Abstract
Water kefir is a fermented beverage employing a natural microbial consortium, which harbours bifidobacteria, namely Bifidobacterium aquikefiri and Bifidobacterium tibiigranuli. However, little information is available on their metabolic properties or role in the consortium. In this study, we combined genomic and physiologic investigations to predict and characterize the properties of these organisms and their possible role in the consortium. When comparing the genomes of these psychrotrophic organisms with that of the three selected mesophilic probiotic Bifidobacterium strains, we could find 143 genes shared by the 3 known isolates of bifidobacteria from water kefir that do not occur in the probiotic strains. These include genes involved in acid and oxygen tolerance. In addition, their genomically predicted carbohydrate usage and transport suggest adaptation to sucrose and other plant-related sugars. Furthermore, they proved prototrophic for all amino acids in vitro, which enables them to cope with the strong amino acid limitation in water kefir.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
Abbreviations
- ANIb:
-
Average nucleotide identity based on BLAST + (ANIb)
- CDM:
-
Chemically defined medium (CDM)
- CDM+AA:
-
Chemically defined medium with all amino acids (CDM + AA)
- CDM−AA:
-
Chemically defined medium without amino acids (CDM–AA)
- DMG:
-
Diagnostic marker gene (DMG)
- F6PPK:
-
Fructose-6-phosphate phosphoketolase (F6PPK)
- GOI:
-
Gene of interest (GOI)
References
Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K et al (2008) The RAST Server: rapid annotations using subsystems technology. BMC Genomics 9:75–75. https://doi.org/10.1186/1471-2164-9-75
Behr J, Geissler AJ, Schmid J, Zehe A, Vogel RF (2016) The identification of novel Diagnostic Marker Genes for the detection of beer spoiling Pediococcus damnosus strains using the BlAst Diagnostic Gene findEr. PLoS ONE 11:e0152747. https://doi.org/10.1371/journal.pone.0152747
Bottacini F, Motherway MOC, Kuczynski J, O’Connell KJ, Serafini F, Duranti S, Milani C et al (2014) Comparative genomics of the Bifidobacterium breve taxon. BMC Genomics 15:170
Bruinenberg PG, De Roo G, Limsowtin G (1997) Purification and characterization of cystathionine (gamma)-lyase from Lactococcus lactis subsp. cremoris SK11: possible role in flavor compound formation during cheese maturation. Appl Environ Microbiol 63:561–566
Cabiscol Català E, Tamarit Sumalla J, Ros Salvador J (2000) Oxidative stress in bacteria and protein damage by reactive oxygen species. Int Microbiol 3:3–8
Cotter PD, Hill C (2003) Surviving the acid test: responses of gram-positive bacteria to low pH. Microbiol Mol Biol Rev 67:429–453. https://doi.org/10.1128/mmbr.67.3.429-453.2003
Cronin M, Zomer A, Fitzgerald G, van Sinderen D (2012) Identification of iron-regulated genes of Bifidobacterium breve UCC2003 as a basis for controlled gene expression. Bioengineered 3:159–169. https://doi.org/10.4161/bbug.18985
Csonka LN, Hanson AD (1991) Prokaryotic osmoregulation: genetics and physiology. Annu Rev Microbiol 45:569–606
Deguchi Y, Morishita T, Mutai M (1985) Comparative studies on synthesis of water-soluble vitamins among human species of Bifidobacteria. Agric Biol Chem 49:13–19. https://doi.org/10.1080/00021369.1985.10866683
Delcenserie V, Gavini F, Beerens H, Tresse O, Franssen C, Daube G (2007) Description of a new species, Bifidobacterium crudilactis sp. nov., isolated from raw milk and raw milk cheeses. Syst Appl Microbiol 30:381–389. https://doi.org/10.1016/j.syapm.2007.01.004
Eckel VPL, Ziegler L-M, Vogel RF, Ehrmann M (2019) Bifidobacterium tibiigranuli sp. nov. isolated from homemade water kefir. Int J Syst Evol Microbiol. https://doi.org/10.1099/ijsem.0.003936
