1
|
Parker JL, Page A, Jacob O, Stanton V, Davis B, Flythe M, Adam EN. Equine fecal microbiota response to short term antibiotic administration. J Equine Vet Sci 2024; 133:104993. [PMID: 38171452 DOI: 10.1016/j.jevs.2023.104993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 12/28/2023] [Accepted: 12/30/2023] [Indexed: 01/05/2024]
Abstract
Though generally safe, research continues to demonstrate negative side effects of antibiotic administration on the gastrointestinal (GIT) microbiota across species. In horses, antibiotic associated diarrhea (AAD) is a life-threatening condition linked to the GIT microbiota. This study tested the hypothesis that short term antibiotic administration to healthy horses would negatively impact the fecal microbiota as measured by their ability to digest nutrients and through fecal shedding of disease-associated-bacteria. Twenty-four horses were assigned to one of four treatment groups: control (CO); potassium penicillin/gentamicin sulfate (KPG); ceftiofur crystalline free acid (EX); trimethoprim/sulfamethoxazole (SMZ); and treated for 4 days. Fecal samples were collected before treatment began (S0), the day after treatment conclusion (S5), and at 10, 14, 21, and 28 days after initiating treatment. Horses had highly individualized responses to antibiotic administration. All horses receiving antibiotics experienced significantly softer stool compared to controls. Lactobacillus spp. were dramatically reduced in all antibiotic treated S5 samples. Horses receiving antibiotics were significantly more likely to test positive for C. difficile or C. perfringens on fecal qPCR. In conclusion, response to antibiotic administration displays high inter-individual variability, but shows changes to the functions of fecal microbiota that may depend on the antibiotic used.
Collapse
Affiliation(s)
- J L Parker
- Department of Veterinary Science, Gluck Equine Research Center, College of Agriculture, Food, and Environment, University of Kentucky, 1400 Nicholasville Rd., Lexington, KY 40546, USA
| | - A Page
- Department of Veterinary Science, Gluck Equine Research Center, College of Agriculture, Food, and Environment, University of Kentucky, 1400 Nicholasville Rd., Lexington, KY 40546, USA
| | - O Jacob
- Department of Veterinary Science, Gluck Equine Research Center, College of Agriculture, Food, and Environment, University of Kentucky, 1400 Nicholasville Rd., Lexington, KY 40546, USA
| | - V Stanton
- Department of Statistics, College of Arts and Sciences, University of Kentucky, 725 Rose St., Lexington, KY 40536, USA
| | - B Davis
- Forage-Animal Production Research Unit, Agricultural Research Service, United States Department of Agriculture, 1100 Nicholasville Rd., Lexington, KY 40546, USA; Department of Animal & Food Sciences, College of Agriculture, Food, and Environment, University of Kentucky, 325 Cooper Dr., Lexington, KY 40546, USA
| | - M Flythe
- Forage-Animal Production Research Unit, Agricultural Research Service, United States Department of Agriculture, 1100 Nicholasville Rd., Lexington, KY 40546, USA; Department of Animal & Food Sciences, College of Agriculture, Food, and Environment, University of Kentucky, 325 Cooper Dr., Lexington, KY 40546, USA
| | - E N Adam
- Department of Veterinary Science, Gluck Equine Research Center, College of Agriculture, Food, and Environment, University of Kentucky, 1400 Nicholasville Rd., Lexington, KY 40546, USA.
| |
Collapse
|
2
|
Sharma N, Agarwal A, Bijoy A, Pandit S, Sharma RK. Ligno cellulolytic extremozymes and their biotechnological applications. Extremophiles 2023; 28:2. [PMID: 37950773 DOI: 10.1007/s00792-023-01314-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 09/26/2023] [Indexed: 11/13/2023]
Abstract
Lignocellulolytic enzymes are used in different industrial and environmental processes. The rigorous operating circumstances of these industries, however, might prevent these enzymes from performing as intended. On the other side, extremozymes are enzymes produced by extremophiles that can function in extremely acidic or basic; hot or cold; under high or low salinity conditions. These severe conditions might denature the normal enzymes that are produced by mesophilic microorganisms. The increased stability of these enzymes has been contributed to a number of conformational modifications in their structures. These modifications may result from a few amino acid substitutions, an improved hydrophobic core, the existence of extra ion pairs and salt bridges, an increase in compactness, or an increase in positively charged amino acids. These enzymes are the best option for industrial and bioremediation activities that must be carried out under difficult conditions due to their improved stability. The review, therefore, discusses lignocellulolytic extremozymes, their structure and mechanisms along with industrial and biotechnological applications.
