Lactobacillus buchneri strain NRRL B-30929 was a contaminant obtained from a commercial ethanol fermentation. This facultative anaerobe is unique because of its rapid growth on xylose and simultaneous fermentation of xylose and glucose. The strain utilizes a broad range of carbohydrate substrates and possesses a high tolerance to ethanol and other stresses, making it an attractive candidate for bioconversion of biomass substrates to various bioproducts. The genome sequence of NRRL B-30929 will provide insight into the unique properties of this lactic acid bacterium

Chertkov, Olga

Copeland, Alex

Goodwin, Lynne

Leathers, Timothy D.

Liu, Siqing

Mills, David A.

English

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University of Nebraska - Lincoln 
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US Department of Energy Publications U.S. Department of Energy 
2011 
Complete Genome Sequence of Lactobacillus buchneri NRRL 
B-30929, a Novel Strain from a Commercial Ethanol Plant 
Siqing Liu 
National Center for Agricultural Utilization Research, Siqing.liu@ars.usda.gov 
Timothy D. Leathers 
National Center for Agricultural Utilization Research 
Alex Copeland 
DOE Joint Genome Institute 
Olga Chertkov 
DOE Joint Genome Institute 
Lynne Goodwin 
DOE Joint Genome Institute 
See next page for additional authors 
Follow this and additional works at: https://digitalcommons.unl.edu/usdoepub 
 Part of the Bioresource and Agricultural Engineering Commons 
Liu, Siqing; Leathers, Timothy D.; Copeland, Alex; Chertkov, Olga; Goodwin, Lynne; and Mills, David A., 
"Complete Genome Sequence of Lactobacillus buchneri NRRL B-30929, a Novel Strain from a Commercial 
Ethanol Plant" (2011). US Department of Energy Publications. 293. 
https://digitalcommons.unl.edu/usdoepub/293 
This Article is brought to you for free and open access by the U.S. Department of Energy at 
DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in US Department of Energy 
Publications by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. 
Authors 
Siqing Liu, Timothy D. Leathers, Alex Copeland, Olga Chertkov, Lynne Goodwin, and David A. Mills 
This article is available at DigitalCommons@University of Nebraska - Lincoln: https://digitalcommons.unl.edu/
usdoepub/293 
JOURNAL OF BACTERIOLOGY, Aug. 2011, p. 4019–4020 Vol. 193, No. 15
0021-9193/11/$12.00 doi:10.1128/JB.05180-11
Copyright © 2011, American Society for Microbiology. All Rights Reserved.
Complete Genome Sequence of Lactobacillus buchneri NRRL
B-30929, a Novel Strain from a Commercial Ethanol Plant
Siqing Liu,1* Timothy D. Leathers,1 Alex Copeland,2 Olga Chertkov,3
Lynne Goodwin,3 and David A. Mills4*
Renewable Product Technology Research Unit, National Center for Agricultural Utilization Research, U.S. Department of
Agriculture, Peoria, Illinois1; DOE Joint Genome Institute, Walnut Creek, California2; DOE Joint Genome Institute,
Los Alamos, New Mexico3; and Department of Viticulture and Enology, Robert Mondavi Institute for
Wine and Food Science, University of California, Davis, California4
Received 28 April 2011/Accepted 10 May 2011
Lactobacillus buchneri strain NRRL B-30929 was a contaminant obtained from a commercial ethanol fer-
mentation. This facultative anaerobe is unique because of its rapid growth on xylose and simultaneous
fermentation of xylose and glucose. The strain utilizes a broad range of carbohydrate substrates and possesses
a high tolerance to ethanol and other stresses, making it an attractive candidate for bioconversion of biomass
substrates to various bioproducts. The genome sequence of NRRL B-30929 will provide insight into the unique
properties of this lactic acid bacterium.
