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

Ingle, Abel T.; Fortney, Nathaniel W.; Myers, Kevin S.; Walters, Kevin A.; Scarborough, Matthew; Donohue, Timothy J.; Noguera, Daniel R.

doi:10.1128/mra.00292-22

Cited by 4 publications

(6 citation statements)

References 19 publications

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“…For microbial community analyses we used a dataset of 217 non-redundant MAGs ( Supplementary Table S1 ), which represent the collective set of metagenomes we have assembled from several fermentation bioreactors seeded with the same inoculum but fed different carbohydrate-rich feedstocks ( Myers et al, 2023 ). In the assembly of this non-redundant dataset we used the 173 MAGs obtained from the UFMP-fed bioreactor described in this study, 105 MAGs from a UFMP-fed upflow sludge blanket bioreactor ( Walters et al, 2022 ), 10 MAGs from a cellulosic ethanol thin stillage bioreactor ( Scarborough et al, 2018a ), 8 MAGs from a xylose-rich synthetic cellulosic medium reactors ( Scarborough et al, 2022b ), 51 MAGs from bioreactors using starch-ethanol thin stillage as the feedstock ( Fortney et al, 2022 ), and 48 MAGs from bioreactors fed dairy manure hydrolysate ( Ingle et al, 2022 ). These MAGs were consolidated by dereplication (dRep, v3.2.2; “dereplicate” command with “–conW 0.5” and” –N50W 5″ custom parameters) ( Olm et al, 2017 ), obtaining the final library of 217 non-redundant MAGs used for further analysis.…”

Section: Methodsmentioning

confidence: 99%

A metagenome-level analysis of a microbial community fermenting ultra-filtered milk permeate

Walters

Mohan

Myers

et al. 2023

Front. Bioeng. Biotechnol.

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Fermentative microbial communities have the potential to serve as biocatalysts for the conversion of low-value dairy coproducts into renewable chemicals, contributing to a more sustainable global economy. To develop predictive tools for the design and operation of industrially relevant strategies that utilize fermentative microbial communities, there is a need to determine the genomic features of community members that are characteristic to the accumulation of different products. To address this knowledge gap, we performed a 282-day bioreactor experiment with a microbial community that was fed ultra-filtered milk permeate, a low-value coproduct from the dairy industry. The bioreactor was inoculated with a microbial community from an acid-phase digester. A metagenomic analysis was used to assess microbial community dynamics, construct metagenome-assembled genomes (MAGs), and evaluate the potential for lactose utilization and fermentation product synthesis of community members represented by the assembled MAGs. This analysis led us to propose that, in this reactor, members of the Actinobacteriota phylum are important in the degradation of lactose, via the Leloir pathway and the bifid shunt, and the production of acetic, lactic, and succinic acids. In addition, members of the Firmicutes phylum contribute to the chain-elongation-mediated production of butyric, hexanoic, and octanoic acids, with different microbes using either lactose, ethanol, or lactic acid as the growth substrate. We conclude that genes encoding carbohydrate utilization pathways, and genes encoding lactic acid transport into the cell, electron confurcating lactate dehydrogenase, and its associated electron transfer flavoproteins, are genomic features whose presence in Firmicutes needs to be established to infer the growth substrate used for chain elongation.

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Section: Methodsmentioning

confidence: 99%

A metagenome-level analysis of a microbial community fermenting ultra-filtered milk permeate

Walters

Mohan

Myers

et al. 2023

Front. Bioeng. Biotechnol.

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“…MAG data was obtained from previously published lab-scale bioreactor studies of microbial communities grown with various agroindustrial residues (Scarborough et al, 2018a;Scarborough et al, 2020;Fortney et al, 2021;Ingle et al, 2021;Fortney et al, 2022;Ingle et al, 2022;Scarborough et al, 2022;Walters et al, 2022). The operational conditions of the bioreactors are summarized in Table 1 and additional information on sample collection can be found in the respective publications.…”

Section: Metagenome Assembled Genome (Mag) Sourcesmentioning

confidence: 99%

“…The operational conditions of the bioreactors are summarized in Table 1 and additional information on sample collection can be found in the respective publications. MAGs were obtained from the inoculum source (two samples, 10 MAGs) (Ingle et al, 2022) and bioreactors fed cellulosic ethanol thin stillage (six samples, 10 MAGs) (Scarborough et al, 2018a;Scarborough et al, 2020), synthetic medium containing xylose as the primary carbon source (three samples, 8 MAGs) (Scarborough et al, 2022), hydrolysate from dairy manure (four samples, 38 MAGs) (Ingle et al, 2021;Ingle et al, 2022), ultra-filtered milk permeate (34 samples, 123 MAGs) (Walters et al, 2022;Walters et al, 2023), and starch ethanol thin stillage (31 samples, 51 MAGs) (Fortney et al, 2021;Fortney et al, 2022). In all cases, only the best-quality representative MAGs determined in each study were used.…”

Section: Metagenome Assembled Genome (Mag) Sourcesmentioning

confidence: 99%

“…Two additional bioreactors complete the set of 10 bioreactors used in this study; one fed a xylose-rich synthetic medium and a second one operated with ultra-filtered milk permeate as the feedstock. The MAGs assembled from all of the bioreactors have been reported and are publicly available (Scarborough et al, 2018a;Fortney et al, 2022;Ingle et al, 2022;Scarborough et al, 2022;Walters et al, 2022). The main fermentation products that accumulated in the medium of these bioreactors include lactic and succinic acids, ethanol, as well as the short chain fatty acids (SCFAs) acetic and propionic acids and the MCFAs butyric, hexanoic, and octanoic acids (Figure 2).…”

Section: Analysis Of the Non-redundant Mag Datasetmentioning

confidence: 99%

“…In other cases, it is proposed that ethanol can be used as an electron donor and act as an intermediate during MCFA production (Agler et al, 2012;Kucek et al, 2016a). To evaluate whether this microbial ecology model can be generalized to conceptually explain MCFA production from a variety of carbohydrate-rich organic residues, we evaluated the microbial communities that were enriched when the same inoculum was used in bioreactor experiments that fermented several agroindustrial residues, including thin stillage from starch ethanol production (Fortney et al, 2021;Fortney et al, 2022), thin stillage from cellulosic ethanol production (Scarborough et al, 2018a;Scarborough et al, 2020), xylose (Scarborough et al, 2022), dairy manure hydrolysate (Ingle et al, 2021;Ingle et al, 2022), and ultrafiltered milk permeate (Walters et al, 2022;Walters et al, 2023). In all cases, the inoculum was from an acid-phase anaerobic digester at the local wastewater treatment plant (Madison, WI, United States).…”

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confidence: 99%

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Comparison of metagenomes from fermentation of various agroindustrial residues suggests a common model of community organization

Myers

Ingle

Walters

et al. 2023

Front. Bioeng. Biotechnol.

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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.

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Metagenome-assembled genomes from microbiomes fermenting dairy coproducts

Walters,

Myers,

Donohue

et al. 2024

Microbiol Resour Announc

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

Cited by 4 publications

References 19 publications

A metagenome-level analysis of a microbial community fermenting ultra-filtered milk permeate

A metagenome-level analysis of a microbial community fermenting ultra-filtered milk permeate

Comparison of metagenomes from fermentation of various agroindustrial residues suggests a common model of community organization

Metagenome-assembled genomes from microbiomes fermenting dairy coproducts

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