PeerJ Preprints: Biotechnologyhttps://peerj.com/preprints/index.atom?journal=peerj&subject=700Biotechnology articles published in PeerJ PreprintsIsolation and characterization of psychrotrophic proteolytic bacteria from landfill site under temperate climatic conditions of Kashmir Himalayahttps://peerj.com/preprints/273912019-12-212019-12-21Basharat HamidArshid JehangirZahoor Ahmad BabaMuneer Ahmad WaniImran Khan
The temperate climatic regions face the problem of waste accumulation due to lower environmental temperatures. However, these regions harbor cold active microbes viz. psychrotrophic proteolytic bacteria that play an important role in the degradation of protenaceous materials of the waste stream. Hence in the present study psychrotrophic proteolytic bacteria were isolated from waste samples collected from landfill site by using random sampling method under environmental temperature of 10oC. By using serial dilution and spread plate technique a total of 8 morphologically different psychrotrophic proteolytic bacteria were isolated on skim milk agar media at pH of 7.0 and temperature of 10°C after 48hours. Under in-vitro conditions all the isolates produced significant quantities of protease over the control and diameters of hydrolysis zones ranged between 2 to 18 mm at temperature range of 5 to 20oC and after 72 hours. The corresponding quantitative protease activities of the isolates was significant that ranged between 0.5 to 2.25 U/ml and the isolate PB2 was most efficient with highest protease activity of 2.25U/ml at 20oC. Based on 16SrRNA analysis the isolate was identified as Pseudomonas florescence with 96% similarity. It was concluded that the isolates can grow in wide ranges of temperature and could be used for enhanced decomposition of organic wastes during lower temperature conditions in cold regions. Further the isolates could have industrial applications due to the production of cold active proteases that would help economic benefits through energy conservation.
The temperate climatic regions face the problem of waste accumulation due to lower environmental temperatures. However, these regions harbor cold active microbes viz. psychrotrophic proteolytic bacteria that play an important role in the degradation of protenaceous materials of the waste stream. Hence in the present study psychrotrophic proteolytic bacteria were isolated from waste samples collected from landfill site by using random sampling method under environmental temperature of 10oC. By using serial dilution and spread plate technique a total of 8 morphologically different psychrotrophic proteolytic bacteria were isolated on skim milk agar media at pH of 7.0 and temperature of 10°C after 48hours. Under in-vitro conditions all the isolates produced significant quantities of protease over the control and diameters of hydrolysis zones ranged between 2 to 18 mm at temperature range of 5 to 20oC and after 72 hours. The corresponding quantitative protease activities of the isolates was significant that ranged between 0.5 to 2.25 U/ml and the isolate PB2 was most efficient with highest protease activity of 2.25U/ml at 20oC. Based on 16SrRNA analysis the isolate was identified as Pseudomonas florescence with 96% similarity. It was concluded that the isolates can grow in wide ranges of temperature and could be used for enhanced decomposition of organic wastes during lower temperature conditions in cold regions. Further the isolates could have industrial applications due to the production of cold active proteases that would help economic benefits through energy conservation.Ethylene induced nitrile and VOC synthesis by soil microbes; Improved root elongation & reduced risk of fungal infection in plants.https://peerj.com/preprints/5432019-09-272019-09-27Guenevere PerryDiane Perry
The scope of the project was to develop a method to induce soil microbes to inhibit fungal infection and improve root elongation. The study was randomized. Gladiolus bulbs selected for the study were visibly inspected to for viability and visible signs of infection. Two trials were conducted from Aug. 5th – Sept. 5th 2014 with 4 replicates per condition over a 7-d period in damp outdoor conditions in late summer. A mixed culture of plant growth promoting rhizobacteria (PGPR) were collected from soil surrounding the roots of young fruit bearing trees. Microbes were mixed with minimal media (no-carbon source), and cultured with an ethylene and used as potting soil. Bulbs planted in ethylene induced soil displayed 0% visible fungal growth, while 38% of bulbs grown in control conditions displayed some form of fungal growth and/or infection. Ethylene induced soil increased root length by 225% in bulbs in 7-d period. GC Mass Spectrophotometry data suggest ethylene may induce soil microbes to synthesize several VOCs including (ethanol, 3-methyl-1-butanol, pentanol) and esters (ethyl acetate), that may have synergistic benefits to lower the risk of fungal infection by soil mold, while nitrile compounds improve root elongation. The findings are preliminary, additional studies are required to understand the mechanism.