Lactobacillus buchneri is a heterofermentative, facultative
anaerobe that belongs to the lactic acid bacteria. Strains of L.
buchneri have been described as having diverse activities, rang-
ing from prevention of silage spoilage by yeasts and molds (1,
2, 10) to histamine production in Swiss cheese (9). Several
strains have been reported to metabolize lactate to produce
1,2-propanediol (5, 7) and to produce 1,3-propanediol from
glycerol (8, 11, 12). A sauerkraut isolate of L. buchneri was
found to produce an antibacterial peptide that inhibited the
growth of selected Gram-positive bacteria (13–15). Interest-
ingly, several isolates of L. buchneri are capable of producing
ferulate esterases, which break down the cross-links between
lignin and hemicellulose (6).
The strain NRRL B-30929 was originally isolated from an
ethanol production plant and can tolerate high ethanol con-
centrations (4). L. buchneri NRRL B-30929 is unique in its
rapid growth on xylose and ability to simultaneously ferment
glucose and xylose. In addition, the strain can utilize a broad
spectrum of monosaccharides, disaccharides, and oligosaccha-
ride substrates, and it can tolerate inhibitors present in ligno-
cellulosic hydrolysates (3).
The general methods of genomic DNA preparation, library
construction, and sequencing can be found on the Joint
Genome Institute (JGI) website (http://www.jgi.doe.gov
/sequencing/protocols/index.html). A whole-genome shotgun
strategy using Roche 454 Titanium pyrosequencing was per-
formed, and DNA sequences were processed and assembled by
the JGI. NRRL B-30929 has one circular chromosome of
2,506,301 bp, with a GC content of 44.4%, and three plas-
mids, pLBU01 (52,697 bp with 38.1% GC), pLBU02 (18,513
bp with 40.4% GC), and pLBU03 (10,798 bp with 37.6%
GC).
The NRRL B-30929 genome contains a total of 2,541 genes
with 2,461 predicted coding sequences (CDSs) and 80 genes
for RNAs, including 63 tRNA and 15 rRNA genes (https:
//merced.jgi-psf.org/cgi-bin/er/main.cgi). There are total of
1,976 CDSs (77.76%) with predicted functions and 485 CDSs
(19.09%) without predicted functions. A total of 1,965 genes
can be associated with clusters of orthologous genes (COGs)
functions belonging to 1,174 COGs. In summary, there are 204
genes for amino acid transport and metabolism, 180 genes for
replication, recombination, and repair, 171 genes for carbohy-
drate transport and metabolism, 161 genes for signal transduc-
tion mechanisms and transcription, 144 genes for translation,
ribosomal structure, and biogenesis, 124 genes involved in cell
wall/membrane/envelope biogenesis, 99 genes for inorganic
ion transport and metabolism, and 93 genes for energy pro-
duction and conversion.
Generation of the genome sequence for NRRL B-30929 will
foster engineering of carbohydrate metabolism and modifica-
tion of end product profiles for biofuels and other platform
chemicals. Moreover, the finished genome sequence will en-
able whole-genome expression studies to better understand the
stress response systems present in this ethanol-tolerant mi-
crobe.
Nucleotide sequence accession numbers. The complete ge-
nome sequence of Lactobacillus buchneri NRRL B-30929 is
available in GenBank under the accession number CP002652.
The accession numbers for the plasmids pLBU01, pLBU02,
and pLBU03 are CP002653, CP002654, and CP002655, respec-
tively.
We thank and acknowledge all of the JGI personnel who partici-
pated in sequencing, assembly, and automated annotation of the L.
buchneri genome project. We thank Joseph Rich for reading the man-
uscript and Jacqueline Zane and Lucy Joseph for their excellent tech-
nical support.
* Corresponding author. Mailing address for Siqing Liu: Renewable
