulolytic protozoan, Polyplastron multivesiculatum, individual plant cell wall-degrading enzymes appear to be secreted into food vacuoles, while the gram-negative bacterium Prevotella bryantii appears to possess a sequestration-type system for the utilization of soluble xylans. The system that is employed for polysaccharide utilization must play a major role in defining the ecological niche that each organism occupies within a complex gut community. 16S rRNA analyses are also revealing uncultured bacterial species closely adherent to fibrous substrates in the rumen and in the large intestine of animals and humans. The true complexity, both at a single organism and community level, of the microbial enzyme systems that allow animals to digest plant material is beginning to become apparent.
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Affiliation(s)
- Harry J Flint
- Microbial Ecology Group, Rowett Research Institute, Greenburn Road, Bucksburn, Aberdeen AB21 9SB, UK.
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26
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Polysaccharide utilization by gut bacteria: potential for new insights from genomic analysis. Nat Rev Microbiol 2008; 6:121-31. [PMID: 18180751 DOI: 10.1038/nrmicro1817] [Citation(s) in RCA: 1074] [Impact Index Per Article: 67.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The microbiota of the mammalian intestine depend largely on dietary polysaccharides as energy sources. Most of these polymers are not degradable by the host, but herbivores can derive 70% of their energy intake from microbial breakdown--a classic example of mutualism. Moreover, dietary polysaccharides that reach the human large intestine have a major impact on gut microbial ecology and health. Insight into the molecular mechanisms by which different gut bacteria use polysaccharides is, therefore, of fundamental importance. Genomic analyses of the gut microbiota could revolutionize our understanding of these mechanisms and provide new biotechnological tools for the conversion of polysaccharides, including lignocellulosic biomass, into monosaccharides.
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27
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OmPraba G, Velmurugan D, Arumugam P, Govindasamy V, Kalaichelvan PT. Homology Model of a Novel Thermostable Xylanase fromBacillus subtilis-AK1. J Biomol Struct Dyn 2007; 25:311-20. [DOI: 10.1080/07391102.2007.10507179] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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28
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Chassard C, Goumy V, Leclerc M, Del'homme C, Bernalier-Donadille A. Characterization of the xylan-degrading microbial community from human faeces. FEMS Microbiol Ecol 2007; 61:121-31. [PMID: 17391327 DOI: 10.1111/j.1574-6941.2007.00314.x] [Citation(s) in RCA: 106] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
In humans, plant cell wall polysaccharides represent an important source of dietary fibres that are digested by gut microorganisms. Despite the extensive degradation of xylan in the colon, the population structure and the taxonomy of the predominant bacteria involved in degradation of this polysaccharide have not been extensively explored. The objective of our study was to characterize the xylanolytic microbial community from human faeces, using xylan from different botanic origins. The xylanolytic population was enumerated at high level in all faecal samples studied. The predominant xylanolytic organisms further isolated (20 strains) were assigned to Roseburia and Bacteroides species. Some Bacteroides isolates corresponded to the two newly described species Bacteroides intestinalis and Bacteroides dorei. Other isolates were closely related to Bacteroides sp. nov., a cellulolytic bacterium recently isolated from human faeces. The remaining Bacteroides strains could be considered to belong to a new species of this genus. Roseburia isolates could be assigned to the species Roseburia intestinalis. The xylanase activity of the Bacteroides and Roseburia isolates was found to be higher than that of other gut xylanolytic species previously identified. Our results provide new insights to the diversity and activity of the human gut xylanolytic community. Four new xylan-degrading Bacteroides species were identified and the xylanolytic capacity of R. intestinalis was further shown.