The scope of the project was to develop a method to induce soil microbes to inhibit fungal infection and improve root elongation. The study was randomized. Gladiolus bulbs selected for the study were visibly inspected to for viability and visible signs of infection. Two trials were conducted from Aug. 5th – Sept. 5th 2014 with 4 replicates per condition over a 7-d period in damp outdoor conditions in late summer. A mixed culture of plant growth promoting rhizobacteria (PGPR) were collected from soil surrounding the roots of young fruit bearing trees. Microbes were mixed with minimal media (no-carbon source), and cultured with an ethylene and used as potting soil. Bulbs planted in ethylene induced soil displayed 0% visible fungal growth, while 38% of bulbs grown in control conditions displayed some form of fungal growth and/or infection. Ethylene induced soil increased root length by 225% in bulbs in 7-d period. GC Mass Spectrophotometry data suggest ethylene may induce soil microbes to synthesize several VOCs including (ethanol, 3-methyl-1-butanol, pentanol) and esters (ethyl acetate), that may have synergistic benefits to lower the risk of fungal infection by soil mold, while nitrile compounds improve root elongation. The findings are preliminary, additional studies are required to understand the mechanism.Ethylene induced soil delays ripening in organic bananas.https://peerj.com/preprints/5062019-09-252019-09-25Guenevere PerryDiane Williams
The scope of the project was to develop a method to induce soil bacteria to biosynthesize compounds that retard the effects of ethylene induced ripening in climacteric fruits. The study was randomized. Organic bananas selected for the study were visibly inspected to ensure the fruit was unripen with no visible signs of bruising, spotting, or infection from a local distributor. Four trials were conducted from June 5th - August 5th 2014 with 3 replicates (3-4 bananas per experimental unit) in 4 trial studies for 3 days at room temperature. A mixed culture of plant growth promoting rhizobacteria (PGPR) were collected from soil surrounding the roots of young fruit bearing trees. Microbes were mixed with no-carbon source media, and cultured with an ethylene for 3 d at room temperature in a closed container. Induced soil was used to delay ripening. Microbes induced with media and ethylene delayed ripening 100% of the time in all experimental units compared to control samples, while microbes cultured with media (no ethylene) delayed ripening less than 10% of the time compared to the control. These cells also appeared to increase the incidence of fungal infection in the fruit. The findings suggest induced microbes may convert ethylene into ethanol then acetaldehyde. The two compounds may form an acetaldehyde/ethanol vapor that delays ripening, and a secondary nitrile compound that inhibits fungal growth.
The scope of the project was to develop a method to induce soil bacteria to biosynthesize compounds that retard the effects of ethylene induced ripening in climacteric fruits. Thestudy was randomized. Organic bananas selected for the study were visibly inspected to ensure the fruit was unripen with no visible signs of bruising, spotting, or infection from a local distributor. Four trials were conducted from June 5th - August 5th 2014 with 3 replicates (3-4 bananas per experimental unit) in 4 trial studies for 3 days at room temperature. A mixed culture of plant growth promoting rhizobacteria (PGPR) were collected from soil surrounding the roots of young fruit bearing trees. Microbes were mixed with no-carbon source media, and cultured with an ethylene for 3 d at room temperature in a closed container. Induced soil was used to delay ripening. Microbes induced with media and ethylene delayed ripening 100% of the time in all experimental units compared to control samples, while microbes cultured with media (no ethylene) delayed ripening less than 10% of the time compared to the control. These cells also appeared to increase the incidence of fungal infection in the fruit. The findings suggest induced microbes may convert ethylene into ethanol then acetaldehyde. The two compounds may form an acetaldehyde/ethanol vapor that delays ripening, and a secondary nitrile compound that inhibits fungal growth.Rhodococcus sp. may convert ethylene to acetaldehyde to slow ripening in climacteric fruit.https://peerj.com/preprints/33982019-09-172019-09-17Guenevere Perry
Pre-Print Update. Previous studies suggested Rhodococcus rhodochrous and Bacillus licheniformis cells converted ethylene to a nitrile compound to delay the effects of ripening, (Perry, G. Nov. 9, 2017). However, there may be an alternative compound that plays a more significant role in induced Rhodococcus and Bacillus ability to delay ripening. It has been known for years that Rhodococcus can convert the alkyne compound acetylene to acetaldehyde and potentially ethanol as a secondary product (DeBont, 1980).