Product Technology Research Unit, National Center for Agricultural
Utilization Research, U.S. Department of Agriculture, Peoria, IL.
Phone: (309) 681-6566. Fax: (309) 681-6040. E-mail: Siqing.liu@ars
.usda.gov. Mailing address for David A. Mills: Department of
Viticulture and Enology, Robert Mondavi Institute for Wine and Food
Science, University of California, Davis, CA. Phone: (530) 754-7821.
Fax: (530) 752-0382. E-mail: damills@ucdavis.edu.
 Published ahead of print on 27 May 2011.
4019
This work conducted by the U.S. Department of Energy Joint Ge-
nome Institute is supported by the Office of Science of the U.S. De-
partment of Energy under contract no. DE-AC02-05CH11231.
Mention of a trade name, proprietary product, or specific equipment
does not constitute a guarantee or warranty by the United States
Department of Agriculture and does not imply its approval to the
exclusion of other products that may be suitable.
REFERENCES
1. Kleinschmit, D. H., R. J. Schmidt, and L. Kung, Jr. 2005. The effects of
various antifungal additives on the fermentation and aerobic stability of corn
silage. J. Dairy Sci. 88:2130–2139.
2. Kung, L., Jr., and N. K. Ranjit. 2001. The effect of Lactobacillus buchneri and
other additives on the fermentation and aerobic stability of barley silage. J.
Dairy Sci. 84:1149–1155.
3. Liu, S., et al. 2009. Conversion of biomass hydrolysates and other substrates
to ethanol and other chemicals by Lactobacillus buchneri. Lett. Appl. Micro-
biol. 48:337–342.
4. Liu, S., K. A. Skinner-Nemec, and T. D. Leathers. 2008. Lactobacillus bu-
chneri strain NRRL B-30929 converts a concentrated mixture of xylose and
glucose into ethanol and other products. J. Ind. Microbiol. Biotechnol. 35:
75–81.
5. Nishino, N., M. Yoshida, H. Shiota, and E. Sakaguchi. 2003. Accumulation
of 1,2-propanediol and enhancement of aerobic stability in whole crop maize
silage inoculated with Lactobacillus buchneri. J. Appl. Microbiol. 94:800–807.
6. Nsereko, V. L., et al. 2006. The American Dairy Science Association annual
meeting abstract.
7. Oude Elferink, S. J., et al. 2001. Anaerobic conversion of lactic acid to acetic
acid and 1, 2-propanediol by Lactobacillus buchneri. Appl. Environ. Micro-
biol. 67:125–132.
8. Schutz, H., and F. Radler. 1984. Anaerobic reduction of glycerol to propane-
diol-1.3 by Lactobacillus brevis and Lactobacillus buchneri. Syst. Appl. Mi-
crobiol. 5:169–178.
9. Sumner, S. S., M. W. Speckhard, E. B. Somers, and S. L. Taylor. 1985.
Isolation of histamine-producing Lactobacillus buchneri from Swiss cheese
implicated in a food poisoning outbreak. Appl. Environ. Microbiol. 50:1094–
1096.
10. Taylor, C. C., N. J. Ranjit, J. A. Mills, J. M. Neylon, and L. Kung, Jr. 2002.
The effect of treating whole-plant barley with Lactobacillus buchneri 40788
on silage fermentation, aerobic stability, and nutritive value for dairy cows.
J. Dairy Sci. 85:1793–1800.
11. Veiga-da-Cunha, M., and M. A. Foster. 1992. 1,3-Propanediol:NAD oxi-
doreductases of Lactobacillus brevis and Lactobacillus buchneri. Appl. Envi-
ron. Microbiol. 58:2005–2010.
12. Veiga da Cunha, M., and M. A. Foster. 1992. Sugar-glycerol cofermentations
in lactobacilli: the fate of lactate. J. Bacteriol. 174:1013–1019.
13. Yildirim, M. 2001. Characterization of buchnericin LB produced by Lacto-
bacillus buchneri LB. Turk. J. Biol. 25:73–82.
14. Yildirim, M. 2001. Purification of buchnericin LB produced by Lactobacillus
buchneri LB. Turk. J. Biol. 25:59–65.
15. Yildirim, Z., Y. K. Avsar, and M. Yildirim. 2002. Factors affecting the
adsorption of buchnericin LB, a bacteriocin produced by Lactobacillus bu-
chneri. Microbiol. Res. 157:103–107.
4020 GENOME ANNOUNCEMENTS J. BACTERIOL.