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Affiliation(s)
- Christophe Chassard
- Unité de Microbiologie, INRA, Centre de Recherches de Clermont-Ferrand/Theix, Saint Genès-Champanelle, France
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29
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Blouzard JC, Bourgeois C, de Philip P, Valette O, Bélaïch A, Tardif C, Bélaïch JP, Pagès S. Enzyme diversity of the cellulolytic system produced by Clostridium cellulolyticum explored by two-dimensional analysis: identification of seven genes encoding new dockerin-containing proteins. J Bacteriol 2007; 189:2300-9. [PMID: 17209020 PMCID: PMC1899368 DOI: 10.1128/jb.00917-06] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The enzyme diversity of the cellulolytic system produced by Clostridium cellulolyticum grown on crystalline cellulose as a sole carbon and energy source was explored by two-dimensional electrophoresis. The cellulolytic system of C. cellulolyticum is composed of at least 30 dockerin-containing proteins (designated cellulosomal proteins) and 30 noncellulosomal components. Most of the known cellulosomal proteins, including CipC, Cel48F, Cel8C, Cel9G, Cel9E, Man5K, Cel9M, and Cel5A, were identified by using two-dimensional Western blot analysis with specific antibodies, whereas Cel5N, Cel9J, and Cel44O were identified by using N-terminal sequencing. Unknown enzymes having carboxymethyl cellulase or xylanase activities were detected by zymogram analysis of two-dimensional gels. Some of these enzymes were identified by N-terminal sequencing as homologs of proteins listed in the NCBI database. Using Trap-Dock PCR and DNA walking, seven genes encoding new dockerin-containing proteins were cloned and sequenced. Some of these genes are clustered. Enzymes encoded by these genes belong to glycoside hydrolase families GH2, GH9, GH10, GH26, GH27, and GH59. Except for members of family GH9, which contains only cellulases, the new modular glycoside hydrolases discovered in this work could be involved in the degradation of different hemicellulosic substrates, such as xylan or galactomannan.
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Affiliation(s)
- Jean-Charles Blouzard
- Laboratoire de Bioénergétique et Ingénierie des Protéines, IBSM, Centre National de la Recherche Scientifique and Université de Provence, Marseille, France
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30
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Ricard G, McEwan NR, Dutilh BE, Jouany JP, Macheboeuf D, Mitsumori M, McIntosh FM, Michalowski T, Nagamine T, Nelson N, Newbold CJ, Nsabimana E, Takenaka A, Thomas NA, Ushida K, Hackstein JHP, Huynen MA. Horizontal gene transfer from Bacteria to rumen Ciliates indicates adaptation to their anaerobic, carbohydrates-rich environment. BMC Genomics 2006; 7:22. [PMID: 16472398 PMCID: PMC1413528 DOI: 10.1186/1471-2164-7-22] [Citation(s) in RCA: 110] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2005] [Accepted: 02/10/2006] [Indexed: 12/04/2022] Open
Abstract
Background The horizontal transfer of expressed genes from Bacteria into Ciliates which live in close contact with each other in the rumen (the foregut of ruminants) was studied using ciliate Expressed Sequence Tags (ESTs). More than 4000 ESTs were sequenced from representatives of the two major groups of rumen Cilates: the order Entodiniomorphida (Entodinium simplex, Entodinium caudatum, Eudiplodinium maggii, Metadinium medium, Diploplastron affine, Polyplastron multivesiculatum and Epidinium ecaudatum) and the order Vestibuliferida, previously called Holotricha (Isotricha prostoma, Isotricha intestinalis and Dasytricha ruminantium). Results A comparison of the sequences with the completely sequenced genomes of Eukaryotes and Prokaryotes, followed by large-scale construction and analysis of phylogenies, identified 148 ciliate genes that specifically cluster with genes from the Bacteria and Archaea. The phylogenetic clustering with bacterial genes, coupled with the absence of close relatives of these genes in the Ciliate Tetrahymena thermophila, indicates that they have been acquired via Horizontal Gene Transfer (HGT) after the colonization of the gut by the rumen Ciliates. Conclusion Among the HGT candidates, we found an over-representation (>75%) of genes involved in metabolism, specifically in the catabolism of complex carbohydrates, a rich food source in the rumen. We propose that the acquisition of these genes has greatly facilitated the Ciliates' colonization of the rumen providing evidence for the role of HGT in the adaptation to new niches.