Collapse
Affiliation(s)
- Nikita Sharma
- Department of Biosciences, Manipal University Jaipur, Jaipur, 303007, Rajasthan, India
| | - Aditi Agarwal
- Department of Biosciences, Manipal University Jaipur, Jaipur, 303007, Rajasthan, India
| | - Ananya Bijoy
- Department of Biosciences, Manipal University Jaipur, Jaipur, 303007, Rajasthan, India
| | - Sunidhi Pandit
- Department of Biosciences, Manipal University Jaipur, Jaipur, 303007, Rajasthan, India
| | - Rakesh Kumar Sharma
- Department of Life Sciences, Chhatrapati Shahu Ji Maharaj University, Kanpur, India.
| |
Collapse
|
3
|
Tan MCY, Zakaria MR, Liew KJ, Chong CS. Draft genome sequence of Hahella sp. CR1 and its ability in producing cellulases for saccharifying agricultural biomass. Arch Microbiol 2023; 205:278. [PMID: 37420023 DOI: 10.1007/s00203-023-03617-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 06/20/2023] [Accepted: 06/23/2023] [Indexed: 07/09/2023]
Abstract
Hahella is a genus that has not been well-studied, with only two identified species. The potential of this genus to produce cellulases is yet to be fully explored. The present study isolated Hahella sp. CR1 from mangrove soil in Tanjung Piai National Park, Malaysia, and performed whole genome sequencing (WGS) using NovaSeq 6000. The final assembled genome consists of 62 contigs, 7,106,771 bp, a GC ratio of 53.5%, and encoded for 6,397 genes. The CR1 strain exhibited the highest similarity with Hahella sp. HN01 compared to other available genomes, where the ANI, dDDH, AAI, and POCP were 97.04%, 75.2%, 97.95%, and 91.0%, respectively. In addition, the CAZymes analysis identified 88 GTs, 54 GHs, 11 CEs, 7 AAs, 2 PLs, and 48 CBMs in the genome of strain CR1. Among these proteins, 11 are related to cellulose degradation. The cellulases produced from strain CR1 were characterized and demonstrated optimal activity at 60 ℃, pH 7.0, and 15% (w/v) sodium chloride. The enzyme was activated by K+, Fe2+, Mg2+, Co2+, and Tween 40. Furthermore, cellulases from strain CR1 improved the saccharification efficiency of a commercial cellulase blend on the tested agricultural wastes, including empty fruit bunch, coconut husk, and sugarcane bagasse. This study provides new insights into the cellulases produced by strain CR1 and their potential to be used in lignocellulosic biomass pre-treatment.
Collapse
Affiliation(s)
- Melvin Chun Yun Tan
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310, Skudai, Johor, Malaysia
| | - Muhammad Ramziuddin Zakaria
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310, Skudai, Johor, Malaysia
| | - Kok Jun Liew
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310, Skudai, Johor, Malaysia
| | - Chun Shiong Chong
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310, Skudai, Johor, Malaysia.
