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Kevin V. Solomon - One of the best experts on this subject based on the ideXlab platform.
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cocultivation of Anaerobic Fungi with rumen bacteria establishes an antagonistic relationship
Mbio, 2021Co-Authors: Candice L Swift, Casey A. Hooker, Kevin V. Solomon, Katherine B Louie, Benjamin P Bowen, Vasanth R Singan, Chris Daum, Christa Pennacchio, Kerrie Barry, V ShutthanandanAbstract:Anaerobic gut Fungi (Neocallimastigomycetes) live in the digestive tract of large herbivores, where they are vastly outnumbered by bacteria. It has been suggested that Anaerobic Fungi challenge growth of bacteria owing to the wealth of biosynthetic genes in fungal genomes, although this relationship has not been experimentally tested. Here, we cocultivated the rumen bacteria Fibrobacter succinogenes strain UWB7 with the Anaerobic gut Fungi Anaeromyces robustus or Caecomyces churrovis on a range of carbon substrates and quantified the bacterial and fungal transcriptomic response. Synthetic cocultures were established for at least 24 h, as verified by active fungal and bacterial transcription. A. robustus upregulated components of its secondary metabolism in the presence of Fibrobacter succinogenes strain UWB7, including six nonribosomal peptide synthetases, one polyketide synthase-like enzyme, and five polyketide synthesis O-type methyltransferases. Both A. robustus and C. churrovis cocultures upregulated S-adenosyl-l-methionine (SAM)-dependent methyltransferases, histone methyltransferases, and an acetyltransferase. Fungal histone 3 lysine 27 trimethylation marks were more abundant in coculture, and heterochromatin protein-1 was downregulated. Together, these findings suggest that fungal chromatin remodeling occurs when bacteria are present. F. succinogenes strain UWB7 upregulated four genes in coculture encoding drug efflux pumps, which likely protect the cell against toxins. Furthermore, untargeted nonpolar metabolomics data revealed at least one novel fungal metabolite enriched in coculture, which may be a defense compound. Taken together, these data suggest that A. robustus and C. churrovis produce antimicrobials when exposed to rumen bacteria and, more broadly, that Anaerobic gut Fungi are a source of novel antibiotics. IMPORTANCE Anaerobic Fungi are outnumbered by bacteria by 4 orders of magnitude in the herbivore rumen. Despite their numerical disadvantage, they are resilient members of the rumen microbiome. Previous studies mining the genomes of Anaerobic Fungi identified genes encoding enzymes to produce natural products, which are small molecules that are often antimicrobials. In this work, we cocultured the Anaerobic fungus Anaeromyces robustus or Caecomyes churrovis with rumen bacteria Fibrobacter succinogenes strain UWB7 and sequenced fungal and bacterial active genes via transcriptome sequencing (RNA-seq). Consistent with production of a fungal defense compound, bacteria upregulated genes encoding drug efflux pumps, which often export toxic molecules, and Fungi upregulated genes encoding biosynthetic enzymes of natural products. Furthermore, tandem mass spectrometry detected an unknown fungal metabolite enriched in the coculture. Together, these findings point to an antagonistic relationship between Anaerobic Fungi and rumen bacteria resulting in the production of a fungal compound with potential antimicrobial activity.
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Anaerobic Fungal Mevalonate Pathway Genomic Biases Lead to Heterologous Toxicity Underpredicted by Codon Adaptation Indices
'MDPI AG', 2021Co-Authors: Ethan T. Hillman, Adrian Ortiz-velez, Elizabeth M. Frazier, Evan K. Shank, Jacob A. Englaender, Kevin V. SolomonAbstract:Anaerobic Fungi are emerging biotechnology platforms with genomes rich in biosynthetic potential. Yet, the heterologous expression of their biosynthetic pathways has had limited success in model hosts like E. coli. We find one reason for this is that the genome composition of Anaerobic Fungi like P. indianae are extremely AT-biased with a particular preference for rare and semi-rare AT-rich tRNAs in E coli, which are not explicitly predicted by standard codon adaptation indices (CAI). Native P. indianae genes with these extreme biases create drastic growth defects in E. coli (up to 69% reduction in growth), which is not seen in genes from other organisms with similar CAIs. However, codon optimization rescues growth, allowing for gene evaluation. In this manner, we demonstrate that Anaerobic fungal homologs such as PI.atoB are more active than S. cerevisiae homologs in a hybrid pathway, increasing the production of mevalonate up to 2.5 g/L (more than two-fold) and reducing waste carbon to acetate by ~90% under the conditions tested. This work demonstrates the bioproduction potential of Anaerobic fungal enzyme homologs and how the analysis of codon utilization enables the study of otherwise difficult to express genes that have applications in biocatalysis and natural product discovery
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Hydrolysis of untreated lignocellulosic feedstock is independent of S-lignin composition in newly classified Anaerobic fungal isolate, Piromyces sp. UH3-1.