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Affiliation(s)
- Guénola Ricard
- Center for Molecular and Biomolecular Informatics, Nijmegen Center for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Toernooiveld 1, 6525 ED Nijmegen, The Netherlands
| | - Neil R McEwan
- Institute of Rural Sciences, University of Wales, Aberystwyth, SY23 3AL, UK
| | - Bas E Dutilh
- Center for Molecular and Biomolecular Informatics, Nijmegen Center for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Toernooiveld 1, 6525 ED Nijmegen, The Netherlands
| | - Jean-Pierre Jouany
- I.N.R.A., Station de Recherches sur la Nutrition des Herbivores, Centre de Recherches de Clermont-Ferrand/Theix, France
| | - Didier Macheboeuf
- I.N.R.A., Station de Recherches sur la Nutrition des Herbivores, Centre de Recherches de Clermont-Ferrand/Theix, France
| | - Makoto Mitsumori
- National Institute of Livestock and Grassland Science, 2 Ikenodai, Kukizaki, Ibaraki, 305-0901, Japan
| | | | - Tadeusz Michalowski
- Kielanowski Institute of Animal Physiology and Nutrition, Polish Academy of Sciences, Jablonna, Warsaw, Poland
| | - Takafumi Nagamine
- Rumen Microbiology Research Team, STAFF-Institute, 446-1 Ippaizuka, Kamiyokoba, Tsukuba 305-0854, Japan
| | - Nancy Nelson
- Rowett Research Institute, Aberdeen, AB21 9SB, UK
| | - Charles J Newbold
- Rumen Microbiology Research Team, STAFF-Institute, 446-1 Ippaizuka, Kamiyokoba, Tsukuba 305-0854, Japan
| | - Eli Nsabimana
- I.N.R.A., Station de Recherches sur la Nutrition des Herbivores, Centre de Recherches de Clermont-Ferrand/Theix, France
| | - Akio Takenaka
- National Institute of Livestock and Grassland Science, 2 Ikenodai, Kukizaki, Ibaraki, 305-0901, Japan
| | | | - Kazunari Ushida
- Laboratory of Animal Science, Kyoto Prefectural University, Shimogamo, Kyoto 606-8522, Japan
| | - Johannes HP Hackstein
- Department of Evolutionary Microbiology, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Martijn A Huynen
- Center for Molecular and Biomolecular Informatics, Nijmegen Center for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Toernooiveld 1, 6525 ED Nijmegen, The Netherlands
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Newbold CJ, McEwan NR, Calza RE, Chareyron EN, Duval SM, Eschenlauer SCP, McIntosh FM, Nelson N, Travis AJ, Wallace RJ. An NAD+-dependent glutamate dehydrogenase cloned from the ruminal ciliate protozoan,Entodinium caudatum. FEMS Microbiol Lett 2005; 247:113-21. [PMID: 15921862 DOI: 10.1016/j.femsle.2005.04.034] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2005] [Revised: 04/21/2005] [Accepted: 04/23/2005] [Indexed: 11/28/2022] Open
Abstract
An NAD(+)-dependent glutamate dehydrogenase (GDH; EC 1.4.1.24) was cloned from the ruminal ciliate protozoan, Entodinium caudatum. The gene had high sequence similarity to GDH genes from the Bacteroides (class)--a class of bacteria which is highly represented in the rumen. When expressed in Escherichia coli the enzyme had a high affinity for ammonia and alpha-ketoglutarate (apparent K(m) of 2.33 and 0.71 mM, respectively) and a low affinity for glutamate (apparent K(m) of 98 mM). GDH activity and GDH mRNA concentration were increased by incubating washed E. caudatum cells with ammonia and antibiotics. These results suggest that the GDH is an anabolic enzyme catalysing the assimilation of ammonia by E. caudatum in the rumen and that the gene was probably acquired by lateral gene transfer from a ruminal bacterium.