This pre-print revisit re-examines the prior data to determine if the tri-phasic system previously discussed in 2017, induced bacteria to convert ethylene and/or propylene into acetaldehyde (a primary product), ethanol (a secondary product), and acetonitrile (a product of ethanol and a subsequent ammoxidation reaction). The acetaldehyde may delay the effects of ripening and inhibit fungal growth, while the nitrile by products enhance early plant development including germination and root elongation. Experimental results suggest an inducible monooxygenase or dioxygenase like enzyme is required to facilitate this process.
Pre-Print Update. Previous studies suggested Rhodococcus rhodochrous and Bacillus licheniformis cells converted ethylene to a nitrile compound to delay the effects of ripening, (Perry, G. Nov. 9, 2017). However, there may be an alternative compound that plays a more significant role in induced Rhodococcus and Bacillus ability to delay ripening. It has been known for years that Rhodococcus can convert the alkyne compound acetylene to acetaldehyde and potentially ethanol as a secondary product (DeBont, 1980).This pre-print revisit re-examines the prior data to determine if the tri-phasic system previously discussed in 2017, induced bacteria to convert ethylene and/or propylene into acetaldehyde (a primary product), ethanol (a secondary product), and acetonitrile (a product of ethanol and a subsequent ammoxidation reaction). The acetaldehyde may delay the effects of ripening and inhibit fungal growth, while the nitrile by products enhance early plant development including germination and root elongation. Experimental results suggest an inducible monooxygenase or dioxygenase like enzyme is required to facilitate this process.MATLAB software for automated calculation of concentration of different compounds using extracted peak area from HPLC data file in pdf formathttps://peerj.com/preprints/278782019-09-032019-09-03Wenfa Ng
Chromatograms represent a class of data difficult to process expeditiously due to the large number of intermediary steps necessary to translate peak detection to a concentration reading of a specific compound. This problem is further exacerbated by the different output file format in which instrument manufacturers present chromatographic data. Steps necessary to convert a detected peak to a concentration reading include identification of compound using retention time, extraction of corresponding peak area, and calculation of concentration of compound by using a calibration curve. This work sought to develop a MATLAB software able to automatically extract peak area from chromatographic readout captured in pdf format and calculate the corresponding concentration values. Given manufacturer-specific formatting features in pdf file, the MATLAB software could only read and handle pdf files of HPLC readouts from Shimadzu’s LabSolutions software. In processing the pdf file of each analyzed sample, entire content of the file was first read as a character string. Subsequently, specific delimiters were used to extract retention time and detected peak area for each compound. This information was subsequently processed to identify specific target compound of interest, where extracted peak area was used to calculate concentration of compound using a calibration plot. Overall, the program generates a database comprising filename, raw retention time and peak area data, as well as concentration values of each target compound in an easy to read format. Finally, to provide ease of access and a permanent file for storage, the program output the above database as an Excel file stored on the hard drive. One important advantage of this software is that it could process multiple pdf files simultaneously and there is no upper limit to the number of pdf files (or samples) that could be processed. Collectively, the MATLAB software capable of automatically extracting peak area and calculating concentration of different compounds would provide significant savings of time in handling large number of pdf files in a typical chromatographic run from a Shimadzu HPLC instrument.
