Comparison of metagenomes from fermentation of various agroindustrial residues suggests a common model of community organization
The liquid residue resulting from various agroindustrial processes is both rich in organic material and an attractive source to produce a variety of chemicals. Using microbial communities to produce chemicals from these liquid residues is an active area of research, but it is unclear how to deploy m...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2023-05-01
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| Series: | Frontiers in Bioengineering and Biotechnology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fbioe.2023.1197175/full |
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| author | Kevin S. Myers Kevin S. Myers Abel T. Ingle Abel T. Ingle Abel T. Ingle Kevin A. Walters Kevin A. Walters Kevin A. Walters Nathaniel W. Fortney Nathaniel W. Fortney Matthew J. Scarborough Timothy J. Donohue Timothy J. Donohue Timothy J. Donohue Daniel R. Noguera Daniel R. Noguera Daniel R. Noguera |
| author_facet | Kevin S. Myers Kevin S. Myers Abel T. Ingle Abel T. Ingle Abel T. Ingle Kevin A. Walters Kevin A. Walters Kevin A. Walters Nathaniel W. Fortney Nathaniel W. Fortney Matthew J. Scarborough Timothy J. Donohue Timothy J. Donohue Timothy J. Donohue Daniel R. Noguera Daniel R. Noguera Daniel R. Noguera |
| author_sort | Kevin S. Myers |
| collection | DOAJ |
| description | The liquid residue resulting from various agroindustrial processes is both rich in organic material and an attractive source to produce a variety of chemicals. Using microbial communities to produce chemicals from these liquid residues is an active area of research, but it is unclear how to deploy microbial communities to produce specific products from the different agroindustrial residues. To address this, we fed anaerobic bioreactors one of several agroindustrial residues (carbohydrate-rich lignocellulosic fermentation conversion residue, xylose, dairy manure hydrolysate, ultra-filtered milk permeate, and thin stillage from a starch bioethanol plant) and inoculated them with a microbial community from an acid-phase digester operated at the wastewater treatment plant in Madison, WI, United States. The bioreactors were monitored over a period of months and sampled to assess microbial community composition and extracellular fermentation products. We obtained metagenome assembled genomes (MAGs) from the microbial communities in each bioreactor and performed comparative genomic analyses to identify common microorganisms, as well as any community members that were unique to each reactor. Collectively, we obtained a dataset of 217 non-redundant MAGs from these bioreactors. This metagenome assembled genome dataset was used to evaluate whether a specific microbial ecology model in which medium chain fatty acids (MCFAs) are simultaneously produced from intermediate products (e.g., lactic acid) and carbohydrates could be applicable to all fermentation systems, regardless of the feedstock. MAGs were classified using a multiclass classification machine learning algorithm into three groups, organisms fermenting the carbohydrates to intermediate products, organisms utilizing the intermediate products to produce MCFAs, and organisms producing MCFAs directly from carbohydrates. This analysis revealed common biological functions among the microbial communities in different bioreactors, and although different microorganisms were enriched depending on the agroindustrial residue tested, the results supported the conclusion that the microbial ecology model tested was appropriate to explain the MCFA production potential from all agricultural residues. |
| first_indexed | 2024-03-13T11:03:02Z |
| format | Article |
| id | doaj.art-069ed0725e5b4681a0796ed0a9306bc6 |
| institution | Directory Open Access Journal |
| issn | 2296-4185 |
| language | English |
| last_indexed | 2024-03-13T11:03:02Z |
| publishDate | 2023-05-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Bioengineering and Biotechnology |
| spelling | doaj.art-069ed0725e5b4681a0796ed0a9306bc62023-05-16T14:52:13ZengFrontiers Media S.A.Frontiers in Bioengineering and Biotechnology2296-41852023-05-011110.3389/fbioe.2023.11971751197175Comparison of metagenomes from fermentation of various agroindustrial residues suggests a common model of community organizationKevin S. Myers0Kevin S. Myers1Abel T. Ingle2Abel T. Ingle3Abel T. Ingle4Kevin A. Walters5Kevin A. Walters6Kevin A. Walters7Nathaniel W. Fortney8Nathaniel W. Fortney9Matthew J. Scarborough10Timothy J. Donohue11Timothy J. Donohue12Timothy J. Donohue13Daniel R. Noguera14Daniel R. Noguera15Daniel R. Noguera16Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, United StatesWisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI, United StatesGreat Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, United StatesWisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI, United StatesDepartment of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, WI, United