Biotechnology for biofuels, 2018Co-Authors: Casey A. Hooker, Ethan T. Hillman, Jonathan C. Overton, Adrian Ortiz-velez, Makayla Schacht, Abigail Hunnicutt, Nathan S. Mosier, Kevin V. SolomonAbstract:Plant biomass is an abundant but underused feedstock for bioenergy production due to its complex and variable composition, which resists breakdown into fermentable sugars. These feedstocks, however, are routinely degraded by many uncommercialized microbes such as Anaerobic gut Fungi. These gut Fungi express a broad range of carbohydrate active enzymes and are native to the digestive tracts of ruminants and hindgut fermenters. In this study, we examine gut fungal performance on these substrates as a function of composition, and the ability of this isolate to degrade inhibitory high syringyl lignin-containing forestry residues. We isolated a novel fungal specimen from a donkey in Independence, Indiana, United States. Phylogenetic analysis of the Internal Transcribed Spacer 1 sequence classified the isolate as a member of the genus Piromyces within the phylum Neocallimastigomycota (Piromyces sp. UH3-1, strain UH3-1). The isolate penetrates the substrate with an extensive rhizomycelial network and secretes many cellulose-binding enzymes, which are active on various components of lignocellulose. These activities enable the fungus to hydrolyze at least 58% of the glucan and 28% of the available xylan in untreated corn stover within 168 h and support growth on crude agricultural residues, food waste, and energy crops. Importantly, UH3-1 hydrolyzes high syringyl lignin-containing poplar that is inhibitory to many Fungi with efficiencies equal to that of low syringyl lignin-containing poplar with no reduction in fungal growth. This behavior is correlated with slight remodeling of the fungal secretome whose composition adapts with substrate to express an enzyme cocktail optimized to degrade the available biomass. Piromyces sp. UH3-1, a newly isolated Anaerobic gut fungus, grows on diverse untreated substrates through production of a broad range of carbohydrate active enzymes that are robust to variations in substrate composition. Additionally, UH3-1 and potentially other Anaerobic Fungi are resistant to inhibitory lignin composition possibly due to changes in enzyme secretion with substrate. Thus, Anaerobic Fungi are an attractive platform for the production of enzymes that efficiently use mixed feedstocks of variable composition for second generation biofuels. More importantly, our work suggests that the study of Anaerobic Fungi may reveal naturally evolved strategies to circumvent common hydrolytic inhibitors that hinder biomass usage.
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Catabolic repression in early-diverging Anaerobic Fungi is partially mediated by natural antisense transcripts.
Fungal Genetics and Biology, 2018Co-Authors: Kevin V. Solomon, Anna Lipzen, Dawn A. ThompsonAbstract:Early-diverging Anaerobic Fungi (order: Neocallimastigomycota), lignocelluolytic chytrid-like Fungi central to fiber degradation in the digestive tracts of large herbivores, are attractive sources of cellulases and hemicellulases for biotechnology. Enzyme expression is tightly regulated and coordinated through mechanisms that remain unelucidated to optimize hydrolytic efficiency. Our analysis of Anaerobic fungal transcriptomes reveals hundreds of cis-natural antisense transcripts (cis-NATs), which we hypothesize play an integral role in this regulation. Through integrated genomic and transcriptomic sequencing on a range of catabolic substrates, we validate these NATs in three species (Anaeromyces robustus, Neocallimasix californiae, and Piromyces finnis), and analyze their expression patterns and prevalence to gain insight into their function. NAT function was diverse and conserved across the three fungal genomes studied, with 10% of all metabolic process NATs associated with lignocellulose hydrolysis. Despite these similarities, however, only eleven gene targets were conserved orthologs. Several NATs were dynamically regulated by lignocellulosic substrates while their gene targets were unregulated. This observation is consistent with a hypothesized, but untested, regulatory mechanism where selected genes are exclusively regulated at the transcriptional/post-transcriptional level by NATs. However, only genes with high NAT relative expression levels displayed this phenomenon, suggesting a selection mechanism that favors larger dynamic ranges for more precise control of gene expression. In addition to this mode, we observed two other possible regulatory fates: canonical transcriptional regulation with no NAT response, and positive co-regulation of target mRNA and cognate NAT, which we hypothesize is a fine-tuning strategy to locally negate control outputs from global regulators. Our work reveals the complex contributions of antisense RNA to the catabolic response in Anaerobic Fungi, highlighting its importance in understanding lignocellulolytic activity for bioenergy applications. More importantly, the relative expression of NAT to target may form a critical determinant of transcriptional vs post-transcriptional (NAT) control of gene expression in primitive Anaerobic Fungi.
