Microbiomes and methods for producing medium-chain fatty acids from organic substrates

Donohue, Timothy James; Scarborough, Matthew; Noguera, Daniel

Title: Microbiomes and methods for producing medium-chain fatty acids from organic substrates

Abstract

Microbiome compositions and uses thereof. The microbiome compositions include a set of microbes. The sets of microbes contain members of Lactobacillaceae, Eubacteriaceae, Lachnospiraceae, and Coriobacteriaceae. The number of individual physical microbes in the set constitutes a certain percentage of the total number of individual physical microbes in the microbiome composition. The microbiome compositions can be used for producing medium-chain fatty acids from organic substrates through anaerobic fermentation in a medium. The medium can include lignocellulosic stillage.

Inventors:: Donohue, Timothy James; Scarborough, Matthew; Noguera, Daniel

Issue Date:: 2022-02-08

Research Org.:: Univ. of Wisconsin, Madison, WI (United States)

Sponsoring Org.:: USDOE

OSTI Identifier:: 1892593

Patent Number(s):: 11242544

Application Number:: 16/433,639

Assignee:: Wisconsin Alumni Research Foundation (Madison, WI)

Patent Classifications (CPCs):: C - CHEMISTRY C12 - BIOCHEMISTRY C12N - MICROORGANISMS OR ENZYMES

C - CHEMISTRY C12 - BIOCHEMISTRY C12P - FERMENTATION OR ENZYME-USING PROCESSES TO SYNTHESISE A DESIRED CHEMICAL COMPOUND OR COMPOSITION OR TO SEPARATE OPTICAL ISOMERS FROM A RACEMIC MIXTURE {

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C - CHEMISTRY C12 - BIOCHEMISTRY C12N - MICROORGANISMS OR ENZYMES
C12N1/20 - Bacteria {

C - CHEMISTRY C12 - BIOCHEMISTRY C12P - FERMENTATION OR ENZYME-USING PROCESSES TO SYNTHESISE A DESIRED CHEMICAL COMPOUND OR COMPOSITION OR TO SEPARATE OPTICAL ISOMERS FROM A RACEMIC MIXTURE {
C12P2203/00 - Fermentation products obtained from optionally pretreated or hydrolyzed cellulosic or lignocellulosic material as the carbon source
C12P7/6409 - {Fatty acids}
C12P7/6463 - {obtained from glyceride producing microorganisms, e.g. single cell oil}

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DOE Contract Number:: FC02-07ER64494; SC0018409

Resource Type:: Patent

Resource Relation:: Patent File Date: 06/06/2019

Country of Publication:: United States

Language:: English

Citation Formats


                    Donohue, Timothy James, Scarborough, Matthew, and Noguera, Daniel. Microbiomes and methods for producing medium-chain fatty acids from organic substrates.  United States: N. p., 2022. 
        Web.

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                    Donohue, Timothy James, Scarborough, Matthew, & Noguera, Daniel. Microbiomes and methods for producing medium-chain fatty acids from organic substrates.  United States.

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                    Donohue, Timothy James, Scarborough, Matthew, and Noguera, Daniel. Tue .  
        "Microbiomes and methods for producing medium-chain fatty acids from organic substrates".  United States.  https://www.osti.gov/servlets/purl/1892593.

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@article{osti_1892593,

  title        = {Microbiomes and methods for producing medium-chain fatty acids from organic substrates},

  author       = {Donohue, Timothy James and Scarborough, Matthew and Noguera, Daniel},

  abstractNote = {Microbiome compositions and uses thereof. The microbiome compositions include a set of microbes. The sets of microbes contain members of Lactobacillaceae, Eubacteriaceae, Lachnospiraceae, and Coriobacteriaceae. The number of individual physical microbes in the set constitutes a certain percentage of the total number of individual physical microbes in the microbiome composition. The microbiome compositions can be used for producing medium-chain fatty acids from organic substrates through anaerobic fermentation in a medium. The medium can include lignocellulosic stillage.},

  doi          = {},

  journal      = {},
number       = ,

  volume       = ,

  place        = {United States},

  year         = {2022},

  month        = {2}

}

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Large-scale production, harvest and logistics of switchgrass ( Panicum virgatum L. ) - current technology and envisioning a mature technology
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Title: Microbiomes and methods for producing medium-chain fatty acids from organic substrates