Chromatograms represent a class of data difficult to process expeditiously due to the large number of intermediary steps necessary to translate peak detection to a concentration reading of a specific compound. This problem is further exacerbated by the different output file format in which instrument manufacturers present chromatographic data. Steps necessary to convert a detected peak to a concentration reading include identification of compound using retention time, extraction of corresponding peak area, and calculation of concentration of compound by using a calibration curve. This work sought to develop a MATLAB software able to automatically extract peak area from chromatographic readout captured in pdf format and calculate the corresponding concentration values. Given manufacturer-specific formatting features in pdf file, the MATLAB software could only read and handle pdf files of HPLC readouts from Shimadzu’s LabSolutions software. In processing the pdf file of each analyzed sample, entire content of the file was first read as a character string. Subsequently, specific delimiters were used to extract retention time and detected peak area for each compound. This information was subsequently processed to identify specific target compound of interest, where extracted peak area was used to calculate concentration of compound using a calibration plot. Overall, the program generates a database comprising filename, raw retention time and peak area data, as well as concentration values of each target compound in an easy to read format. Finally, to provide ease of access and a permanent file for storage, the program output the above database as an Excel file stored on the hard drive. One important advantage of this software is that it could process multiple pdf files simultaneously and there is no upper limit to the number of pdf files (or samples) that could be processed. Collectively, the MATLAB software capable of automatically extracting peak area and calculating concentration of different compounds would provide significant savings of time in handling large number of pdf files in a typical chromatographic run from a Shimadzu HPLC instrument.Candidate genes in coffee (Coffea arabica L.) leaves associated with rust (Hemileia vastatrix Berk. & Br) stresshttps://peerj.com/preprints/279232019-08-282019-08-28Fabián Echeverría-BeiruteSeth C. MurrayBenoit BertrandPatricia E. Klein
Background. Coffee leaf rust (CLR) caused by Hemileia vastatrix Berk. & Br, is one of the most threatening diseases for Coffea arabica L. It is hypothesized that host tolerance to CLR relies on non-race-specific resistance genes.
Methods. This study evaluated gene expression in leaves of two susceptible coffee cultivars (one inbred and one F1 hybrid) under different stress conditions: rust control (fungicide and untreated) and fruit thinning (thinned and un-thinned) treatments. RNA-seq analysis focused on the association of differentially expressed genes (DEGs) with CLR and associated the effect of the most significant genes into the phenotype, using regression and prediction statistical models.
Results. Gene expression and gene ontology (GO) analysis allowed identification of 100 genes associated with quantitative traits. From these, 88 were correlated with rust incidence, rust severity, and rust sporulation. The expression of genes coding for pathogenesis-related proteins increased positively with rust incidence in the inbred, while genes involved in homoeostasis and broader cell wall structuring processes were upregulated in the F1 hybrid. The enriched gene functions and associations revealed that a possible hypersensitive response (HR) in the inbred and a systemic acquired resistance (SAR) in the F1 hybrid were involved in the tolerance mechanisms to CLR stress. This is the first study to demonstrate the specific interactions between CLR and host at a molecular level, useful for identifying control targets for breeding perennial species.