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Hydrolysis of untreated lignocellulosic feedstock is independent of S-lignin composition in newly classified Anaerobic fungal isolate, Piromyces sp. UH3-1
BMC, 2018Co-Authors: Casey A. Hooker, Ethan T. Hillman, Jonathan C. Overton, Adrian Ortiz-velez, Makayla Schacht, Abigail Hunnicutt, Nathan S. Mosier, Kevin V. SolomonAbstract:Abstract Background Plant biomass is an abundant but underused feedstock for bioenergy production due to its complex and variable composition, which resists breakdown into fermentable sugars. These feedstocks, however, are routinely degraded by many uncommercialized microbes such as Anaerobic gut Fungi. These gut Fungi express a broad range of carbohydrate active enzymes and are native to the digestive tracts of ruminants and hindgut fermenters. In this study, we examine gut fungal performance on these substrates as a function of composition, and the ability of this isolate to degrade inhibitory high syringyl lignin-containing forestry residues. Results We isolated a novel fungal specimen from a donkey in Independence, Indiana, United States. Phylogenetic analysis of the Internal Transcribed Spacer 1 sequence classified the isolate as a member of the genus Piromyces within the phylum Neocallimastigomycota (Piromyces sp. UH3-1, strain UH3-1). The isolate penetrates the substrate with an extensive rhizomycelial network and secretes many cellulose-binding enzymes, which are active on various components of lignocellulose. These activities enable the fungus to hydrolyze at least 58% of the glucan and 28% of the available xylan in untreated corn stover within 168 h and support growth on crude agricultural residues, food waste, and energy crops. Importantly, UH3-1 hydrolyzes high syringyl lignin-containing poplar that is inhibitory to many Fungi with efficiencies equal to that of low syringyl lignin-containing poplar with no reduction in fungal growth. This behavior is correlated with slight remodeling of the fungal secretome whose composition adapts with substrate to express an enzyme cocktail optimized to degrade the available biomass. Conclusions Piromyces sp. UH3-1, a newly isolated Anaerobic gut fungus, grows on diverse untreated substrates through production of a broad range of carbohydrate active enzymes that are robust to variations in substrate composition. Additionally, UH3-1 and potentially other Anaerobic Fungi are resistant to inhibitory lignin composition possibly due to changes in enzyme secretion with substrate. Thus, Anaerobic Fungi are an attractive platform for the production of enzymes that efficiently use mixed feedstocks of variable composition for second generation biofuels. More importantly, our work suggests that the study of Anaerobic Fungi may reveal naturally evolved strategies to circumvent common hydrolytic inhibitors that hinder biomass usage
Anil Kumar Puniya - One of the best experts on this subject based on the ideXlab platform.
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Anaerobic Fungi past present and future
Frontiers in Microbiology, 2020Co-Authors: Matthias Hess, Anil Kumar Puniya, S.s. Paul, Mark Van Der Giezen, Joan E. Edwards, Claire Shaw, Katerina FliegerovaAbstract:Anaerobic Fungi (AF) play an essential role in feed conversion due to their potent fiber degrading enzymes and invasive growth. Much has been learned about this unusual fungal phylum since the paradigm shifting work of Colin Orpin in the 1970s, when he characterized the first AF. Molecular approaches targeting specific phylogenetic marker genes have facilitated taxonomic classification of AF, which had been previously been complicated by the complex life cycles and associated morphologies. Although we now have a much better understanding of their diversity, it is believed that there are still numerous genera of AF that remain to be described in gut ecosystems. Recent marker-gene based studies have shown that fungal diversity in the herbivore gut is much like the bacterial population, driven by host phylogeny, host genetics and diet. Since AF are major contributors to the degradation of plant material ingested by the host animal, it is understandable that there has been great interest in exploring the enzymatic repertoire of these microorganisms in order to establish a better understanding of how AF, and their enzymes, can be used to improve host health and performance, while simultaneously reducing the ecological footprint of the livestock industry. A detailed understanding of AF and their interaction with other gut microbes as well as the host animal is essential, especially when production of affordable high-quality protein and other animal-based products needs to meet the demands of an increasing human population. Such a mechanistic understanding, leading to more sustainable livestock practices, will be possible with recently developed -omics technologies that have already provided first insights into the different contributions of the fungal and bacterial population in the rumen during plant cell wall hydrolysis.
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A new Anaerobic fungus (Oontomyces anksri gen. nov., sp. nov.) from the digestive tract of the Indian camel (Camelus dromedarius).
Fungal biology, 2015Co-Authors: Sumit Singh Dagar, Gareth W Griffith, Sanjay Kumar, Tony M. Callaghan, Joan E. Edwards, Rameshwar Singh, Ashok K. Nagpal, Anil Kumar PuniyaAbstract:Two cultures of Anaerobic Fungi were isolated from the forestomach of an Indian camel (Camelus dromedarius). Phylogenetic analysis using both the internal transcribed spacer (ITS) and large-subunit (LSU) regions of the rRNA locus demonstrated that these isolates were identical and formed a distinct clade within the Anaerobic Fungi (phylum Neocallimastigomycota). Morphological examination showed that these Fungi formed monocentric thalli with filamentous rhizoids and uniflagellate zoospores, broadly similar to members of the genus Piromyces. However, distinctive morphological features were observed, notably the pinching of the cytoplasm in the sporangiophore and the formation of intercalary rhizoidal swellings. Since genetic analyses demonstrated this fungus was only distantly related to Piromyces spp. and closer to the polycentric Anaeromyces clade, we have assigned it to a new genus and species Oontomyces anksri gen. nov., sp. nov. Interrogation of the GenBank database identified several closely related ITS sequences, which were all environmental sequences obtained from camels, raising the possibility that this fungus may be specific to camelids.