Fels L, Jakob F, Vogel RF, Wefers D (2018) Structural characterization of the exopolysaccharides from water kefir. Carbohydr Polym 189:296–303. https://doi.org/10.1016/j.carbpol.2018.02.037
Ferrario C, Duranti S, Milani C, Mancabelli L, Lugli GA, Turroni F, Mangifesta M et al (2015) Exploring amino acid auxotrophy in Bifidobacterium bifidum PRL2010. Front Microbiol. https://doi.org/10.3389/fmicb.2015.01331
Gardy JL, Laird MR, Chen F, Rey S, Walsh CJ, Ester M, Brinkman FSL (2004) PSORTb vol 2.0: Expanded prediction of bacterial protein subcellular localization and insights gained from comparative proteome analysis. Bioinformatics 21:617–623. https://doi.org/10.1093/bioinformatics/bti057
Giaever H, Styrvold OB, Kaasen I, Strøm A (1988) Biochemical and genetic characterization of osmoregulatory trehalose synthesis in Escherichia coli. J Bacteriol 170:2841–2849
Goldman BS, Gabbert KK, Kranz RG (1996) The temperature-sensitive growth and survival phenotypes of Escherichia coli cydDC and cydAB strains are due to deficiencies in cytochrome bd and are corrected by exogenous catalase and reducing agents. J Bacteriol 178:6348–6351. https://doi.org/10.1128/jb.178.21.6348-6351.1996
Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P, Tiedje JM (2007) DNA–DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 57:81–91. https://doi.org/10.1099/ijs.0.64483-0
Gulitz A, Stadie J, Wenning M, Ehrmann MA, Vogel RF (2011) The microbial diversity of water kefir. Int J Food Microbiol 151:284–288
Gulitz A, Stadie J, Ehrmann MA, Ludwig W, Vogel RF (2013) Comparative phylobiomic analysis of the bacterial community of water kefir by 16S rRNA gene amplicon sequencing and ARDRA analysis. J Appl Microbiol 114:1082–1091. https://doi.org/10.1111/jam.12124
Holyoake LV, Hunt S, Sanguinetti G, Cook GM, Howard MJ, Rowe ML, Poole RK et al (2016) CydDC-mediated reductant export in Escherichia coli controls the transcriptional wiring of energy metabolism and combats nitrosative stress. Biochem J 473:693–701. https://doi.org/10.1042/BJ20150536
Jungersen M, Wind A, Johansen E, Christensen JE, Stuer-Lauridsen B, Eskesen D (2014) The science behind the probiotic strain Bifidobacterium animalis subsp. lactis BB-12®. Microorganisms 2:92–110
Larsen PI, Sydnes LK, Landfald B, Strøm AR (1987) Osmoregulation in Escherichia coli by accumulation of organic osmolytes: betaines, glutamic acid, and trehalose. Arch Microbiol 147:1–7. https://doi.org/10.1007/BF00492896
Laureys D, De Vuyst L (2014) Microbial species diversity, community dynamics, and metabolite kinetics of water kefir fermentation. Appl Environ Microbiol 80:2564–2572. https://doi.org/10.1128/aem.03978-13
Laureys D, Cnockaert M, De Vuyst L, Vandamme P (2016) Bifidobacterium aquikefiri sp. nov., isolated from water kefir. Int J Syst Evol Microbiol 66:1281–1286. https://doi.org/10.1099/ijsem.0.000877
LeBlanc JG, Milani C, de Giori GS, Sesma F, van Sinderen D, Ventura M (2013) Bacteria as vitamin suppliers to their host: a gut microbiota perspective. Curr Opin Biotechnol 24:160–168. https://doi.org/10.1016/j.copbio.2012.08.005
Lee J-H, O'Sullivan DJ (2010) Genomic insights into Bifidobacteria. Microbiol Mol Biol Rev 74:378–416. https://doi.org/10.1128/mmbr.00004-10
Lee AY, Karplus PA, Ganem B, Clardy J (1995) Atomic structure of the buried catalytic pocket of Escherichia coli chorismate mutase. J Am Chem Soc 117:3627–3628. https://doi.org/10.1021/ja00117a038
Lee J-H, Karamychev VN, Kozyavkin SA, Mills D, Pavlov AR, Pavlova NV, Polouchine NN et al (2008) Comparative genomic analysis of the gut bacterium Bifidobacterium longum reveals loci susceptible to deletion during pure culture growth. BMC Genomics 9:247–247. https://doi.org/10.1186/1471-2164-9-247