Background. Coffee leaf rust (CLR) caused by Hemileia vastatrix Berk. & Br, is one of the most threatening diseases for Coffea arabica L. It is hypothesized that host tolerance to CLR relies on non-race-specific resistance genes.Methods. This study evaluated gene expression in leaves of two susceptible coffee cultivars (one inbred and one F1 hybrid) under different stress conditions: rust control (fungicide and untreated) and fruit thinning (thinned and un-thinned) treatments. RNA-seq analysis focused on the association of differentially expressed genes (DEGs) with CLR and associated the effect of the most significant genes into the phenotype, using regression and prediction statistical models.Results. Gene expression and gene ontology (GO) analysis allowed identification of 100 genes associated with quantitative traits. From these, 88 were correlated with rust incidence, rust severity, and rust sporulation. The expression of genes coding for pathogenesis-related proteins increased positively with rust incidence in the inbred, while genes involved in homoeostasis and broader cell wall structuring processes were upregulated in the F1 hybrid. The enriched gene functions and associations revealed that a possible hypersensitive response (HR) in the inbred and a systemic acquired resistance (SAR) in the F1 hybrid were involved in the tolerance mechanisms to CLR stress. This is the first study to demonstrate the specific interactions between CLR and host at a molecular level, useful for identifying control targets for breeding perennial species.A novel computational approach to the silencing of Sugarcane Bacilliform Guadeloupe A Virus determines potential host-derived MicroRNAs in sugarcane (Saccharum officinarum L.)https://peerj.com/preprints/278422019-07-042019-07-04Fakiha AshrafMuhammad Aleem AshrafXiaowen HuShuzhen Zhang
Sugarcane Bacilliform Guadeloupe A Virus (SCBGAV, genus Badnavirus, family Caulimoviridae) is an emerging, deleterious pathogen of sugarcane which presents a substantial barrier to producing high sugarcane earnings. The circular, double-stranded (ds) DNA genome of SCBGAV (7.4 Kb) is composed of three open reading frames (ORF) that replicate by a reverse transcriptase. In the current study, we used miRNA target prediction algorithms to identify and comprehensively analyze the genome-wide sugarcane (Saccharum officinarum L.)-encoded microRNA (miRNA) targets against the SCBGAV. A total of 28 potential mature target miRNAs were retrieved from the miRBase database and were further analyzed for hybridization to the SCBGAV genome. Multiple computational approaches—including miRNA-target seed pairing, multiple target positions, minimum free energy, target site accessibility, maximum complementarity, pattern recognition and minimum folding energy for attachments— were considered by all algorithms. Only 4 sugarcane miRNAs are selected for SCBGAV silencing. Among those 4, sof-miR396 was identified as the top effective candidate, capable of targeting the vital ORF3 which encodes polyprotein of the SCBGAV genome. miRanda, RNA22 and RNAhybrid algorithms predicted hybridization of sof-miR396 at common locus position 3394. A Circos plot was created to study the network visualization of sugarcane-encoded miRNAs with SCBGAV genes determines detailed evidence for any ideal targets of SCBGAV ORFs by precise miRNAs. The present study concludes a comprehensive report towards the creation of SCBGAV-resistant sugarcane through the expression analysis of the identified miRNAs.
Sugarcane Bacilliform Guadeloupe A Virus (SCBGAV, genus Badnavirus, family Caulimoviridae) is an emerging, deleterious pathogen of sugarcane which presents a substantial barrier to producing high sugarcane earnings. The circular, double-stranded (ds) DNA genome of SCBGAV (7.4 Kb) is composed of three open reading frames (ORF) that replicate by a reverse transcriptase. In the current study, we used miRNA target prediction algorithms to identify and comprehensively analyze the genome-wide sugarcane (Saccharum officinarum L.)-encoded microRNA (miRNA) targets against the SCBGAV. A total of 28 potential mature target miRNAs were retrieved from the miRBase database and were further analyzed for hybridization to the SCBGAV genome. Multiple computationalapproaches—including miRNA-target seed pairing, multiple target positions, minimum free energy, target site accessibility, maximum complementarity, pattern recognition and minimum folding energy for attachments— were considered by all algorithms. Only4 sugarcane miRNAs are selected for SCBGAV silencing. Among those 4, sof-miR396 was identified as the top effective candidate, capable of targeting the vital ORF3 which encodes polyprotein of the SCBGAV genome. miRanda, RNA22 and RNAhybrid algorithms predicted hybridization of sof-miR396 at common locus position 3394. A Circos plot was created to study the network visualization of sugarcane-encoded miRNAs with SCBGAV genes determines detailed evidence for any ideal targets of SCBGAV ORFs by precise miRNAs. The present study concludes a comprehensive report towards the creation of SCBGAV-resistant sugarcane through the expression analysis of the identified miRNAs.Current methods for inhibiting antibiotic resistant bacteria by targeting bacterial cell metabolism and disrupting antibiotic elimination through the AcrAB-Tolc efflux pumphttps://peerj.com/preprints/278402019-07-042019-07-04Tatiana Hillman