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Affiliation(s)
- C James Newbold
- Rowett Research Institute, Greenburn Road, Aberdeen AB21 9SB, Scotland, United Kingdom
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32
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Béra-Maillet C, Devillard E, Cezette M, Jouany JP, Forano E. Xylanases and carboxymethylcellulases of the rumen protozoaPolyplastron multivesiculatum,Eudiplodinium maggiiandEntodiniumsp. FEMS Microbiol Lett 2005; 244:149-56. [PMID: 15727834 DOI: 10.1016/j.femsle.2005.01.035] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2004] [Revised: 10/27/2004] [Accepted: 01/20/2005] [Indexed: 11/20/2022] Open
Abstract
Endoglucanase and xylanase activities of three rumen protozoa, Polyplastron multivesiculatum, Eudiplodinium maggii, and Entodinium sp. were compared qualitatively by zymograms and quantitatively by measuring specific activities against different polysaccharides. A set of carboxymethylcellulases and xylanases was produced by the large ciliates whereas no band of activity was observed for Entodinium sp. in zymograms. Specific activity of endoglucanases from P. multivesiculatum (1.3 micromol mg prot(-1) min(-1)) was twice that of E. maggii, whereas xylanase specific activity (4.5 micromol mg prot(-1) min(-1)) was only half. Very weak activities were observed for Entodinium sp. A new xylanase gene, xyn11D, from P. multivesiculatum was reported and its gene product compared to 33 other family 11 xylanases. Phylogenetic analysis showed that xylanase sequences from rumen protozoa are closely related to those of bacteria.
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Affiliation(s)
- Christel Béra-Maillet
- Unité de Microbiologie, INRA, Centre de Recherches de Clermont-Ferrand-Theix, 63122 Saint-Genès-Champanelle, France.
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33
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Béra-Maillet C, Ribot Y, Forano E. Fiber-degrading systems of different strains of the genus Fibrobacter. Appl Environ Microbiol 2004; 70:2172-9. [PMID: 15066810 PMCID: PMC383150 DOI: 10.1128/aem.70.4.2172-2179.2004] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The S85 type strain of Fibrobacter succinogenes, a major ruminal fibrolytic species, was isolated 49 years ago from a bovine rumen and has been used since then as a model for extensive studies. To assess the validity of this model, we compared the cellulase- and xylanase-degrading activities of several other F. succinogenes strains originating from different ruminants, including recently isolated strains, and looked for the presence of 10 glycoside hydrolase genes previously identified in S85. The NR9 F. intestinalis type strain, representative of the second species of the genus, was also included in this study. DNA-DNA hybridization and 16S rRNA gene sequencing first classified the strains and provided the phylogenetic positions of isolates of both species. Cellulase and xylanase activity analyses revealed similar activity profiles for all F. succinogenes strains. However, the F(E) strain, phylogenetically close to S85, presented a poor xylanolytic system and weak specific activities. Furthermore, the HM2 strain, genetically distant from the other F. succinogenes isolates, displayed a larger cellulolytic profile on zymograms and higher cellulolytic specific activity. F. intestinalis NR9 presented a higher cellulolytic specific activity and a stronger extracellular xylanolytic activity. Almost all glycoside hydrolase genes studied were found in the F. succinogenes isolates by PCR, except in the HM2 strain, and few of them were detected in F. intestinalis NR9. As expected, the fibrolytic genes of strains of the genus Fibrobacter as well as the cellulase and xylanase activities are better conserved in closely related phylogenetic isolates.