Complete Genome Sequence of \u3ci\u3eLactobacillus buchneri\u3c/i\u3e NRRL
B-30929, a Novel Strain from a Commercial Ethanol Plant

DigitalCommons@University of Nebraska

University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln US Department of Energy Publications U.S. Department of Energy 2011 Complete Genome Sequence of Lactobacillus buchneri NRRL B-30929, a Novel Strain from a Commercial Ethanol Plant Siqing Liu National Center for Agricultural Utilization Research, Siqing.liu@ars.usda.gov Timothy D. Leathers National Center for Agricultural Utilization Research Alex Copeland DOE Joint Genome Institute Olga Chertkov DOE Joint Genome Institute Lynne Goodwin DOE Joint Genome Institute See next page for additional authors Follow this and additional works at: https://digitalcommons.unl.edu/usdoepub  Part of the Bioresource and Agricultural Engineering Commons Liu, Siqing; Leathers, Timothy D.; Copeland, Alex; Chertkov, Olga; Goodwin, Lynne; and Mills, David A., "Complete Genome Sequence of Lactobacillus buchneri NRRL B-30929, a Novel Strain from a Commercial Ethanol Plant" (2011). US Department of Energy Publications. 293. https://digitalcommons.unl.edu/usdoepub/293 This Article is brought to you for free and open access by the U.S. Department of Energy at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in US Department of Energy Publications by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. Authors Siqing Liu, Timothy D. Leathers, Alex Copeland, Olga Chertkov, Lynne Goodwin, and David A. Mills This article is available at DigitalCommons@University of Nebraska - Lincoln: https://digitalcommons.unl.edu/usdoepub/293 JOURNAL OF BACTERIOLOGY, Aug. 2011, p. 4019–4020 Vol. 193, No. 150021-9193/11/$12.00 doi:10.1128/JB.05180-11Copyright © 2011, American Society for Microbiology. All Rights Reserved.Complete Genome Sequence of Lactobacillus buchneri NRRLB-30929, a Novel Strain from a Commercial Ethanol PlantSiqing Liu,1* Timothy D. Leathers,1 Alex Copeland,2 Olga Chertkov,3Lynne Goodwin,3 and David A. Mills4*Renewable Product Technology Research Unit, National Center for Agricultural Utilization Research, U.S. Department ofAgriculture, Peoria, Illinois1; DOE Joint Genome Institute, Walnut Creek, California2; DOE Joint Genome Institute,Los Alamos, New Mexico3; and Department of Viticulture and Enology, Robert Mondavi Institute forWine and Food Science, University of California, Davis, California4Received 28 April 2011/Accepted 10 May 2011Lactobacillus buchneri strain NRRL B-30929 was a contaminant obtained from a commercial ethanol fer-mentation. This facultative anaerobe is unique because of its rapid growth on xylose and simultaneousfermentation of xylose and glucose. The strain utilizes a broad range of carbohydrate substrates and possessesa high tolerance to ethanol and other stresses, making it an attractive candidate for bioconversion of biomasssubstrates to various bioproducts. The genome sequence of NRRL B-30929 will provide insight into the uniqueproperties of this lactic acid bacterium.Lactobacillus buchneri is a heterofermentative, facultativeanaerobe that belongs to the lactic acid bacteria. Strains of L.buchneri have been described as having diverse activities, rang-ing from prevention of silage spoilage by yeasts and molds (1,2, 10) to histamine production in Swiss cheese (9). Severalstrains have been reported to metabolize lactate to produce1,2-propanediol (5, 7) and to produce 1,3-propanediol fromglycerol (8, 11, 12). A sauerkraut isolate