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role of live microbial feed supplements with reference to Anaerobic Fungi in ruminant productivity a review
Journal of Integrative Agriculture, 2015Co-Authors: Anil Kumar Puniya, Gareth W Griffith, Monica Puniya, S. Rao Ravella, Sumit Singh Dagar, Abdelfattah Z M Salem, Sanjay Kumar, Nikhil KumarAbstract:Abstract To keep the concept of a safe food supply to the consumers, animal feed industries world over are showing an increasing interest in the direct-fed microbials (DFM) for improved animal performance in terms of growth or productivity. This becomes all the more essential in a situation, where a number of the residues of antibiotics and/or other growth stimulants reach in milk and meat with a number of associated potential risks for the consumers. Hence, in the absence of growth stimulants, a positive manipulation of the rumen microbial ecosystem to enhance the feedstuff utilization for improved production efficiency by ruminants has become of much interest to the researchers and entrepreneurs. A few genera of live microbes (i.e., bacteria, Fungi and yeasts in different types of formulations from paste to powder) are infrequently used as DFM for the domestic ruminants. These DFM products are live microbial feed supplements containing naturally occurring microbes in the rumen. Among different DFM possibilities, Anaerobic rumen Fungi (ARF) based additives have been found to improve ruminant productivity consistently during feeding trials. Administration of ARF during the few trials conducted, led to the increased weight gain, milk production, and total tract digestibility of feed components in ruminants. Anaerobic Fungi in the rumen display very strong cell-wall degrading cellulolytic and xylanolytic activities through rhizoid development, resulting in the physical disruption of feed structure paving the way for bacterial action. Significant improvements in the fiber digestibility were found to coincide with increases in ARF in the rumen indicating their role. Most of the researches based on DFM have indicated a positive response in nutrient digestion and methane reducing potential during in vivo and/or in vitro supplementation of ARF as DFM. Therefore, DFM especially ARF will gain popularity but it is necessary that all the strains are thoroughly studied for their beneficial properties to have a confirmed ‘generally regarded as safe’ status for ruminants.
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role of Anaerobic Fungi in wheat straw degradation and effects of plant feed additives on rumen fermentation parameters in vitro
Beneficial Microbes, 2015Co-Authors: Sumit Singh Dagar, Sanjay Kumar, N Singh, Navneet Goel, Anil Kumar PuniyaAbstract:In the present study, rumen microbial groups, i.e. total rumen microbes (TRM), total Anaerobic Fungi (TAF), avicel enriched bacteria (AEB) and neutral detergent fibre enriched bacteria (NEB) were evaluated for wheat straw (WS) degradability and different fermentation parameters in vitro. Highest WS degradation was shown for TRM, followed by TAF, NEB and least by AEB. Similar patterns were observed with total gas production and short chain fatty acid profiles. Overall, TAF emerged as the most potent individual microbial group. In order to enhance the fibrolytic and rumen fermentation potential of TAF, we evaluated 18 plant feed additives in vitro. Among these, six plant additives namely Albizia lebbeck, Alstonia scholaris, Bacopa monnieri, Lawsonia inermis, Psidium guajava and Terminalia arjuna considerably improved WS degradation by TAF. Further evaluation showed A. lebbeck as best feed additive. The study revealed that TAF plays a significant role in WS degradation and their fibrolytic activities can be improved by inclusion of A. lebbeck in fermentation medium. Further studies are warranted to elucidate its active constituents, effect on fungal population and in vivo potential in animal system.
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Role of live microbial feed supplements with reference to Anaerobic Fungi in ruminant productivity: A review
'Elsevier BV', 2015Co-Authors: Anil Kumar Puniya, Salem A.z.m., Kumar Sanjay, Dagar, Sumit Singh, Griffith W Gareth, Puniya Monica, Ravella R Sreenivas, Kumar Nikhil, Dhewa Tejpal, Kumar RavinderAbstract:To keep the concept of a safe food supply to the consumers, animal feed industries world over are showing an increasing interest in the direct-fed microbials (DFM) for improved animal performance in terms of growth or productivity. This becomes all the more essential in a situation, where a number of the residues of antibiotics and/or other growth stimulants reach in milk and meat with a number of associated potential risks for the consumers. Hence, in the absence of growth stimulants, a positive manipulation of the rumen microbial ecosystem to enhance the feedstuff utilization for improved production efficiency by ruminants has become of much interest to the researchers and entrepreneurs. A few genera of live microbes (i.e., bacteria, Fungi and yeasts in different types of formulations from paste to powder) are infrequently used as DFM for the domestic ruminants. These DFM products are live microbial feed supplements containing naturally occurring microbes in the rumen. Among different DFM possibilities, Anaerobic rumen Fungi (ARF) based additives have been found to improve ruminant productivity consistently during feeding trials. Administration of ARF during the few trials conducted, led to the increased weight gain, milk production, and total tract digestibility of feed components in ruminants. Anaerobic Fungi in the rumen display very strong cell-wall degrading cellulolytic and xylanolytic activities through rhizoid development, resulting in the physical disruption of feed structure paving the way for bacterial action. Significant improvements in the fiber digestibility were found to coincide with increases in ARF in the rumen indicating their role. Most of the researches based on DFM have indicated a positive response in nutrient digestion and methane reducing potential during in vivo and/or in vitro supplementation of ARF as DFM. Therefore, DFM especially ARF will gain popularity but it is necessary that all the strain
Sumit Singh Dagar - One of the best experts on this subject based on the ideXlab platform.