| |
Collapse
|
4
|
Sim JXF, Drigo B, Doolette CL, Vasileiadis S, Karpouzas DG, Lombi E. Impact of twenty pesticides on soil carbon microbial functions and community composition. Chemosphere 2022; 307:135820. [PMID: 35944675 DOI: 10.1016/j.chemosphere.2022.135820] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 07/20/2022] [Accepted: 07/21/2022] [Indexed: 05/20/2023]
Abstract
Pesticides are known to affect non-targeted soil microorganisms. Still, studies comparing the effect of multiple pesticides on a wide range of microbial endpoints associated with carbon cycling are scarce. Here, we employed fluorescence enzymatic assay and real-time PCR to evaluate the effect of 20 commercial pesticides, applied at their recommended dose and five times their recommended dose, on soil carbon cycling related enzymatic activities (α-1,4-glucosidase, β-1,4-glucosidase, β-d-cellobiohydrolase and β-xylosidase), and on the absolute abundance of functional genes (cbhl and chiA), in three different South Australian agricultural soils. The effects on cellulolytic and chitinolytic microorganisms, and the total microbial community composition were determined using shotgun metagenomic sequencing in selected pesticide-treated and untreated samples. The application of insecticides significantly increased the cbhl and chiA genes absolute abundance in the acidic soil. At the community level, insecticide fipronil had the greatest stimulating effect on cellulolytic and chitinolytic microorganisms, followed by fungicide metalaxyl-M and insecticide imidacloprid. A shift towards a fungal dominated microbial community was observed in metalaxyl-M treated soil. Overall, our results suggest that the application of pesticides might affect the soil carbon cycle and may disrupt the formation of soil organic matter and structure stabilisation.
Collapse
Affiliation(s)
- Jowenna X F Sim
- Future Industries Institute, University of South Australia, Mawson Lakes, SA, 5095, Australia.
| | - Barbara Drigo
- Future Industries Institute, University of South Australia, Mawson Lakes, SA, 5095, Australia
| | - Casey L Doolette
- Future Industries Institute, University of South Australia, Mawson Lakes, SA, 5095, Australia
| | - Sotirios Vasileiadis
- University of Thessaly, Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, Larissa, Viopolis, 41500, Greece
| | - Dimitrios G Karpouzas
- University of Thessaly, Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, Larissa, Viopolis, 41500, Greece
| | - Enzo Lombi
- Future Industries Institute, University of South Australia, Mawson Lakes, SA, 5095, Australia; University of South Australia, UniSA STEM, Mawson Lakes, South Australia, 5095, Australia
| |
Collapse
|
5
|
Máté R, Kutasi J, Bata-Vidács I, Kosztik J, Kukolya J, Tóth E, Bóka K, Táncsics A, Kovács G, Nagy I, Tóth Á. Flavobacterium hungaricum sp. nov. a novel soil inhabitant, cellulolytic bacterium isolated from plough field. Arch Microbiol 2022; 204:301. [PMID: 35524012 DOI: 10.1007/s00203-022-02905-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 04/05/2022] [Accepted: 04/06/2022] [Indexed: 11/15/2022]
Abstract
A Gram-negative bacterial strain, named Kb82, was isolated from agricultural soil and a polyphasic approach was used for characterisation and to determine its taxonomic position. Based on 16S rRNA gene sequence analysis, the highest similarity was found with Flavobacterium artemisiae SYP-B1015 (98.2%). The highest ANI (83.3%) and dDDH (26.5%) values were found with Flavobacterium ginsenosidimutans THG 01 and Flavobacterium fluviale HYN0086T, respectively. The isolate is aerobic with rod-shaped cells, positive for catalase and negative for oxidase tests. The DNA G+C content is 34.7 mol%. The only isoprenoid quinone is menaquinone 6 (MK-6). The major fatty acids are iso-C15:0, summed feature 3 (C16:1ω7c/C16:1ω6c) and iso-C17:0 3OH. The major polar lipid is phosphatidylethanolamine. On the bases of phenotypic characteristics and analysis of 16S rRNA gene sequences, it is concluded that strain Kb82T represents a novel species in the Flavobacterium genus, for which the name Flavobacterium hungaricum sp. nov. is proposed. The type strain of the species is strain Kb82T (= LMG 31576T = NCAIM B.02635T).