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Affiliation(s)
- Christel Béra-Maillet
- Unité de Microbiologie, INRA CR de Clermont-Ferrand-Theix, 63122 Saint-Genès-Champanelle, France
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van den Eede G, Aarts H, Buhk HJ, Corthier G, Flint HJ, Hammes W, Jacobsen B, Midtvedt T, van der Vossen J, von Wright A, Wackernagel W, Wilcks A. The relevance of gene transfer to the safety of food and feed derived from genetically modified (GM) plants. Food Chem Toxicol 2004; 42:1127-56. [PMID: 15123384 DOI: 10.1016/j.fct.2004.02.001] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2003] [Accepted: 02/04/2004] [Indexed: 12/31/2022]
Abstract
In 2000, the thematic network ENTRANSFOOD was launched to assess four different topics that are all related to the testing or assessment of food containing or produced from genetically modified organisms (GMOs). Each of the topics was linked to a European Commission (EC)-funded large shared cost action (see http://www.entransfood.com). Since the exchange of genetic information through horizontal (lateral) gene transfer (HGT) might play a more important role, in quantity and quality, than hitherto imagined, a working group dealing with HGT in the context of food and feed safety was established. This working group was linked to the GMOBILITY project (GMOBILITY, 2003) and the results of the deliberations are laid down in this review paper. HGT is reviewed in relation to the potential risks of consuming food or feed derived from transgenic crops. First, the mechanisms for obtaining transgenic crops are described. Next, HGT mechanisms and its possible evolutionary role are described. The use of marker genes is presented in detail as a special case for genes that may pose a risk. Furthermore, the exposure to GMOs and in particular to genetically modified (GM) deoxyribonucleic acid (DNA) is discussed as part of the total risk assessment. The review finishes off with a number of conclusions related to GM food and feed safety. The aim of this paper is to provide a comprehensive overview to assist risk assessors as well as regulators and the general public in understanding the safety issues related to these mechanisms.
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Affiliation(s)
- G van den Eede
- European Commission Directorate General Joint Research Centre, Institute for Health and Consumer Protection, Biotechnology and GMOs Unit, Via E. Fermi 1-T.P. 331, I-21020 Ispra (VA), Italy.
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Isolation and characterization of the Pseudobutyrivibrio xylanivorans Mz5T xylanase XynT—the first family 11 endoxylanase from rumen Butyrivibrio-related bacteria. Enzyme Microb Technol 2004. [DOI: 10.1016/j.enzmictec.2003.10.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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36
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Flint HJ. Polysaccharide Breakdown by Anaerobic Microorganisms Inhabiting the Mammalian Gut. ADVANCES IN APPLIED MICROBIOLOGY 2004; 56:89-120. [PMID: 15566977 DOI: 10.1016/s0065-2164(04)56003-3] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Harry J Flint
- Microbial Genetics Group Rowett Research Institute Bucksburn, Aberdeen, AB21 9SB, United Kingdom.
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37
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Robert CÃ, Bernalier-Donadille A. The cellulolytic microflora of the human colon: evidence of microcrystalline cellulose-degrading bacteria in methane-excreting subjects. FEMS Microbiol Ecol 2003; 46:81-9. [DOI: 10.1016/s0168-6496(03)00207-1] [Citation(s) in RCA: 121] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
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38
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Devillard E, Bera-Maillet C, Flint HJ, Scott KP, Newbold CJ, Wallace RJ, Jouany JP, Forano E. Characterization of XYN10B, a modular xylanase from the ruminal protozoan Polyplastron multivesiculatum, with a family 22 carbohydrate-binding module that binds to cellulose. Biochem J 2003; 373:495-503. [PMID: 12693992 PMCID: PMC1223500 DOI: 10.1042/bj20021784] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2002] [Revised: 04/04/2003] [Accepted: 04/14/2003] [Indexed: 11/17/2022]
Abstract
A new xylanase gene, xyn10B, was isolated from the ruminal protozoan Polyplastron multivesiculatum and the gene product was characterized. XYN10B is the first protozoan family 10 glycoside hydrolase characterized so far and is a modular enzyme comprising a family 22 carbohydrate-binding module (CBM) preceding the catalytic domain. The CBM22 was shown to be a true CBM. It showed high affinity for soluble arabinoxylan and is the first example of a CBM22 that binds strongly to celluloses of various crystallinities. The enzymic properties of XYN10B were also analysed. Its optimal temperature and pH for activity were 39 degrees C and 7.0 respectively; these values being close to those of the ruminal ecosystem. The phylogenetic relationships between the XYN10B CBM22 or catalytic domain and related sequences from ruminal and non-ruminal bacteria and eukaryotes are reported. The xyn10B gene is shown to lack introns.