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A new Anaerobic fungus (Oontomyces anksri gen. nov., sp. nov.) from the digestive tract of the Indian camel (Camelus dromedarius).
Fungal biology, 2015Co-Authors: Sumit Singh Dagar, Gareth W Griffith, Sanjay Kumar, Tony M. Callaghan, Joan E. Edwards, Rameshwar Singh, Ashok K. Nagpal, Anil Kumar PuniyaAbstract:Two cultures of Anaerobic Fungi were isolated from the forestomach of an Indian camel (Camelus dromedarius). Phylogenetic analysis using both the internal transcribed spacer (ITS) and large-subunit (LSU) regions of the rRNA locus demonstrated that these isolates were identical and formed a distinct clade within the Anaerobic Fungi (phylum Neocallimastigomycota). Morphological examination showed that these Fungi formed monocentric thalli with filamentous rhizoids and uniflagellate zoospores, broadly similar to members of the genus Piromyces. However, distinctive morphological features were observed, notably the pinching of the cytoplasm in the sporangiophore and the formation of intercalary rhizoidal swellings. Since genetic analyses demonstrated this fungus was only distantly related to Piromyces spp. and closer to the polycentric Anaeromyces clade, we have assigned it to a new genus and species Oontomyces anksri gen. nov., sp. nov. Interrogation of the GenBank database identified several closely related ITS sequences, which were all environmental sequences obtained from camels, raising the possibility that this fungus may be specific to camelids.
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role of live microbial feed supplements with reference to Anaerobic Fungi in ruminant productivity a review
Journal of Integrative Agriculture, 2015Co-Authors: Anil Kumar Puniya, Gareth W Griffith, Monica Puniya, S. Rao Ravella, Sumit Singh Dagar, Abdelfattah Z M Salem, Sanjay Kumar, Nikhil KumarAbstract:Abstract To keep the concept of a safe food supply to the consumers, animal feed industries world over are showing an increasing interest in the direct-fed microbials (DFM) for improved animal performance in terms of growth or productivity. This becomes all the more essential in a situation, where a number of the residues of antibiotics and/or other growth stimulants reach in milk and meat with a number of associated potential risks for the consumers. Hence, in the absence of growth stimulants, a positive manipulation of the rumen microbial ecosystem to enhance the feedstuff utilization for improved production efficiency by ruminants has become of much interest to the researchers and entrepreneurs. A few genera of live microbes (i.e., bacteria, Fungi and yeasts in different types of formulations from paste to powder) are infrequently used as DFM for the domestic ruminants. These DFM products are live microbial feed supplements containing naturally occurring microbes in the rumen. Among different DFM possibilities, Anaerobic rumen Fungi (ARF) based additives have been found to improve ruminant productivity consistently during feeding trials. Administration of ARF during the few trials conducted, led to the increased weight gain, milk production, and total tract digestibility of feed components in ruminants. Anaerobic Fungi in the rumen display very strong cell-wall degrading cellulolytic and xylanolytic activities through rhizoid development, resulting in the physical disruption of feed structure paving the way for bacterial action. Significant improvements in the fiber digestibility were found to coincide with increases in ARF in the rumen indicating their role. Most of the researches based on DFM have indicated a positive response in nutrient digestion and methane reducing potential during in vivo and/or in vitro supplementation of ARF as DFM. Therefore, DFM especially ARF will gain popularity but it is necessary that all the strains are thoroughly studied for their beneficial properties to have a confirmed ‘generally regarded as safe’ status for ruminants.