Collapse
|
6
|
Liu GH, Narsing Rao MP, Wang XY, Chu TW, Liu B, Li WJ. Bacillus alkalicellulosilyticus sp. nov., isolated from extremely alkaline bauxite residue (red mud) site. Arch Microbiol 2020; 203:719-723. [PMID: 33047173 DOI: 10.1007/s00203-020-02063-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 08/28/2020] [Accepted: 09/30/2020] [Indexed: 11/30/2022]
Abstract
A Gram-stain-negative, rod-shaped, facultatively anaerobic, motile and spore-forming strain designated FJAT-44921T was isolated from red mud collected from Chiping County, Shandong Province, China. The 16S rRNA gene sequence result showed that strain FJAT-44921T shared a low sequence identity (96.6%) with the members of the genus Bacillus. Growth was observed at pH 8.0-10.0 (optimum pH 9.0), 10-40 °C (optimum 20-25 °C) with 0-8% (v/w %) NaCl (optimum 4-6 v/w %). FJAT-44921T consists of MK-7 as the isoprenoid quinone and meso-2,6-diaminopimelic acid as the cell-wall diamino acid. The predominant fatty acids were anteiso-C15:0, iso-C15:0, C16:0, and anteiso-C17:0. The polar lipids were diphosphatidylglycerol, phosphatidyl glycerol, phosphatidylmethylethanolamine, unidentified phospholipid, and unidentified aminophospholipid. The genomic DNA G + C content was 37.3 mol%. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between FJAT-44921T and other closely related Bacillus members were lower than the recognized threshold values of ANI (95-96%) and dDDH (70%) recommended as the criterion for interspecies identity. The type strain is FJAT-44921T (=CCTCC AB 2016196T =DSM 104630T).
Collapse
Affiliation(s)
- Guo-Hong Liu
- Agricultural Bio-Resources Institute, Fujian Academy of Agricultural Sciences, Fuzhou, 350003, PR China
| | - Manik Prabhu Narsing Rao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Xiao-Ying Wang
- Agricultural Bio-Resources Institute, Fujian Academy of Agricultural Sciences, Fuzhou, 350003, PR China
| | - Tong-Wei Chu
- Chiping Agricultural Bureau, Chiping, 252100, PR China
| | - Bo Liu
- Agricultural Bio-Resources Institute, Fujian Academy of Agricultural Sciences, Fuzhou, 350003, PR China.
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China. .,State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, PR China.
| |
Collapse
|
7
|
Malgas S, Chandra R, Van Dyk JS, Saddler JN, Pletschke BI. Formulation of an optimized synergistic enzyme cocktail, HoloMix, for effective degradation of various pre-treated hardwoods. Bioresour Technol 2017; 245:52-65. [PMID: 28892706 DOI: 10.1016/j.biortech.2017.08.186] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 08/25/2017] [Accepted: 08/29/2017] [Indexed: 06/07/2023]
Abstract
In this study, two selected hardwoods were subjected to sodium chlorite delignification and steam explosion, and the impact of pre-treatments on synergistic enzymatic saccharification evaluated. A cellulolytic core-set, CelMix, and a xylanolytic core-set, XynMix, optimised for glucose and xylose release, respectively, were used to formulate HoloMix cocktail for optimal saccharification of various pre-treated hardwoods. For delignified biomass, the optimized HoloMix consisted of 75%:25% protein dosage, CelMix: XynMix, while for untreated and steam exploded biomass the HoloMix consisted of 93.75%:6.25% protein dosage. Saccharification by HoloMix (27.5mgprotein/gbiomass) for 24h achieved 70-100% sugar yields. Pre-treatment of the hardwoods (especially those with a higher proportion of lignin) with a laccase, improved saccharification by HoloMix. This study provided insights into enzymatic hydrolysis of various pre-treated hardwood substrates and showed the same lignocellulolytic cocktail comparable to/if not better than commercial enzyme preparations can be used to efficiently hydrolyse different hardwood species.