StatesGreat Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, United StatesWisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI, United StatesDepartment of Bacteriology, University of Wisconsin-Madison, Madison, WI, United StatesGreat Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, United StatesWisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI, United StatesDepartment of Civil and Environmental Engineering, University of Vermont, Burlington, VT, United StatesGreat Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, United StatesWisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI, United StatesDepartment of Bacteriology, University of Wisconsin-Madison, Madison, WI, United StatesGreat Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, United StatesWisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI, United StatesDepartment of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, WI, United StatesThe liquid residue resulting from various agroindustrial processes is both rich in organic material and an attractive source to produce a variety of chemicals. Using microbial communities to produce chemicals from these liquid residues is an active area of research, but it is unclear how to deploy microbial communities to produce specific products from the different agroindustrial residues. To address this, we fed anaerobic bioreactors one of several agroindustrial residues (carbohydrate-rich lignocellulosic fermentation conversion residue, xylose, dairy manure hydrolysate, ultra-filtered milk permeate, and thin stillage from a starch bioethanol plant) and inoculated them with a microbial community from an acid-phase digester operated at the wastewater treatment plant in Madison, WI, United States. The bioreactors were monitored over a period of months and sampled to assess microbial community composition and extracellular fermentation products. We obtained metagenome assembled genomes (MAGs) from the microbial communities in each bioreactor and performed comparative genomic analyses to identify common microorganisms, as well as any community members that were unique to each reactor. Collectively, we obtained a dataset of 217 non-redundant MAGs from these bioreactors. This metagenome assembled genome dataset was used to evaluate whether a specific microbial ecology model in which medium chain fatty acids (MCFAs) are simultaneously produced from intermediate products (e.g., lactic acid) and carbohydrates could be applicable to all fermentation systems, regardless of the feedstock. MAGs were classified using a multiclass classification machine learning algorithm into three groups, organisms fermenting the carbohydrates to intermediate products, organisms utilizing the intermediate products to produce MCFAs, and organisms producing MCFAs directly from carbohydrates. This analysis revealed common biological functions among the microbial communities in different bioreactors, and although different microorganisms were enriched depending on the agroindustrial residue tested, the results supported the conclusion that the microbial ecology model tested was appropriate to explain the MCFA production potential from all agricultural residues.https://www.frontiersin.org/articles/10.3389/fbioe.2023.1197175/fullmicrobiomefermentationchain elongationagroindustrial residuemetagenomics |
| spellingShingle | Kevin S. Myers Kevin S. Myers Abel T. Ingle Abel T. Ingle Abel T. Ingle Kevin A. Walters Kevin A. Walters Kevin A. Walters Nathaniel W. Fortney Nathaniel W. Fortney Matthew J. Scarborough Timothy J. Donohue Timothy J. Donohue Timothy J. Donohue Daniel R. Noguera Daniel R. Noguera Daniel R. Noguera Comparison of metagenomes from fermentation of various agroindustrial residues suggests a common model of community organization Frontiers in Bioengineering and Biotechnology microbiome fermentation chain elongation agroindustrial residue metagenomics |
| title | Comparison of metagenomes from fermentation of various agroindustrial residues suggests a common model of community organization |
| title_full | Comparison of metagenomes from fermentation of various agroindustrial residues suggests a common model of community organization |
| title_fullStr | Comparison of metagenomes from fermentation of various agroindustrial residues suggests a common model of community organization |
| title_full_unstemmed | Comparison of metagenomes from fermentation of various agroindustrial residues suggests a common model of community organization |
| title_short | Comparison of metagenomes from fermentation of various agroindustrial residues suggests a common model of community organization |
| title_sort | comparison of metagenomes from fermentation of various agroindustrial residues suggests a common model of community organization |
| topic | microbiome fermentation chain elongation agroindustrial residue metagenomics |
| url | https://www.frontiersin.org/articles/10.3389/fbioe.2023.1197175/full |
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