Abstract

Citation Formats

Chain elongation in anaerobic reactor microbiomes to recover resources from waste journal, June 2014

Integrated acidogenic digestion and carboxylic acid separation by nanofiltration membranes for the lignocellulosic carboxylate platform journal, September 2015

Microbial synthesis of medium-chain chemicals from renewables journal, December 2017

Xylose utilization in ethanol production: a patent landscape: Xylose Utilization in Ethanol Production: A Patent Landscape journal, July 2016

Metabolic and microbial community dynamics during the anaerobic digestion of maize silage in a two-phase process journal, September 2015

Proposal of Roseburia faecis sp. nov., Roseburia hominis sp. nov. and Roseburia inulinivorans sp. nov., based on isolates from human faeces journal, October 2006

Lactobacillus odoratitofui sp. nov., isolated from stinky tofu brine journal, January 2010

Metabolic network analysis reveals microbial community interactions in anammox granules journal, May 2017

Characterization of a novel Atopobium isolate from the human vagina: description of Atopobium vaginae sp. nov. journal, October 1999

Production of drop-in fuels from biomass at high selectivity by combined microbial and electrochemical conversion journal, January 2017

Production of high-concentration n-caproic acid from lactate through fermentation using a newly isolated Ruminococcaceae bacterium CPB6 journal, April 2017

Coupled Ferredoxin and Crotonyl Coenzyme A (CoA) Reduction with NADH Catalyzed by the Butyryl-CoA Dehydrogenase/Etf Complex from Clostridium kluyveri journal, November 2007

MUSCLE: multiple sequence alignment with high accuracy and high throughput journal, March 2004

Olsenella umbonata sp. nov., a microaerotolerant anaerobic lactic acid bacterium from the sheep rumen and pig jejunum, and emended descriptions of Olsenella, Olsenella uli and Olsenella profusa journal, April 2010

Metabolism of Multiple Aromatic Compounds in Corn Stover Hydrolysate by Rhodopseudomonas palustris journal, July 2015

Switchgrass (Panicum vigratum, L.) delivery to a biorefinery using integrated biomass supply analysis and logistics (IBSAL) model journal, March 2007

Lactobacillus durianis Leisner et al. 2002 is a later heterotypic synonym of Lactobacillus vaccinostercus Kozaki and Okada 1983 journal, August 2006

PyNAST: a flexible tool for aligning sequences to a template alignment journal, November 2009

Increasing the economic value of lignocellulosic stillage through medium-chain fatty acid production journal, July 2018

Clustal W and Clustal X version 2.0 journal, September 2007

Superheat: An R Package for Creating Beautiful and Extendable Heatmaps for Visualizing Complex Data journal, July 2018

Microbiome-based carboxylic acids production: from serum bottles to bioreactors journal, January 2017

Amended description of Ramibacterium alactolyticum Prevot and Taffanel with proposal of a neotype strain journal, October 1967

Two-stage medium chain fatty acid (MCFA) production from municipal solid waste and ethanol journal, March 2014

Carboxylic acid production from brewer’s spent grain via mixed culture fermentation journal, April 2015

Electrolytic extraction drives volatile fatty acid chain elongation through lactic acid and replaces chemical pH control in thin stillage fermentation journal, December 2015

Process Design and Economics for Biochemical Conversion of Lignocellulosic Biomass to Ethanol: Dilute-Acid Pretreatment and Enzymatic Hydrolysis of Corn Stover report, March 2011

The synthesis of n-caproate from lactate: a new efficient process for medium-chain carboxylates production journal, September 2015

Lactobacillus diolivorans sp. nov., a 1,2-propanediol-degrading bacterium isolated from aerobically stable maize silage. journal, March 2002

JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison journal, November 2015

QIIME allows analysis of high-throughput community sequencing data journal, April 2010

Synergistic Bacterial Compositions and Methods of Production and Use Thereof patent-application, July 2014

SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data journal, October 2012

Microbiota Restoration Therapy (MRT), Compositions and Methods of Manufacture patent-application, February 2015

Substrate specificity of pullulanase journal, April 1970

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools journal, November 2012

Engineering and Two-Stage Evolution of a Lignocellulosic Hydrolysate-Tolerant Saccharomyces cerevisiae Strain for Anaerobic Fermentation of Xylose from AFEX Pretreated Corn Stover journal, September 2014