Bacteria have a complex and lengthy evolutionary history of antibiotic resistance. For millions of years, bacteria have evolved a gene pool filled with multiple drug resistant genes. However, for the past 50 years, bacteria have been mutating and evolving vigorously and rapidly. Those 50 years predate to the time of the first use of antibiotic drugs in the 1940s. Since the 1940s, with the wide-spread use of the first antibiotic, penicillin, bacteria have effectively developed resistance to multiple antibiotic drugs. Bacteria develop antibiotic resistance after acquiring antibiotic resistant genes from conjugation and a horizontal transfer of those genes. Bacteria also have innate properties, structure, and functions that can increase their resistance of antibiotics. Bacteria cells can mutate its genes and block the binding of antibiotic drugs to its DNA. If the bacteria effectively impede the activity of an antibiotic through a DNA mutation, then the same mutation is shared with other bacterial cell strains through horizontal transfer. Antibiotics can be expelled from bacteria cells by efflux pumps called AcrBC-Tolc channels from the resistance-nodulation division (RND) family. Targeting the cell metabolism or the expression of efflux pumps may deter or impede the proliferation of antibiotic resistance. Researchers cultured E. tarda with glucose and alanine, and the uptake of kanamycin increased, eliminating approximately 3,000 times the amount of MDR bacterial cells compared to the cells only treated with kanamycin. Another researcher named Dr. Li mutated a gene of the AcrAB-Tolc binding site, forming a replacement for the highly non-polar phenylalanine amino acid residue with an alanine. His mutagenesis of the efflux pumps binding sites for AcrAB-Tolc inhibited the exit of antibiotics through the AcrAB-Tolc efflux pumps. Therefore, the review serves to discuss the new, novel, and current methods for reducing the spread of antibiotic resistant bacteria by targeting bacterial cell metabolism and its antibiotic resistant genes.
Bacteria have a complex and lengthy evolutionary history of antibiotic resistance. For millions of years, bacteria have evolved a gene pool filled with multiple drug resistant genes. However, for the past 50 years, bacteria have been mutating and evolving vigorously and rapidly. Those 50 years predate to the time of the first use of antibiotic drugs in the 1940s. Since the 1940s, with the wide-spread use of the first antibiotic, penicillin, bacteria have effectively developed resistance to multiple antibiotic drugs. Bacteria develop antibiotic resistance after acquiring antibiotic resistant genes from conjugation and a horizontal transfer of those genes. Bacteria also have innate properties, structure, and functions that can increase their resistance of antibiotics. Bacteria cells can mutate its genes and block the binding of antibiotic drugs to its DNA. If the bacteria effectively impede the activity of an antibiotic through a DNA mutation, then the same mutation is shared with other bacterial cell strains through horizontal transfer. Antibiotics can be expelled from bacteria cells by efflux pumps called AcrBC-Tolc channels from the resistance-nodulation division (RND) family. Targeting the cell metabolism or the expression of efflux pumps may deter or impede the proliferation of antibiotic resistance. Researchers cultured E. tarda with glucose and alanine, and the uptake of kanamycin increased, eliminating approximately 3,000 times the amount of MDR bacterial cells compared to the cells only treated with kanamycin. Another researcher named Dr. Li mutated a gene of the AcrAB-Tolc binding site, forming a replacement for the highly non-polar phenylalanine amino acid residue with an alanine. His mutagenesis of the efflux pumps binding sites for AcrAB-Tolc inhibited the exit of antibiotics through the AcrAB-Tolc efflux pumps. Therefore, the review serves to discuss the new, novel, and current methods for reducing the spread of antibiotic resistant bacteria by targeting bacterial cell metabolism and its antibiotic resistant genes.Molecular weight calculator for organic compounds in biotechnologyhttps://peerj.com/preprints/278362019-07-022019-07-02Wenfa Ng
Automated calculation of molecular weight of chemical compounds would provide savings in time and effort, especially in handling large number of compounds common in chemical or biotechnology workflow. In this work, a molecular weight calculator was developed using MATLAB and is capable of handling the chemical elements: carbon, hydrogen, oxygen, nitrogen, phosphorus, and sulphur that constitute organic compounds common in biotechnology. Such compounds would typically come across as either substrates or products of fermentation, where automated calculation of molecular weight would feed into mass/charge calculations that facilitate workflow involving their mass spectrometric detection. Specifically, chemical formulas of molecular ion are necessary information for identifying particular mass peaks in mass spectrometry, to which automated molecular weight calculation would greatly simplify peak identification. Thus, the molecular weight calculator developed in this work could be used as a subroutine for more complex software that provides identification of mass peaks in mass spectrometry workflow detecting organic compounds in fermentation.