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role of Anaerobic Fungi in wheat straw degradation and effects of plant feed additives on rumen fermentation parameters in vitro
Beneficial Microbes, 2015Co-Authors: Sumit Singh Dagar, Sanjay Kumar, N Singh, Navneet Goel, Anil Kumar PuniyaAbstract:In the present study, rumen microbial groups, i.e. total rumen microbes (TRM), total Anaerobic Fungi (TAF), avicel enriched bacteria (AEB) and neutral detergent fibre enriched bacteria (NEB) were evaluated for wheat straw (WS) degradability and different fermentation parameters in vitro. Highest WS degradation was shown for TRM, followed by TAF, NEB and least by AEB. Similar patterns were observed with total gas production and short chain fatty acid profiles. Overall, TAF emerged as the most potent individual microbial group. In order to enhance the fibrolytic and rumen fermentation potential of TAF, we evaluated 18 plant feed additives in vitro. Among these, six plant additives namely Albizia lebbeck, Alstonia scholaris, Bacopa monnieri, Lawsonia inermis, Psidium guajava and Terminalia arjuna considerably improved WS degradation by TAF. Further evaluation showed A. lebbeck as best feed additive. The study revealed that TAF plays a significant role in WS degradation and their fibrolytic activities can be improved by inclusion of A. lebbeck in fermentation medium. Further studies are warranted to elucidate its active constituents, effect on fungal population and in vivo potential in animal system.
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Anaerobic Fungi (phylum Neocallimastigomycota): advances in understanding their taxonomy, life cycle, ecology, role and biotechnological potential
FEMS Microbiology Ecology, 2014Co-Authors: Robert J. Gruninger, Gareth W Griffith, Sumit Singh Dagar, Anil Kumar Puniya, Tony M. Callaghan, Joan E. Edwards, Noha H. Youssef, Katerina Fliegerova, Robert J. Forster, Adrian TsangAbstract:Anaerobic Fungi (phylum Neocallimastigomycota) inhabit the gastrointestinal tract of mammalian herbivores, where they play an important role in the degradation of plant material. The Neocallimastigomycota represent the earliest diverging lineage of the zoosporic Fungi; however, understanding of the relationships of the different taxa (both genera and species) within this phylum is in need of revision. Issues exist with the current approaches used for their identification and classification, and recent evidence suggests the presence of several novel taxa (potential candidate genera) that remain to be characterised. The life cycle and role of Anaerobic Fungi has been well characterised in the rumen, but not elsewhere in the ruminant alimentary tract. Greater understanding of the 'resistant' phase(s) of their life cycle is needed, as is study of their role and significance in other herbivores. Biotechnological application of Anaerobic Fungi, and their highly active cellulolytic and hemi-cellulolytic enzymes, has been a rapidly increasing area of research and development in the last decade. The move towards understanding of Anaerobic Fungi using -omics based (genomic, transcriptomic and proteomic) approaches is starting to yield valuable insights into the unique cellular processes, evolutionary history, metabolic capabilities and adaptations that exist within the Neocallimastigomycota.
Mostafa S Elshahed - One of the best experts on this subject based on the ideXlab platform.
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comparative genomics and divergence time estimation of the Anaerobic Fungi in herbivorous mammals
bioRxiv, 2018Co-Authors: Yan Wang, Noha H. Youssef, Radwa A Hanafy, Mostafa S Elshahed, M B Couger, Jason E StajichAbstract:The Anaerobic gut Fungi (AGF) or Neocallimastigomycota inhabit the rumen of herbivorous mammals where they support plant fiber degradation. These obligate anaerobes have large and AT-biased genomes, which have limited genome-wide studies and the phylogenomic analyses of these Fungi. Using newly generated genomes and transcriptomes of 27 Neocallimastigomycota taxa, we have explored their evolutionary relationships, divergence time, and gene content. The most recent common ancestor of the AGF is estimated to have diverged 73.5+/-5 million years ago (Mya), which coincides with the estimated ages of grasses (Poaceae) and evolution of mammalian herbivory. Comparative genomics identified lineage-specific genes and protein family domains including three that may have been acquired through horizontal gene transfer from animal hosts, plants, and rumen gut bacteria. The concordance of independently estimated divergence times of Neocallimastigomycota Fungi, grasses, and ruminate lineages suggest AGF were important in shaping the success of modern ruminants and enabling their efficient acquisition of energy from recalcitrant plant material.
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transcriptomic analysis of lignocellulosic biomass degradation by the Anaerobic fungal isolate orpinomyces sp strain c1a
Biotechnology for Biofuels, 2015Co-Authors: M B Couger, Noha H. Youssef, Christopher G Struchtemeyer, Audra S Liggenstoffer, Mostafa S ElshahedAbstract:Background Anaerobic Fungi reside in the rumen and alimentary tract of herbivores where they play an important role in the digestion of ingested plant biomass. The Anaerobic fungal isolate Orpinomyces sp. strain C1A is an efficient biomass degrader, capable of simultaneous saccharification and fermentation of the cellulosic and hemicellulosic fractions in multiple types of lignocellulosic biomass. To understand the mechanistic and regulatory basis of biomass deconstruction in Anaerobic Fungi, we analyzed the transcriptomic profiles of C1A when grown on four different types of lignocellulosic biomass (alfalfa, energy cane, corn stover, and sorghum) versus a soluble sugar monomer (glucose).
