Metagenomes and Metagenome-Assembled Genomes from Microbiomes Metabolizing Thin Stillage from an Ethanol Biorefinery

Abstract

Here, we report the metagenomes from five anaerobic bioreactors, operated under different conditions, that were fed carbohydrate-rich thin stillage from a corn starch ethanol plant. The putative functions of the abundant taxa identified here will inform future studies of microbial communities involved in valorizing this and other low-value agroindustrial residues.

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

“…In contrast, the lactic acid producing bacteria enriched in a xylose-rich lignocellulosic feedstock were primarily Firmicutes in the Lactobacillaceae family and encoded pathways for pentose utilization ( Scarborough et al, 2018a ). Likewise, members of the Lactobacillaceae family were enriched in a bioreactor fed thin stillage derived from a starch ethanol production ( Fortney et al, 2021 ; Fortney et al, 2022 ). Within microbial communities fed food waste extract, the dominant lactic acid producing bacteria differed based on the organic loading rate, with Firmicutes in the Streptococcaceae family being dominant at low loading rates and Actinobacteriota within the Atopobiaceae family being dominant at high loading rates ( Crognale et al, 2021 ).…”

“…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.…”

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

“…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.…”

“…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.…”

“…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).…”