Automated calculation of molecular weight of chemical compounds would provide savings in time and effort, especially in handling large number of compounds common in chemical or biotechnology workflow. In this work, a molecular weight calculator was developed using MATLAB and is capable of handling the chemical elements: carbon, hydrogen, oxygen, nitrogen, phosphorus, and sulphur that constitute organic compounds common in biotechnology. Such compounds would typically come across as either substrates or products of fermentation, where automated calculation of molecular weight would feed into mass/charge calculations that facilitate workflow involving their mass spectrometric detection. Specifically, chemical formulas of molecular ion are necessary information for identifying particular mass peaks in mass spectrometry, to which automated molecular weight calculation would greatly simplify peak identification. Thus, the molecular weight calculator developed in this work could be used as a subroutine for more complex software that provides identification of mass peaks in mass spectrometry workflow detecting organic compounds in fermentation.A mechanistic overview of ruminal fibre digestion.https://peerj.com/preprints/278312019-06-282019-06-28Adrian E NaasPhillip B Pope
Ruminants have co-evolved with symbiotic rumen microbiota, which readily convert ingested plant fibres into the nutrients they need to sustain their growth and maintenance. Fibre degradation within the rumen microbiome has been attributed to a limited number of cultivable representatives, which has restricted our ability to understand the different enzymatic machineries that exist. However, via a combination of culturing, meta-omics, bioinformatics, biochemistry and enzymology, we are beginning to expand our insight into the different fibre-digesting strategies that rumen microbiota employ. We discuss findings from studies on well-known Ruminococcus, Fibrobacter and Prevotella isolates, as well as those from poorly understood and as-yet uncultured Bacteroidetes lineages. Collectively, these approaches have revealed new mechanistic information related to the hydrolytic capacity of cellulosomes, free enzymes, outer membrane vesicles, polysaccharide utilization loci and large multi-modular enzymes, which are generating deeper insights into the intricate microbial networks that engage in ruminal fibre digestion.
Ruminants have co-evolved with symbiotic rumen microbiota, which readily convert ingested plant fibres into the nutrients they need to sustain their growth and maintenance. Fibre degradation within the rumen microbiome has been attributed to a limited number of cultivable representatives, which has restricted our ability to understand the different enzymatic machineries that exist. However, via a combination of culturing, meta-omics, bioinformatics, biochemistry and enzymology, we are beginning to expand our insight into the different fibre-digesting strategies that rumen microbiota employ. We discuss findings from studies on well-known Ruminococcus, Fibrobacter and Prevotella isolates, as well as those from poorly understood and as-yet uncultured Bacteroidetes lineages. Collectively, these approaches have revealed new mechanistic information related to the hydrolytic capacity of cellulosomes, free enzymes, outer membrane vesicles, polysaccharide utilization loci and large multi-modular enzymes, which are generating deeper insights into the intricate microbial networks that engage in ruminal fibre digestion.