of L. buchneri wasfound to produce an antibacterial peptide that inhibited thegrowth of selected Gram-positive bacteria (13–15). Interest-ingly, several isolates of L. buchneri are capable of producingferulate esterases, which break down the cross-links betweenlignin and hemicellulose (6).The strain NRRL B-30929 was originally isolated from anethanol production plant and can tolerate high ethanol con-centrations (4). L. buchneri NRRL B-30929 is unique in itsrapid growth on xylose and ability to simultaneously fermentglucose and xylose. In addition, the strain can utilize a broadspectrum of monosaccharides, disaccharides, and oligosaccha-ride substrates, and it can tolerate inhibitors present in ligno-cellulosic hydrolysates (3).The general methods of genomic DNA preparation, libraryconstruction, and sequencing can be found on the JointGenome Institute (JGI) website (http://www.jgi.doe.gov/sequencing/protocols/index.html). A whole-genome shotgunstrategy using Roche 454 Titanium pyrosequencing was per-formed, and DNA sequences were processed and assembled bythe JGI. NRRL B-30929 has one circular chromosome of2,506,301 bp, with a GC content of 44.4%, and three plas-mids, pLBU01 (52,697 bp with 38.1% GC), pLBU02 (18,513bp with 40.4% GC), and pLBU03 (10,798 bp with 37.6%GC).The NRRL B-30929 genome contains a total of 2,541 geneswith 2,461 predicted coding sequences (CDSs) and 80 genesfor RNAs, including 63 tRNA and 15 rRNA genes (https://merced.jgi-psf.org/cgi-bin/er/main.cgi). There are total of1,976 CDSs (77.76%) with predicted functions and 485 CDSs(19.09%) without predicted functions. A total of 1,965 genescan be associated with clusters of orthologous genes (COGs)functions belonging to 1,174 COGs. In summary, there are 204genes for amino acid transport and metabolism, 180 genes forreplication, recombination, and repair, 171 genes for carbohy-drate transport and metabolism, 161 genes for signal transduc-tion mechanisms and transcription, 144 genes for translation,ribosomal structure, and biogenesis, 124 genes involved in cellwall/membrane/envelope biogenesis, 99 genes for inorganicion transport and metabolism, and 93 genes for energy pro-duction and conversion.Generation of the genome sequence for NRRL B-30929 willfoster engineering of carbohydrate metabolism and modifica-tion of end product profiles for biofuels and other platformchemicals. Moreover, the finished genome sequence will en-able whole-genome expression studies to better understand thestress response systems present in this ethanol-tolerant mi-crobe.Nucleotide sequence accession numbers. The complete ge-nome sequence of Lactobacillus buchneri NRRL B-30929 isavailable in GenBank under the accession number CP002652.The accession numbers for the plasmids pLBU01, pLBU02,and pLBU03 are CP002653, CP002654, and CP002655, respec-tively.We thank and acknowledge all of the JGI personnel who partici-pated in sequencing, assembly, and automated annotation of the L.buchneri genome project. We thank Joseph Rich for reading the man-uscript and Jacqueline Zane and Lucy Joseph for their excellent tech-nical support.