LeGall J, Prickril BC, Moura I, Xavier AV, Moura JJG, Huynh Boi H (1988) Isolation and characterization of rubrerythrin, a non-heme iron protein from Desulfovibrio vulgaris that contains rubredoxin centers and a hemerythrin-like binuclear iron cluster. Biochemistry 27:1636–1642. https://doi.org/10.1021/bi00405a037
Lehmann Y, Meile L, Teuber M (1996) Rubrerythrin from Clostridium perfringens: cloning of the gene, purification of the protein, and characterization of its superoxide dismutase function. J Bacteriol 178:7152–7158. https://doi.org/10.1128/jb.178.24.7152-7158.1996
Liu Y, Bauer SC, Imlay JA (2011) The YaaA protein of the Escherichia coli OxyR regulon lessens hydrogen peroxide toxicity by diminishing the amount of intracellular unincorporated iron. J Bacteriol 193:2186–2196
Lo R, Turner MS, Barry DG, Sreekumar R, Walsh TP, Giffard PM (2009) Cystathionine γ-lyase is a component of cystine-mediated oxidative defense in Lactobacillus reuteri BR11. J Bacteriol 191:1827–1837. https://doi.org/10.1128/jb.01553-08
Madden T (2013) The BLAST sequence analysis tool. In: The NCBI handbook, 2nd edn. National Center for Biotechnology Information (US), Bethesda
Martí-Arbona R, Xu C, Steele S, Weeks A, Kuty GF, Seibert CM, Raushel FM (2006) Annotating enzymes of unknown function: N-formimino-l-glutamate deiminase is a member of the amidohydrolase superfamily. Biochemistry 45:1997–2005. https://doi.org/10.1021/bi0525425
Moore T, Sparling PF (1996) Interruption of the gpxA gene increases the sensitivity of Neisseria meningitidis to paraquat. J Bacteriol 178:4301–4305
Nagasawa T, Kanzaki H, Yamada H (1984) Cystathionine gamma-lyase of Streptomyces phaeochromogenes. The occurrence of cystathionine gamma-lyase in filamentous bacteria and its purification and characterization. J Biol Chem 259:10393–10403
Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ, Disz T, Edwards RA et al (2014) The SEED and the rapid annotation of microbial genomes using subsystems technology (RAST). Nucleic Acids Res 42:D206–D214. https://doi.org/10.1093/nar/gkt1226
Parche S, Beleut M, Rezzonico E, Jacobs D, Arigoni F, Titgemeyer F, Jankovic I (2006) Lactose-over-glucose preference in Bifidobacterium longum NCC2705: glcP, encoding a glucose transporter, is subject to lactose repression. J Bacteriol 188:1260–1265. https://doi.org/10.1128/JB.188.4.1260-1265.2006
Pericone CD, Park S, Imlay JA, Weiser JN (2003) Factors contributing to hydrogen peroxide resistance in Streptococcus pneumoniae include pyruvate oxidase (SpxB) and avoidance of the toxic effects of the Fenton reaction. J Bacteriol 185:6815–6825
Petry S, Furlan S, Crepeau MJ, Cerning J, Desmazeaud M (2000) Factors affecting exocellular polysaccharide production by Lactobacillus delbrueckii subsp. bulgaricus grown in a chemically defined medium. Appl Environ Microbiol 66:3427–3431
Pidoux M, De Ruiter G, Brooker B, Colquhoun I, Morris V (1990) Microscopic and chemical studies of a gelling polysaccharide from Lactobacillus hilgardii. Carbohydr Polym 13:351–362
Pittman MS, Robinson HC, Poole RK (2005) A bacterial glutathione transporter (Escherichia coli CydDC) exports reductant to the periplasm. J Biol Chem 280:32254–32261. https://doi.org/10.1074/jbc.M503075200
Pokusaeva K, Fitzgerald GF, van Sinderen D (2011) Carbohydrate metabolism in Bifidobacteria. Genes Nutr 6:285–306. https://doi.org/10.1007/s12263-010-0206-6
Pophaly SD, Singh R, Pophaly SD, Kaushik JK, Tomar SK (2012) Current status and emerging role of glutathione in food grade lactic acid bacteria. Microb Cell Fact 11:114–114. https://doi.org/10.1186/1475-2859-11-114
