Metagenome-Assembled Genomes from a Microbiome Grown in Dairy Manure Hydrolysate

Abel T Ingle^{1

2

3}, Nathaniel W Fortney^{1

2}, Kevin S Myers^{1

2}, Kevin A Walters^{1

2

4}, Matthew J Scarborough⁵, Timothy J Donohue^{1

2

4}, Daniel R Noguera^{1

2

3}

Affiliations

¹ Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA.
² Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA.
³ Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA.
⁴ Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA.
⁵ Department of Civil and Environmental Engineering, University of Vermont, Burlington, Vermont, USA.

PMID: 35894622
PMCID: PMC9387265
DOI: 10.1128/mra.00292-22

Metagenome-Assembled Genomes from a Microbiome Grown in Dairy Manure Hydrolysate

Abel T Ingle et al. Microbiol Resour Announc. 2022.

. 2022 Aug 18;11(8):e0029222.

doi: 10.1128/mra.00292-22. Epub 2022 Jul 27.

Authors

Abel T Ingle^{1

2

3}, Nathaniel W Fortney^{1

2}, Kevin S Myers^{1

2}, Kevin A Walters^{1

2

4}, Matthew J Scarborough⁵, Timothy J Donohue^{1

2

4}, Daniel R Noguera^{1

2

3}

Affiliations

¹ Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA.
² Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA.
³ Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA.
⁴ Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA.
⁵ Department of Civil and Environmental Engineering, University of Vermont, Burlington, Vermont, USA.

PMID: 35894622
PMCID: PMC9387265
DOI: 10.1128/mra.00292-22

Abstract

Anaerobic microbiomes can be used to recover the chemical energy in agroindustrial and municipal wastes as useful products. Here, we report a total of 109 draft metagenome-assembled genomes from a bioreactor-fed carbohydrate-rich dairy manure hydrolysate. Studying these genomes will aid us in deciphering the metabolic networks in anaerobic microbiomes.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

**FIG 1**
Phylogeny of dRep-identified representative MAGs. Strain code abbreviations are as follows: ACET, *Acetobacter*; ATO, *Atopobiaceae*; ACT, *Actinomycetaceae*; ACUT, *Acutalibacteraceae*; ANA, *Anaerotignaceae*; BAC, *Bacillus*; BACIL, *Bacilli*; BACTE, *Bacteroidales*; BIF, *Bifidobacteriaceae*; BURK, *Burkholderiaceae*; CLOS, *Clostridium*; DIAL, *Dialister*; ENTER, *Enterococcaceae*; FLAV, *Flavobacteriales*; LAC, *Lactobacillus*; LACCAS, *Lacticaseibacillus*; LCO, *Lachnospiraceae*; LENLAC, *Lentilactobacillus*; LEUC, *Leuconostoc*; LIMLAC, *Limosilactobacillus*; LIGLAC, *Ligilactobacillus*; LIQLAC, *Liquorilactobacillus*; MEG, *Megasphaera*; PREV, *Prevotella*; PSEUD, Pseudomonas; SACCH, *Saccharofermentans*; SCHLAC, *Schleiferilactobacillus*; SPHING, *Sphingobium*; SPOR, *Sporolactobacillus*; XAN, *Xanthomonadaceae*. The higher taxonomic levels are labeled P, phylum; C, class; and F, family. Phylum abbreviations: *Bacter*., *Bacteroidota*; *Fir*., *Firmicutes_C*. Class abbreviations: *Gamma*., *Gammaproteobacteria*; *Alpha*., *Alphaproteobacteria*; *Bact*., *Bacteroidia*; *Actin*., *Actinobacteria*; *Cor*., *Coriobacteriia*; *Neg*., *Negativicutes*. Family abbreviations: Xa., *Xanthomonadaceae*; Ac., *Acetobacter*; *Bifidobac.*, *Bifidobacteriaceae*; At., *Atopobiaceae*; An., *Anaerotignaceae*; *Clo*., *Clostridiaceae*; *Acutali*., *Acutalibacteraceae*. The shaded strain code abbreviations indicate representative genomes from the inoculum. The phylogenetic tree was generated in RAxML-NG with 500 bootstraps using the concatenation of 120 bacterial single-copy housekeeping genes generated using GTDB-Tk. Bootstrap values greater than 50 are shown. The scale bar indicates the number of nucleotide substitutions per sequence site.

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References

1. Scarborough MJ, Myers KS, Donohue TJ, Noguera DR. 2020. Medium-chain fatty acid synthesis by “Candidatus Weimeria bifida” gen. nov., sp. nov., and “Candidatus Pseudoramibacter fermentans” sp. nov. Appl Environ Microbiol 86:2796. doi:10.1128/AEM.02242-19. - DOI - PMC - PubMed
1. Fortney NW, Hanson NJ, Rosa PRF, Donohue TJ, Noguera DR. 2021. Diverse profile of fermentation byproducts from thin stillage. Front Bioeng Biotechnol 9:695306. doi:10.3389/fbioe.2021.695306. - DOI - PMC - PubMed
1. Ingle AT, Fortney NW, Walters KA, Donohue TJ, Noguera DR. 2021. Mixed acid fermentation of carbohydrate-rich dairy manure hydrolysate. Front Bioeng Biotechnol 9:724304. doi:10.3389/fbioe.2021.724304. - DOI - PMC - PubMed
1. Scarborough MJ, Lawson CE, Hamilton JJ, Donohue TJ, Noguera DR. 2018. Metatranscriptomic and thermodynamic insights into medium-chain fatty acid production using an anaerobic microbiome. mSystems 3:e00221-18. doi:10.1128/mSystems.00221-18. - DOI - PMC - PubMed
1. Scarborough MJ, Lynch G, Dickson M, McGee M, Donohue TJ, Noguera DR. 2018. Increasing the economic value of lignocellulosic stillage through medium-chain fatty acid production. Biotechnol Biofuels 11:200. doi:10.1186/s13068-018-1193-x. - DOI - PMC - PubMed

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Metagenome-Assembled Genomes from a Microbiome Grown in Dairy Manure Hydrolysate

Affiliations

Metagenome-Assembled Genomes from a Microbiome Grown in Dairy Manure Hydrolysate

Authors

Affiliations

Abstract

Conflict of interest statement

Figures

References

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