Measurement of protein using bicinchoninic acid journal, October 1985

HTSeq--a Python framework to work with high-throughput sequencing data journal, September 2014

Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons journal, January 2011

Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies journal, August 2012

Cells and methods for producing fatty alcohols patent, July 2017

Lactobacillus mucosae sp. nov., a new species with in vitro mucus-binding activity isolated from pig intestine journal, January 2000

PhyloSift: phylogenetic analysis of genomes and metagenomes journal, January 2014

Comparative sequence analyses of the 16S rRNA genes of Lactobacillus minutus, Lactobacillus rimae and Streptococcus parvulus : Proposal for the creation of a new genus Atopobium journal, August 1992

Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes journal, May 2014

Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology journal, November 2012

Promoting chain elongation in mixed culture acidification reactors by addition of ethanol journal, January 2013

Anaerobic digestion for treatment of stillage from cellulosic bioethanol production journal, September 2013

Electron transfer in syntrophic communities of anaerobic bacteria and archaea journal, August 2009

Production of medium-chain carboxylic acids by Megasphaera sp. MH with supplemental electron acceptors journal, June 2016

Life cycle assessment of lignocellulosic ethanol: a review of key factors and methods affecting calculated GHG emissions and energy use journal, April 2016

Energy conservation via electron bifurcating ferredoxin reduction and proton/Na+ translocating ferredoxin oxidation journal, February 2013

Recovery of multiple compounds and recyclable water from thin stillage patent, September 2014

Anvi’o: an advanced analysis and visualization platform for ‘omics data journal, January 2015

Lignocellulosic Biomass Pretreatment Using AFEX book, January 2009

Olsenella scatoligenes sp. nov., a 3-methylindole- (skatole) and 4-methylphenol- (p-cresol) producing bacterium isolated from pig faeces journal, April 2015

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes journal, May 2015

FLASH: fast length adjustment of short reads to improve genome assemblies journal, September 2011

Modeling product formation in anaerobic mixed culture fermentations journal, January 2006

Bioavailability of Carbohydrate Content in Natural and Transgenic Switchgrasses for the Extreme Thermophile Caldicellulosiruptor bescii journal, June 2017

Inhibition of microbial biofuel production in drought-stressed switchgrass hydrolysate journal, November 2016

Mixed Carboxylic Acid Production by Megasphaera elsdenii from Glucose and Lignocellulosic Hydrolysate journal, March 2017

Glycerol production by microbial fermentation journal, June 2001

Waste to bioproduct conversion with undefined mixed cultures: the carboxylate platform journal, February 2011

Impact of dissolved hydrogen partial pressure on mixed culture fermentations journal, September 2012

Chain Elongation with Reactor Microbiomes: Open-Culture Biotechnology To Produce Biochemicals journal, February 2016

The estimation of carbohydrates in plant extracts by anthrone journal, July 1954

Carboxylate Platform: The MixAlco Process Part 1: Comparison of Three Biomass Conversion Platforms journal, January 2009

T-coffee: a novel method for fast and accurate multiple sequence alignment 1 1Edited by J. Thornton journal, September 2000

Exo-Arabinanase of Penicillium chrysogenum Able To Release Arabinobiose from -1,5-L-Arabinan journal, July 2001

Roseburia intestinalis sp. nov., a novel saccharolytic, butyrate-producing bacterium from human faeces. journal, September 2002

Characterization of novel human oral isolates and cloned 16S rDNA sequences that fall in the family Coriobacteriaceae: description of Olsenella gen. nov., reclassification of Lactobacillus uli as Olsenella uli comb. nov. and description of Olsenella profusa sp. nov journal, September 2001

The semiquinone swing in the bifurcating electron transferring flavoprotein/butyryl-CoA dehydrogenase complex from Clostridium difficile journal, November 2017

metaSPAdes: a new versatile metagenomic assembler journal, March 2017

Roseburia cecicola gen. nov., sp. nov., a Motile, Obligately Anaerobic Bacterium from a Mouse Cecum journal, July 1983

Freeze Dried Fecal Microbiota for Use in Fecal Microbial Transplantation patent-application, December 2015

Chain elongation in anaerobic reactor microbiomes to recover resources from waste
journal, June 2014

Integrated acidogenic digestion and carboxylic acid separation by nanofiltration membranes for the lignocellulosic carboxylate platform
journal, September 2015

Microbial synthesis of medium-chain chemicals from renewables
journal, December 2017