Collapse
Affiliation(s)
- S Malgas
- Enzyme Science Programme (ESP), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown 6140, Eastern Cape, South Africa
| | - R Chandra
- Forest Products Biotechnology Group, University of British Columbia, 2424 Main Mall, Vancouver, British Columbia V6T1Z4, Canada
| | - J S Van Dyk
- Forest Products Biotechnology Group, University of British Columbia, 2424 Main Mall, Vancouver, British Columbia V6T1Z4, Canada
| | - J N Saddler
- Forest Products Biotechnology Group, University of British Columbia, 2424 Main Mall, Vancouver, British Columbia V6T1Z4, Canada
| | - B I Pletschke
- Enzyme Science Programme (ESP), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown 6140, Eastern Cape, South Africa.
| |
Collapse
|
8
|
Speda J, Johansson MA, Odnell A, Karlsson M. Enhanced biomethane production rate and yield from lignocellulosic ensiled forage ley by in situ anaerobic digestion treatment with endogenous cellulolytic enzymes. Biotechnol Biofuels 2017; 10:129. [PMID: 28523077 PMCID: PMC5434626 DOI: 10.1186/s13068-017-0814-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 05/08/2017] [Indexed: 05/15/2023]
Abstract
BACKGROUND Enzymatic treatment of lignocellulosic material for increased biogas production has so far focused on pretreatment methods. However, often combinations of enzymes and different physicochemical treatments are necessary to achieve a desired effect. This need for additional energy and chemicals compromises the rationale of using enzymes for low energy treatment to promote biogas production. Therefore, simpler and less energy intensive in situ anaerobic digester treatment with enzymes is desirable. However, investigations in which exogenous enzymes are added to treat the material in situ have shown mixed success, possibly because the enzymes used originated from organisms not evolutionarily adapted to the environment of anaerobic digesters. In this study, to examine the effect of enzymes endogenous to methanogenic microbial communities, cellulolytic enzymes were instead overproduced and collected from a dedicated methanogenic microbial community. By this approach, a solution with very high endogenous microbial cellulolytic activity was produced and tested for the effect on biogas production from lignocellulose by in situ anaerobic digester treatment. RESULTS Addition of enzymes, endogenous to the environment of a mixed methanogenic microbial community, to the anaerobic digestion of ensiled forage ley resulted in significantly increased rate and yield of biomethane production. The enzyme solution had an instant effect on more readily available cellulosic material. More importantly, the induced enzyme solution also affected the biogas production rate from less accessible cellulosic material in a second slower phase of lignocellulose digestion. Notably, this effect was maintained throughout the experiment to completely digested lignocellulosic substrate. CONCLUSIONS The induced enzyme solution collected from a microbial methanogenic community contained enzymes that were apparently active and stable in the environment of anaerobic digestion. The enzymatic activity had a profound effect on the biogas production rate and yield, comparable with the results of many pretreatment methods. Thus, application of such enzymes could enable efficient low energy in situ anaerobic digester treatment for increased biomethane production from lignocellulosic material.
Collapse
Affiliation(s)
- Jutta Speda
- Molecular Biotechnology, Department of Physics, Chemistry and Biology, Linköping University, 581 83 Linköping, Sweden
| | - Mikaela A. Johansson
- Molecular Biotechnology, Department of Physics, Chemistry and Biology, Linköping University, 581 83 Linköping, Sweden
| | - Anna Odnell
- Molecular Biotechnology, Department of Physics, Chemistry and Biology, Linköping University, 581 83 Linköping, Sweden
- Karshult Municipal Waste Water Treatment Plant, 591 86 Motala, Sweden
| | - Martin Karlsson
- Molecular Biotechnology, Department of Physics, Chemistry and Biology, Linköping University, 581 83 Linköping, Sweden
- InZymes Biotech AB, Gjuterigatan 1B, 582 73 Linköping, Sweden
| |
Collapse
|
9
|