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transcriptomic analysis of lignocellulosic biomass degradation by the Anaerobic fungal isolate orpinomyces sp strain c1a
Biotechnology for Biofuels, 2015Co-Authors: M B Couger, Noha H. Youssef, Christopher G Struchtemeyer, Audra S Liggenstoffer, Mostafa S ElshahedAbstract:Anaerobic Fungi reside in the rumen and alimentary tract of herbivores where they play an important role in the digestion of ingested plant biomass. The Anaerobic fungal isolate Orpinomyces sp. strain C1A is an efficient biomass degrader, capable of simultaneous saccharification and fermentation of the cellulosic and hemicellulosic fractions in multiple types of lignocellulosic biomass. To understand the mechanistic and regulatory basis of biomass deconstruction in Anaerobic Fungi, we analyzed the transcriptomic profiles of C1A when grown on four different types of lignocellulosic biomass (alfalfa, energy cane, corn stover, and sorghum) versus a soluble sugar monomer (glucose). A total of 468.2 million reads (70.2 Gb) were generated and assembled into 27,506 distinct transcripts. CAZyme transcripts identified included 385, 246, and 44 transcripts belonging to 44, 13, and 8 different glycoside hydrolases (GH), carbohydrate esterases, and polysaccharide lyases families, respectively. Examination of CAZyme transcriptional patterns indicates that strain C1A constitutively transcribes a high baseline level of CAZyme transcripts on glucose. Although growth on lignocellulosic biomass substrates was associated with a significant increase in transcriptional levels in few GH families, including the highly transcribed GH1 β-glucosidase, GH6 cellobiohydrolase, and GH9 endoglucanase, the transcriptional levels of the majority of CAZyme families and transcripts were not significantly altered in glucose-grown versus lignocellulosic biomass-grown cultures. Further, strain C1A co-transcribes multiple functionally redundant enzymes for cellulose and hemicellulose saccharification that are mechanistically and structurally distinct. Analysis of fungal dockerin domain-containing transcripts strongly suggests that Anaerobic fungal cellulosomes represent distinct catalytic units capable of independently attacking and converting intact plant fibers to sugar monomers. Collectively, these results demonstrate that strain C1A achieves fast, effective biomass degradation by the simultaneous employment of a wide array of constitutively-transcribed cellulosome-bound and free enzymes with considerable functional overlap. We argue that the utilization of this indiscriminate strategy could be justified by the evolutionary history of Anaerobic Fungi, as well as their functional role within their natural habitat in the herbivorous gut.
Adrian Tsang - One of the best experts on this subject based on the ideXlab platform.
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Application of Transcriptomics to Compare the Carbohydrate Active Enzymes That Are Expressed by Diverse Genera of Anaerobic Fungi to Degrade Plant Cell Wall Carbohydrates
Frontiers in Microbiology, 2018Co-Authors: Robert J. Gruninger, Jay Yanke, Thi Truc Minh Nguyen, Denis W Abbott, Adrian Tsang, Ian Reid, Pan Wang, Tim A. McallisterAbstract:The efficiency with which the Anaerobic Fungi (phylum Neocallimastigomycota) degrade plant biomass is well-recognized and in recent years has received renewed interest. To further understand the biological mechanisms that are utilized by the rumen Anaerobic Fungi to break down lignocellulose, we have used a transcriptomic approach to examine carbohydrate digestion by Neocallimastix frontalis, Piromyces rhizinflata, Orpinomyces joyonii, and Anaeromyces mucronatus cultured on several carbon sources. The number of predicted unique transcripts ranged from 6,633 to 12,751. Pfam domains were identified in 62-70% of the fungal proteins and were linked to gene ontology terms to infer the biological function of the transcripts. Most of the predicted functions are consistent across species suggesting a similar overall strategy evolved for successful colonization of the rumen. However, the presence of differential profiles in enzyme classes suggests that there may be also be niche specialization. All fungal species were found to express an extensive array of transcripts encoding carbohydrate active enzymes (CAZymes) ranging from 8.3 to 11.3% of the transcriptome. CAZyme families involved in hemicellulose digestion were the most abundant across all four Fungi. This study provides additional insight into how Anaerobic Fungi have evolved to become specialists at breaking down the plant cell wall in the complex and, strictly Anaerobic rumen ecosystem.
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Data_Sheet_2_Application of Transcriptomics to Compare the Carbohydrate Active Enzymes That Are Expressed by Diverse Genera of Anaerobic Fungi to Degrade Plant Cell Wall Carbohydrates.XLSX
2018Co-Authors: Robert J. Gruninger, Thi Truc Minh Nguyen, Denis W Abbott, Adrian Tsang, Pan Wang, Ian D. Reid, Jay L. Yanke, Tim McallisterAbstract:The efficiency with which the Anaerobic Fungi (phylum Neocallimastigomycota) degrade plant biomass is well-recognized and in recent years has received renewed interest. To further understand the biological mechanisms that are utilized by the rumen Anaerobic Fungi to break down lignocellulose, we have used a transcriptomic approach to examine carbohydrate digestion by Neocallimastix frontalis, Piromyces rhizinflata, Orpinomyces joyonii, and Anaeromyces mucronatus cultured on several carbon sources. The number of predicted unique transcripts ranged from 6,633 to 12,751. Pfam domains were identified in 62–70% of the fungal proteins and were linked to gene ontology terms to infer the biological function of the transcripts. Most of the predicted functions are consistent across species suggesting a similar overall strategy evolved for successful colonization of the rumen. However, the presence of differential profiles in enzyme classes suggests that there may be also be niche specialization. All fungal species were found to express an extensive array of transcripts encoding carbohydrate active enzymes (CAZymes) ranging from 8.3 to 11.3% of the transcriptome. CAZyme families involved in hemicellulose digestion were the most abundant across all four Fungi. This study provides additional insight into how Anaerobic Fungi have evolved to become specialists at breaking down the plant cell wall in the complex and, strictly Anaerobic rumen ecosystem.