* Corresponding author. Mailing address for Siqing Liu: RenewableProduct Technology Research Unit, National Center for AgriculturalUtilization Research, U.S. Department of Agriculture, Peoria, IL.Phone: (309) 681-6566. Fax: (309) 681-6040. E-mail: Siqing.liu@ars.usda.gov. Mailing address for David A. Mills: Department ofViticulture and Enology, Robert Mondavi Institute for Wine and FoodScience, University of California, Davis, CA. Phone: (530) 754-7821.Fax: (530) 752-0382. E-mail: damills@ucdavis.edu. Published ahead of print on 27 May 2011.4019This work conducted by the U.S. Department of Energy Joint Ge-nome Institute is supported by the Office of Science of the U.S. De-partment of Energy under contract no. DE-AC02-05CH11231.Mention of a trade name, proprietary product, or specific equipmentdoes not constitute a guarantee or warranty by the United StatesDepartment of Agriculture and does not imply its approval to theexclusion of other products that may be suitable.REFERENCES1. Kleinschmit, D. H., R. J. Schmidt, and L. Kung, Jr. 2005. The effects ofvarious antifungal additives on the fermentation and aerobic stability of cornsilage. J. Dairy Sci. 88:2130–2139.2. Kung, L., Jr., and N. K. Ranjit. 2001. The effect of Lactobacillus buchneri andother additives on the fermentation and aerobic stability of barley silage. J.Dairy Sci. 84:1149–1155.3. Liu, S., et al. 2009. Conversion of biomass hydrolysates and other substratesto ethanol and other chemicals by Lactobacillus buchneri. Lett. Appl. Micro-biol. 48:337–342.4. Liu, S., K. A. Skinner-Nemec, and T. D. Leathers. 2008. Lactobacillus bu-chneri strain NRRL B-30929 converts a concentrated mixture of xylose andglucose into ethanol and other products. J. Ind. Microbiol. Biotechnol. 35:75–81.5. Nishino, N., M. Yoshida, H. Shiota, and E. Sakaguchi. 2003. Accumulationof 1,2-propanediol and enhancement of aerobic stability in whole crop maizesilage inoculated with Lactobacillus buchneri. J. Appl. Microbiol. 94:800–807.6. Nsereko, V. L., et al. 2006. The American Dairy Science Association annualmeeting abstract.7. Oude Elferink, S. J., et al. 2001. Anaerobic conversion of lactic acid to aceticacid and 1, 2-propanediol by Lactobacillus buchneri. Appl. Environ. Micro-biol. 67:125–132.8. Schutz, H., and F. Radler. 1984. Anaerobic reduction of glycerol to propane-diol-1.3 by Lactobacillus brevis and Lactobacillus buchneri. Syst. Appl. Mi-crobiol. 5:169–178.9. Sumner, S. S., M. W. Speckhard, E. B. Somers, and S. L. Taylor. 1985.Isolation of histamine-producing Lactobacillus buchneri from Swiss cheeseimplicated in a food poisoning outbreak. Appl. Environ. Microbiol. 50:1094–1096.10. Taylor, C. C., N. J. Ranjit, J. A. Mills, J. M. Neylon, and L. Kung, Jr. 2002.The effect of treating whole-plant barley with Lactobacillus buchneri 40788on silage fermentation, aerobic stability, and nutritive value for dairy cows.J. Dairy Sci. 85:1793–1800.11. Veiga-da-Cunha, M., and M. A. Foster. 1992. 1,3-Propanediol:NAD oxi-doreductases of Lactobacillus brevis and Lactobacillus buchneri. Appl. Envi-ron. Microbiol. 58:2005–2010.12. Veiga da Cunha, M., and M. A. Foster. 1992. Sugar-glycerol cofermentationsin lactobacilli: the fate of lactate. J. Bacteriol. 174:1013–1019.13. Yildirim, M. 2001. Characterization of buchnericin LB produced by Lacto-bacillus buchneri LB. Turk. J. Biol. 25:73–82.14. Yildirim, M. 2001. Purification of buchnericin LB produced by Lactobacillusbuchneri LB. Turk. J. Biol. 25:59–65.15. Yildirim, Z., Y. K. Avsar, and M. Yildirim. 2002. Factors affecting theadsorption of buchnericin LB, a bacteriocin produced by Lactobacillus bu-chneri. Microbiol. Res. 157:103–107.4020 GENOME ANNOUNCEMENTS J. BACTERIOL.

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Complete Genome Sequence of \u3ci\u3eLactobacillus buchneri\u3c/i\u3e NRRL B-30929, a Novel Strain from a Commercial Ethanol Plant

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