Manhar AK, Bashir Y, Saikia D, Nath D, Gupta K, Konwar BK, Kumar R, Namsa ND, Mandal M. Cellulolytic potential of probiotic Bacillus Subtilis AMS6 isolated from traditional fermented soybean (Churpi): An in-vitro study with regards to application as an animal feed additive. Microbiol Res 2016; 186-187:62-70. [PMID: 27242144 DOI: 10.1016/j.micres.2016.03.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 02/23/2016] [Accepted: 03/22/2016] [Indexed: 12/18/2022]
Abstract
The aim of the present study is to evaluate the probiotic attributes of Bacillus subtilis AMS6 isolated from fermented soybean (Churpi). This isolate exhibited tolerance to low pH (pH 2.0) and bile salt (0.3%), capability to autoaggregate and coaggregate. AMS6 also showed highest antibacterial activity against the pathogenic indicator strain Salmonella enterica typhimurium (MTCC 1252) and susceptibility towards different antibiotics tested. The isolate was effective in inhibiting the adherence of food borne pathogens to Caco-2 epithelial cell lines, and was also found to be non-hemolytic which further strengthen the candidature of the isolate as a potential probiotic. Further studies revealed B. subtilis AMS6 showed cellulolytic activity (0.54±0.05 filter paper units mL(-1)) at 37°C. The isolate was found to hydrolyze carboxymethyl cellulose, filter paper and maize (Zea mays) straw. The maize straw digestion was confirmed by scanning electron microscopy studies. The isolate was able to degrade filter paper within 96h of incubation. A full length cellulase gene of AMS6 was amplified using degenerate primers consisting of 1499 nucleotides. The ORF encoded for a protein of 499 amino acids residues with a predicted molecular mass of 55.04kDa. The amino acids sequence consisted of a glycosyl hydrolase family 5 domain at N-terminal; Glycosyl hydrolase catalytic core and a CBM-3 cellulose binding domain at its C terminal. The study suggests potential probiotic B. subtilis AMS6 as a promising candidate envisaging its application as an animal feed additive for enhanced fiber digestion and gut health of animal.
Collapse
Affiliation(s)
- Ajay K Manhar
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur 784028, Assam, India
| | - Yasir Bashir
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur 784028, Assam, India
| | - Devabrata Saikia
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur 784028, Assam, India
| | - Dhrubajyoti Nath
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur 784028, Assam, India
| | - Kuldeep Gupta
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur 784028, Assam, India
| | - Bolin K Konwar
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur 784028, Assam, India
| | - Rahul Kumar
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur 784028, Assam, India
| | - Nima D Namsa
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur 784028, Assam, India
| | - Manabendra Mandal
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur 784028, Assam, India.
| |
Collapse
|
10
|
Zhang Q, Li H, Zhu X, Lai F, Zhai Z, Wang Y. Exploration of the key functional proteins from an efficient cellulolytic microbial consortium using dilution-to-extinction approach. J Environ Sci (China) 2016; 43:199-207. [PMID: 27155425 DOI: 10.1016/j.jes.2015.09.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 09/21/2015] [Accepted: 09/23/2015] [Indexed: 06/05/2023]
Abstract
In the present study, the cellulose binding proteins (CBPs) secreted by a putative cellulolytic microbial consortium were isolated and purified by affinity digestion. The purified CBPs were subsequently separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). Using mass spectrometric analyses, eight CBPs were identified and annotated to be similar to known proteins secreted by Clostridium clariflavum DSM 19732 and Paenibacillus sp. W-61. In addition, in combination with dilution-to-extinction approach and zymogram analysis technique, CBPs 6 (97kDa) and 12 (52kDa) were confirmed to be the key functional proteins that influence cellulolytic activities. Moreover, structural domain analyses and enzymatic activity detection indicated that CBPs 6 and 12 contained glycoside hydrolase families (GH) 9 and 48 catalytic modules, which both revealed endoglucandase and xylanase activities. It was suggested that the coexistence of GH9 and GH48 catalytic domains present in these two proteins could synergistically promote the efficient degradation of cellulose.
