Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2022 Jul 21;11(7):e0029322.
doi: 10.1128/mra.00293-22. Epub 2022 Jun 30.

Metagenomes and Metagenome-Assembled Genomes from Microbial Communities Fermenting Ultrafiltered Milk Permeate

Kevin A Walters  1   2   3 , Kevin S Myers  1   2 , Hui Wang  4 , Nathaniel W Fortney  1   2 , Abel T Ingle  1   2   4 , Matthew J Scarborough  5 , Timothy J Donohue  1   2   3 , Daniel R Noguera  1   2   4
Affiliations

Metagenomes and Metagenome-Assembled Genomes from Microbial Communities Fermenting Ultrafiltered Milk Permeate

Kevin A Walters et al. Microbiol Resour Announc. .

Abstract

Fermentative microbial communities can be utilized for the conversion of various agroindustrial residues into valuable chemicals. Here, we report 34 metagenomes from anaerobic bioreactors fed lactose-rich ultrafiltered milk permeate and 278 metagenome-assembled genomes (MAGs). These MAGs can inform future studies aimed at generating renewable chemicals from dairy and other agroindustrial residues.

PubMed Disclaimer

Conflict of interest statement

The authors declare no conflict of interest.

Figures

FIG 1
FIG 1
Phylogenic tree of dRep representative bacterial MAGs and their presence in two bioreactors (CSTR and USB) fermenting ultrafiltered milk permeate. ACET, Acetobacter; ACID, Acidaminococcaceae; ACT, Actinomycetaceae; ACUT, Acutalibacteraceae; AGRLAC, Agrilactobacillus; ANA, Anaerovoracaceae; ATO, Atopobiaceae; BACIL, Bacilli; BACTE, Bacteroidales; BIF, Bifidobacterium; BUL, Bulleidia; BURK, Burkholderiaceae; CARN, Carnobacteriaceae; CAUL, Caulobacteraceae; CLOS, Clostridium; EGG, Eggerthellaceae; ENTER, Enterobacteriaceae; LAC, Lactobacillus; LCO, Lachnospiraceae; LENLAC, Lentilactobacillus; LEUC, Lecuonostoc; LIQLAC, Liquorilactobacillus; MEG, Megasphaera; MIC, Microbacteriaceae; MORAX, Moraxellaceae; MUR, Muribaculaceae; MYC, Mycobacteriaceae; OSCL, Oscillospiraceae; PREV, Prevotella; PROP, Propionibacteriaceae; RUM, Ruminococcaceae; SACCH, Saccharofermentans; SCHLAC, Schleiferilactobacillus; SELEN, Selenomonadaceae; SPH, Sphaerochaetaceae; SPHING, Sphingobium; SPOR, Sporolactobacillaceae; STREP, Streptococcaceae; TREP, Treponema. Higher taxonomic levels are labeled, from left to right, family (F), order (O), class (C), and phylum (P). Spiro., Spirochaetota; Alphapr., Alphaproteobacteria; Spiro., Spirochaetia; Acida., Acidaminococcales; Clos., Clostridiales; Erys., Erysipelotrichales; Lachno., Lachnospirales; Pepto., Peptostreptococcales; Veillonella., Veillonellales; Acida., Acidaminococcaceae; Acutali., Acutalibacteraceae; Anaer., Anaerovoracaceae; Clos., Clostridiaceae; Erys., Erysipelotrichaceae; Lachno, Lachnospiraceae; Megasph., Megasphaeraceae; Oscil., Oscillospiraceae; Strep., Streptococcaceae. The phylogenetic tree was generated in RAxML-ng (14) with 500 bootstraps using the concatenation of 120 bacterial single-copy marker genes (Bac120) identified by GTDB-Tk (13). Bootstrap values greater than 50 are shown. The scale bar represents evolutionary distance and indicates the number of nucleotide substitutions per sequence site.
See this image and copyright information in PMC

References

    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. Clum A, Huntemann M, Bushnell B, Foster B, Foster B, Roux S, Hajek PP, Varghese N, Mukherjee S, Reddy TBK, Daum C, Yoshinaga Y, O’Malley R, Seshadri R, Kyrpides NC, Eloe-Fadrosh EA, Chen I-MA, Copeland A, Ivanova NN. 2021. DOE JGI Metagenome Workflow. mSystems 6:e00804-20. doi:10.1128/mSystems.00804-20. - DOI - PMC - PubMed
    1. Bushnell B. 2014. BBMap: a fast, accurate, splice-aware aligner. https://sourceforge.net/projects/bbmap.
    1. Nurk S, Meleshko D, Korobeynikov A, Pevzner PA. 2017. metaSPAdes: a new versatile metagenomic assembler. Genome Res 27:824–834. doi:10.1101/gr.213959.116. - DOI - PMC - PubMed
    1. Kolmogorov M, Bickhart DM, Behsaz B, Gurevich A, Rayko M, Shin SB, Kuhn K, Yuan J, Polevikov E, Smith TPL, Pevzner PA. 2020. metaFlye: scalable long-read metagenome assembly using repeat graphs. Nat Methods 17:1103–1110. doi:10.1038/s41592-020-00971-x. - DOI - PMC - PubMed

LinkOut - more resources