Xylose utilization in ethanol production: a patent landscape: Xylose Utilization in Ethanol Production: A Patent Landscape
journal, July 2016

Metabolic and microbial community dynamics during the anaerobic digestion of maize silage in a two-phase process
journal, September 2015

Proposal of Roseburia faecis sp. nov., Roseburia hominis sp. nov. and Roseburia inulinivorans sp. nov., based on isolates from human faeces
journal, October 2006

Lactobacillus odoratitofui sp. nov., isolated from stinky tofu brine
journal, January 2010

Metabolic network analysis reveals microbial community interactions in anammox granules
journal, May 2017

Characterization of a novel Atopobium isolate from the human vagina: description of Atopobium vaginae sp. nov.
journal, October 1999

Production of drop-in fuels from biomass at high selectivity by combined microbial and electrochemical conversion
journal, January 2017

Production of high-concentration n-caproic acid from lactate through fermentation using a newly isolated Ruminococcaceae bacterium CPB6
journal, April 2017

Coupled Ferredoxin and Crotonyl Coenzyme A (CoA) Reduction with NADH Catalyzed by the Butyryl-CoA Dehydrogenase/Etf Complex from Clostridium kluyveri
journal, November 2007

MUSCLE: multiple sequence alignment with high accuracy and high throughput
journal, March 2004

Olsenella umbonata sp. nov., a microaerotolerant anaerobic lactic acid bacterium from the sheep rumen and pig jejunum, and emended descriptions of Olsenella, Olsenella uli and Olsenella profusa
journal, April 2010

Metabolism of Multiple Aromatic Compounds in Corn Stover Hydrolysate by Rhodopseudomonas palustris
journal, July 2015

Switchgrass (Panicum vigratum, L.) delivery to a biorefinery using integrated biomass supply analysis and logistics (IBSAL) model
journal, March 2007

Lactobacillus durianis Leisner et al. 2002 is a later heterotypic synonym of Lactobacillus vaccinostercus Kozaki and Okada 1983
journal, August 2006

PyNAST: a flexible tool for aligning sequences to a template alignment
journal, November 2009

Increasing the economic value of lignocellulosic stillage through medium-chain fatty acid production
journal, July 2018

Clustal W and Clustal X version 2.0
journal, September 2007

Superheat: An R Package for Creating Beautiful and Extendable Heatmaps for Visualizing Complex Data
journal, July 2018

Microbiome-based carboxylic acids production: from serum bottles to bioreactors
journal, January 2017

Amended description of Ramibacterium alactolyticum Prevot and Taffanel with proposal of a neotype strain
journal, October 1967

Two-stage medium chain fatty acid (MCFA) production from municipal solid waste and ethanol
journal, March 2014

Carboxylic acid production from brewer’s spent grain via mixed culture fermentation
journal, April 2015

Electrolytic extraction drives volatile fatty acid chain elongation through lactic acid and replaces chemical pH control in thin stillage fermentation
journal, December 2015

Process Design and Economics for Biochemical Conversion of Lignocellulosic Biomass to Ethanol: Dilute-Acid Pretreatment and Enzymatic Hydrolysis of Corn Stover
report, March 2011

The synthesis of n-caproate from lactate: a new efficient process for medium-chain carboxylates production
journal, September 2015

Lactobacillus diolivorans sp. nov., a 1,2-propanediol-degrading bacterium isolated from aerobically stable maize silage.
journal, March 2002

JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison
journal, November 2015

QIIME allows analysis of high-throughput community sequencing data
journal, April 2010

Synergistic Bacterial Compositions and Methods of Production and Use Thereof
patent-application, July 2014

SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data
journal, October 2012

Microbiota Restoration Therapy (MRT), Compositions and Methods of Manufacture
patent-application, February 2015

Substrate specificity of pullulanase
journal, April 1970

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools
journal, November 2012

Engineering and Two-Stage Evolution of a Lignocellulosic Hydrolysate-Tolerant Saccharomyces cerevisiae Strain for Anaerobic Fermentation of Xylose from AFEX Pretreated Corn Stover
journal, September 2014

Measurement of protein using bicinchoninic acid
journal, October 1985

HTSeq--a Python framework to work with high-throughput sequencing data
journal, September 2014

Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons
journal, January 2011

Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies
journal, August 2012

Cells and methods for producing fatty alcohols
patent, July 2017

Lactobacillus mucosae sp. nov., a new species with in vitro mucus-binding activity isolated from pig intestine
journal, January 2000