Collapse
Affiliation(s)
- Qinghua Zhang
- College of Bioscience and Engineering, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang 330045, China.
| | - Hanguang Li
- College of Bioscience and Engineering, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang 330045, China.
| | - Xiangdong Zhu
- College of Bioscience and Engineering, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang 330045, China
| | - Fenju Lai
- College of Bioscience and Engineering, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang 330045, China
| | - Zhijun Zhai
- College of Bioscience and Engineering, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang 330045, China
| | - Yuanxiu Wang
- College of Bioscience and Engineering, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang 330045, China
| |
Collapse
|
11
|
Zhuang W, Zhang S, Xia X, Wang G. Draft genome sequence of Cellulomonas carbonis T26(T) and comparative analysis of six Cellulomonas genomes. Stand Genomic Sci 2015; 10:104. [PMID: 26587181 PMCID: PMC4652355 DOI: 10.1186/s40793-015-0096-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 11/09/2015] [Indexed: 11/28/2022] Open
Abstract
Most Cellulomonas strains are cellulolytic and this feature may be applied in straw degradation and bioremediation. In this study, Cellulomonas carbonis T26T, Cellulomonas bogoriensis DSM 16987T and Cellulomonas cellasea 20108T were sequenced. Here we described the draft genomic information of C. carbonis T26T and compared it to the related Cellulomonas genomes. Strain T26T has a 3,990,666 bp genome size with a G + C content of 73.4 %, containing 3418 protein-coding genes and 59 RNA genes. The results showed good correlation between the genotypes and the physiological phenotypes. The information are useful for the better application of the Cellulomonas strains.
Collapse
Affiliation(s)
- Weiping Zhuang
- State Key Laboratory of Agricultural Microbiology, College of Life Sciences and Technology, Huazhong Agricultural University, Wuhan, 430070 P. R. China
| | - Shengzhe Zhang
- State Key Laboratory of Agricultural Microbiology, College of Life Sciences and Technology, Huazhong Agricultural University, Wuhan, 430070 P. R. China
| | - Xian Xia
- State Key Laboratory of Agricultural Microbiology, College of Life Sciences and Technology, Huazhong Agricultural University, Wuhan, 430070 P. R. China
| | - Gejiao Wang
- State Key Laboratory of Agricultural Microbiology, College of Life Sciences and Technology, Huazhong Agricultural University, Wuhan, 430070 P. R. China
| |
Collapse
|
12
|
Chua P, Har ZM, Austin CM, Yule CM, Dykes GA, Lee SM. Genome sequencing and annotation of Aeromonas sp. HZM. Genom Data 2015; 5:38-9. [PMID: 26484220 PMCID: PMC4583981 DOI: 10.1016/j.gdata.2015.05.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 05/09/2015] [Accepted: 05/10/2015] [Indexed: 11/16/2022]
Abstract
We report the draft genome sequence of Aeromonas sp. strain HZM, isolated from tropical peat swamp forest soil. The draft genome size is 4,451,364 bp with a G + C content of 61.7% and contains 10 rRNA sequences (eight copies of 5S rRNA genes, single copy of 16S and 23S rRNA each). The genome sequence can be accessed at DDBJ/EMBL/GenBank under the accession no. JEMQ00000000.
Collapse
Affiliation(s)
- Patric Chua
- School of Science, Monash University, Selangor, Malaysia
| | - Zi Mei Har
- School of Science, Monash University, Selangor, Malaysia
| | | | | | - Gary A Dykes
- School of Science, Monash University, Selangor, Malaysia
| | - Sui Mae Lee
- School of Science, Monash University, Selangor, Malaysia
| |
Collapse
|
13
|
Koeck DE, Maus I, Wibberg D, Winkler A, Zverlov VV, Liebl W, Pühler A, Schwarz WH, Schlüter A. Draft genome sequence of Herbinix hemicellulosilytica T3/55 T, a new thermophilic cellulose degrading bacterium isolated from a thermophilic biogas reactor. J Biotechnol 2015; 214:59-60. [PMID: 26253960 DOI: 10.1016/j.jbiotec.2015.07.022] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Accepted: 07/30/2015] [Indexed: 11/20/2022]
Abstract
A novel bacterial species was isolated from an industrial-scale biogas plant. The isolate Herbinix hemicellulosilytica T3/55(T) is able to degrade crystalline cellulose. Comparative 16S rRNA gene sequencing demonstrated that the isolate is closely related to environmental samples forming a hitherto unknown sub-cluster within the family Lachnospiraceae. The draft genome sequence of strain T3/55(T) was established and now provides the genetic basis for application of this microorganism in thermophilic degradation of lignocellulosic biomass.