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Affiliation(s)
- Estelle Devillard
- Rowett Research Institute, Greenburn Road, Bucksburn, Aberdeen AB21 9SB, UK
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39
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Ding SY, Rincon MT, Lamed R, Martin JC, McCrae SI, Aurilia V, Shoham Y, Bayer EA, Flint HJ. Cellulosomal scaffoldin-like proteins from Ruminococcus flavefaciens. J Bacteriol 2001; 183:1945-53. [PMID: 11222592 PMCID: PMC95089 DOI: 10.1128/jb.183.6.1945-1953.2001] [Citation(s) in RCA: 118] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2000] [Accepted: 12/14/2000] [Indexed: 11/20/2022] Open
Abstract
Two tandem cellulosome-associated genes were identified in the cellulolytic rumen bacterium, Ruminococcus flavefaciens. The deduced gene products represent multimodular scaffoldin-related proteins (termed ScaA and ScaB), both of which include several copies of explicit cellulosome signature sequences. The scaB gene was completely sequenced, and its upstream neighbor scaA was partially sequenced. The sequenced portion of scaA contains repeating cohesin modules and a C-terminal dockerin domain. ScaB contains seven relatively divergent cohesin modules, two extremely long T-rich linkers, and a C-terminal domain of unknown function. Collectively, the cohesins of ScaA and ScaB are phylogenetically distinct from the previously described type I and type II cohesins, and we propose that they define a new group, which we designated here type III cohesins. Selected modules from both genes were overexpressed in Escherichia coli, and the recombinant proteins were used as probes in affinity-blotting experiments. The results strongly indicate that ScaA serves as a cellulosomal scaffoldin-like protein for several R. flavefaciens enzymes. The data are supported by the direct interaction of a recombinant ScaA cohesin with an expressed dockerin-containing enzyme construct from the same bacterium. The evidence also demonstrates that the ScaA dockerin binds to a specialized cohesin(s) on ScaB, suggesting that ScaB may act as an anchoring protein, linked either directly or indirectly to the bacterial cell surface. This study is the first direct demonstration in a cellulolytic rumen bacterium of a cellulosome system, mediated by distinctive cohesin-dockerin interactions.
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Affiliation(s)
- S Y Ding
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot, Israel
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40
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McEwan NR, Eschenlauer SC, Calza RE, Wallace RJ, Newbold CJ. The 3' untranslated region of messages in the rumen protozoan Entodinium caudatum. Protist 2000; 151:139-46. [PMID: 10965953 DOI: 10.1078/1434-4610-00014] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The 3' untranslated regions of a number of cDNAs from the rumen protozoal species Entodinium caudatum were studied with a view to characterising their preference for stop codons, general length, nucleotide composition and polyadenylation signals. Unlike a number of ciliates, Entodinium caudatum uses UAA as a stop codon, rather than as a codon for glutamine. In addition, the 3' untranslated region of the message is generally less than 100 nucleotides in length, extremely A+T rich, and does not appear to utilise any of the conventional polyadenylation signals described in other organisms.
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Affiliation(s)
- N R McEwan
- Rowett Research Institute, Bucksburn, Aberdeen, Scotland.
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