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Table_1_Application of Transcriptomics to Compare the Carbohydrate Active Enzymes That Are Expressed by Diverse Genera of Anaerobic Fungi to Degrade Plant Cell Wall Carbohydrates.DOCX
2018Co-Authors: Robert J. Gruninger, Thi Truc Minh Nguyen, Denis W Abbott, Adrian Tsang, Pan Wang, Ian D. Reid, Jay L. Yanke, Tim McallisterAbstract:The efficiency with which the Anaerobic Fungi (phylum Neocallimastigomycota) degrade plant biomass is well-recognized and in recent years has received renewed interest. To further understand the biological mechanisms that are utilized by the rumen Anaerobic Fungi to break down lignocellulose, we have used a transcriptomic approach to examine carbohydrate digestion by Neocallimastix frontalis, Piromyces rhizinflata, Orpinomyces joyonii, and Anaeromyces mucronatus cultured on several carbon sources. The number of predicted unique transcripts ranged from 6,633 to 12,751. Pfam domains were identified in 62–70% of the fungal proteins and were linked to gene ontology terms to infer the biological function of the transcripts. Most of the predicted functions are consistent across species suggesting a similar overall strategy evolved for successful colonization of the rumen. However, the presence of differential profiles in enzyme classes suggests that there may be also be niche specialization. All fungal species were found to express an extensive array of transcripts encoding carbohydrate active enzymes (CAZymes) ranging from 8.3 to 11.3% of the transcriptome. CAZyme families involved in hemicellulose digestion were the most abundant across all four Fungi. This study provides additional insight into how Anaerobic Fungi have evolved to become specialists at breaking down the plant cell wall in the complex and, strictly Anaerobic rumen ecosystem.
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Anaerobic Fungi (phylum Neocallimastigomycota): advances in understanding their taxonomy, life cycle, ecology, role and biotechnological potential
FEMS Microbiology Ecology, 2014Co-Authors: Robert J. Gruninger, Gareth W Griffith, Sumit Singh Dagar, Anil Kumar Puniya, Tony M. Callaghan, Joan E. Edwards, Noha H. Youssef, Katerina Fliegerova, Robert J. Forster, Adrian TsangAbstract:Anaerobic Fungi (phylum Neocallimastigomycota) inhabit the gastrointestinal tract of mammalian herbivores, where they play an important role in the degradation of plant material. The Neocallimastigomycota represent the earliest diverging lineage of the zoosporic Fungi; however, understanding of the relationships of the different taxa (both genera and species) within this phylum is in need of revision. Issues exist with the current approaches used for their identification and classification, and recent evidence suggests the presence of several novel taxa (potential candidate genera) that remain to be characterised. The life cycle and role of Anaerobic Fungi has been well characterised in the rumen, but not elsewhere in the ruminant alimentary tract. Greater understanding of the 'resistant' phase(s) of their life cycle is needed, as is study of their role and significance in other herbivores. Biotechnological application of Anaerobic Fungi, and their highly active cellulolytic and hemi-cellulolytic enzymes, has been a rapidly increasing area of research and development in the last decade. The move towards understanding of Anaerobic Fungi using -omics based (genomic, transcriptomic and proteomic) approaches is starting to yield valuable insights into the unique cellular processes, evolutionary history, metabolic capabilities and adaptations that exist within the Neocallimastigomycota.
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formulation of enzyme blends to maximize the hydrolysis of alkaline peroxide pretreated alfalfa hay and barley straw by rumen enzymes and commercial cellulases
BMC Biotechnology, 2014Co-Authors: Ajay Badhan, Robert J. Gruninger, Yuxi Wang, Donald Patton, Justin Powlowski, Adrian TsangAbstract:Background Efficient conversion of lignocellulosic biomass to fermentable sugars requires the synergistic action of multiple enzymes; consequently enzyme mixtures must be properly formulated for effective hydrolysis. The nature of an optimal enzyme blends depends on the type of pretreatment employed as well the characteristics of the substrate. In this study, statistical experimental design was used to develop mixtures of recombinant glycosyl hydrolases from thermophilic and Anaerobic Fungi that enhanced the digestion of alkaline peroxide treated alfalfa hay and barley straw by mixed rumen enzymes as well as commercial cellulases (Accelerase 1500, A1500; Accelerase XC, AXC).