Collapse
|
14
|
Manhar AK, Saikia D, Bashir Y, Mech RK, Nath D, Konwar BK, Mandal M. In vitro evaluation of celluloytic Bacillus amyloliquefaciens AMS1 isolated from traditional fermented soybean (Churpi) as an animal probiotic. Res Vet Sci 2015; 99:149-56. [PMID: 25660401 DOI: 10.1016/j.rvsc.2015.01.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Revised: 12/07/2014] [Accepted: 01/16/2015] [Indexed: 02/06/2023]
Abstract
A microorganism showing probiotic attributes and hydrolyzing carboxymethylcellulose was isolated from traditional fermented soybean (Churpi) and identified as Bacillus amyloliquefaciens by analysis of 16S rRNA gene sequence and named as B. amyloliquefaciens AMS1. The potentiality of this isolate as probiotic was investigated in vitro and it showed gastrointestinal transit tolerance, cell surface hydrophobicity, cell aggregation and antimicrobial activity. The isolate was found to be non-hemolytic which further strengthens its candidature as a potential probiotic. The maize straw digestion was confirmed by scanning electron microscopy studies. The isolate was able to degrade filter paper within 96 hours of incubation. This study explores the possibility of combining the cellulase degrading ability of a microbe with its probiotic attributes to enhance gut health of animal and digestibility of the feed.
Collapse
Affiliation(s)
- Ajay K Manhar
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur 784028, Assam, India
| | - Devabrata Saikia
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur 784028, Assam, India
| | - Yasir Bashir
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur 784028, Assam, India
| | - Reba K Mech
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur 784028, Assam, India
| | - Dhrubajyoti Nath
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur 784028, Assam, India
| | - Bolin K Konwar
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur 784028, Assam, India
| | - Manabendra Mandal
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur 784028, Assam, India.
| |
Collapse
|
15
|
Sharma R, Kocher GS, Bhogal RS, Oberoi HS. Cellulolytic and xylanolytic enzymes from thermophilic Aspergillus terreus RWY. J Basic Microbiol 2014; 54:1367-77. [PMID: 25047723 DOI: 10.1002/jobm.201400187] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2014] [Accepted: 06/10/2014] [Indexed: 11/05/2022]
Abstract
Thermophilic Aspergillus terreus RWY produced cellulases and xylanases in optimal concentrations at 45 °C in solid state fermentation process, though enzyme production was also observed at 50 and 55 °C. Filter paper cellulase (FP), endoglucanase (EG), β-glucosidase (BGL), cellobiohydrolase (CBH), xylanase, β-xylosidase, α-L-arabinofuranosidase and xylan esterase activities for A. terreus RWY at 45 °C in 72 h were 11.3 ± 0.65, 103 ± 6.4, 122.5 ± 8.7, 10.3 ± 0.66, 872 ± 22.5, 22.1 ± 0.75, 126.4 ± 8.4 and 907 ± 15.5 U (g-ds)(-1) , respectively. Enzyme was optimally active at temperatures and pH ranging between 50-60 °C and 4.0-6.0, respectively. The half life (T1/2 ) of 270 and 240 min at 70 and 75 °C, respectively for the enzyme indicates its stability at higher temperatures. The addition of MnCl2 , CoCl2 , and FeCl3 significantly enhanced cellulase activity. Enzyme demonstrated multiplicity by having seven, one and three isoform(s) for EG, CBH and BGL, respectively. Significant production of functionally active consortium of cellulolytic and xylanolytic enzymes from A. terreus RWY makes it a potential candidate in bioprocessing applications.
Collapse
Affiliation(s)
- Reetika Sharma
- Central Institute of Post-Harvest Engineering and Technology, P.O. PAU, Ludhiana, Punjab, India; Department of Microbiology, Punjab Agricultural University, Ludhiana, Punjab, India
| | | | | | | |
Collapse
|