PhyloSift: phylogenetic analysis of genomes and metagenomes
journal, January 2014

Comparative sequence analyses of the 16S rRNA genes of Lactobacillus minutus, Lactobacillus rimae and Streptococcus parvulus : Proposal for the creation of a new genus Atopobium
journal, August 1992

Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes
journal, May 2014

Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology
journal, November 2012

Promoting chain elongation in mixed culture acidification reactors by addition of ethanol
journal, January 2013

Anaerobic digestion for treatment of stillage from cellulosic bioethanol production
journal, September 2013

Electron transfer in syntrophic communities of anaerobic bacteria and archaea
journal, August 2009

Production of medium-chain carboxylic acids by Megasphaera sp. MH with supplemental electron acceptors
journal, June 2016

Life cycle assessment of lignocellulosic ethanol: a review of key factors and methods affecting calculated GHG emissions and energy use
journal, April 2016

Energy conservation via electron bifurcating ferredoxin reduction and proton/Na+ translocating ferredoxin oxidation
journal, February 2013

Recovery of multiple compounds and recyclable water from thin stillage
patent, September 2014

Anvi’o: an advanced analysis and visualization platform for ‘omics data
journal, January 2015

Lignocellulosic Biomass Pretreatment Using AFEX
book, January 2009

Olsenella scatoligenes sp. nov., a 3-methylindole- (skatole) and 4-methylphenol- (p-cresol) producing bacterium isolated from pig faeces
journal, April 2015

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes
journal, May 2015

FLASH: fast length adjustment of short reads to improve genome assemblies
journal, September 2011

Modeling product formation in anaerobic mixed culture fermentations
journal, January 2006

Bioavailability of Carbohydrate Content in Natural and Transgenic Switchgrasses for the Extreme Thermophile Caldicellulosiruptor bescii
journal, June 2017

Inhibition of microbial biofuel production in drought-stressed switchgrass hydrolysate
journal, November 2016

Mixed Carboxylic Acid Production by Megasphaera elsdenii from Glucose and Lignocellulosic Hydrolysate
journal, March 2017

Glycerol production by microbial fermentation
journal, June 2001

Waste to bioproduct conversion with undefined mixed cultures: the carboxylate platform
journal, February 2011

Impact of dissolved hydrogen partial pressure on mixed culture fermentations
journal, September 2012

Chain Elongation with Reactor Microbiomes: Open-Culture Biotechnology To Produce Biochemicals
journal, February 2016

The estimation of carbohydrates in plant extracts by anthrone
journal, July 1954

Carboxylate Platform: The MixAlco Process Part 1: Comparison of Three Biomass Conversion Platforms
journal, January 2009

T-coffee: a novel method for fast and accurate multiple sequence alignment 1 1Edited by J. Thornton
journal, September 2000

Exo-Arabinanase of Penicillium chrysogenum Able To Release Arabinobiose from -1,5-L-Arabinan
journal, July 2001

Roseburia intestinalis sp. nov., a novel saccharolytic, butyrate-producing bacterium from human faeces.
journal, September 2002

Characterization of novel human oral isolates and cloned 16S rDNA sequences that fall in the family Coriobacteriaceae: description of Olsenella gen. nov., reclassification of Lactobacillus uli as Olsenella uli comb. nov. and description of Olsenella profusa sp. nov
journal, September 2001

The semiquinone swing in the bifurcating electron transferring flavoprotein/butyryl-CoA dehydrogenase complex from Clostridium difficile
journal, November 2017

metaSPAdes: a new versatile metagenomic assembler
journal, March 2017

Roseburia cecicola gen. nov., sp. nov., a Motile, Obligately Anaerobic Bacterium from a Mouse Cecum
journal, July 1983

Freeze Dried Fecal Microbiota for Use in Fecal Microbial Transplantation
patent-application, December 2015

A Clostridium Group IV Species Dominates and Suppresses a Mixed Culture Fermentation by Tolerance to Medium Chain Fatty Acids Products
journal, February 2017

Long-Term n -Caproic Acid Production from Yeast-Fermentation Beer in an Anaerobic Bioreactor with Continuous Product Extraction
journal, June 2015

Comparative assessment of single-stage and two-stage anaerobic digestion for the treatment of thin stillage
journal, May 2012