Reid SJ, Abratt VR (2005) Sucrose utilisation in bacteria: genetic organisation and regulation. Appl Microbiol Biotechnol 67:312–321
Richter M, Rosselló-Móra R, Oliver Glöckner F, Peplies J (2016) JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 32:929–931. https://doi.org/10.1093/bioinformatics/btv681
Rimaux T, Vrancken G, Pothakos V, Maes D, De Vuyst L, Leroy F (2011) The kinetics of the arginine deiminase pathway in the meat starter culture Lactobacillus sakei CTC 494 are pH-dependent. Food Microbiol 28:597–604. https://doi.org/10.1016/j.fm.2010.11.016
Sayers EW, Beck J, Brister JR, Bolton EE, Canese K, Comeau DC, Funk K et al (2019) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 48:D9–D16. https://doi.org/10.1093/nar/gkz899
Scandalios JG (1993) Oxygen stress and superoxide dismutases. Plant Physiol 101:7
Scardovi V (1986) Genus Bifidobacterium In: Bergey's manual of systematic bacteriology, Williams & Wilkins, Baltimore, pp 1418–1434
Schell MA, Karmirantzou M, Snel B, Vilanova D, Berger B, Pessi G, Zwahlen MC et al (2002) The genome sequence of Bifidobacterium longum reflects its adaptation to the human gastrointestinal tract. Proc Natl Acad Sci USA 99:14422–14427. https://doi.org/10.1073/pnas.212527599
Simpson PJ, Ross RP, Fitzgerald GF, Stanton C (2004) Bifidobacterium psychraerophilum sp. nov. and Aeriscardovia aeriphila gen. nov., sp. nov., isolated from a porcine caecum. Int J Syst Evol Microbiol 54:401–406. https://doi.org/10.1099/ijs.0.02667-0
Stadie J (2013) Metabolic activity and symbiotic interaction of bacteria and yeasts in water kefir. Dissertation. Technische Universität München, München
Toft C, Andersson SGE (2010) Evolutionary microbial genomics: insights into bacterial host adaptation. Nat Rev Genet 11:465–475. https://doi.org/10.1038/nrg2798
Tonon T, Lonvaud-Funel A (2002) Arginine metabolism by wine Lactobacilli isolated from wine. Food Microbiol 19:451–461. https://doi.org/10.1006/fmic.2002.0502
Trindade MI, Abratt VR, Reid SJ (2003) Induction of sucrose utilization genes from Bifidobacterium lactis by sucrose and raffinose. Appl Environ Microbiol 69:24–32. https://doi.org/10.1128/aem.69.1.24-32.2003
Verce M, De Vuyst L, Weckx S (2019) Shotgun metagenomics of a water Kefir fermentation ecosystem reveals a novel Oenococcus Species. Front Microbiol 10:479
Waldherr FW, Doll VM, Meissner D, Vogel RF (2010) Identification and characterization of a glucan-producing enzyme from Lactobacillus hilgardii TMW 1.828 involved in granule formation of water kefir. Food Microbiol 27:672–678. https://doi.org/10.1016/j.fm.2010.03.013
Ward HMV (1892) The ginger-beer plant, and the organisms composing it: a contribution to the study of fermentation-yeasts and bacteria. Philos Trans R Soc London Ser B:125–197
Watanabe K, Makino H, Sasamoto M, Kudo Y, Fujimoto J, Demberel S (2009) Bifidobacterium mongoliense sp. nov., from airag, a traditional fermented mare's milk product from Mongolia. Int J Syst Evol Microbiol 59:1535–1540. https://doi.org/10.1099/ijs.0.006247-0
Wei X, Guo Y, Shao C, Sun Z, Zhurina D, Liu D, Liu W et al (2012) Fructose uptake in Bifidobacterium longum NCC2705 is mediated by an ATP-binding cassette transporter. J Biol Chem 287:357–367. https://doi.org/10.1074/jbc.M111.266213
Xu D, Bechtner J, Behr J, Eisenbach L, Geißler AJ, Vogel RF (2019a) Lifestyle of Lactobacillus hordei isolated from water kefir based on genomic, proteomic and physiological characterization. Int J Food Microbiol 290:141–149. https://doi.org/10.1016/j.ijfoodmicro.2018.10.004
Xu D, Behr J, Geißler AJ, Bechtner J, Ludwig C, Vogel RF (2019b) Label-free quantitative proteomic analysis reveals the lifestyle of Lactobacillus hordei in the presence of Sacchromyces cerevisiae. Int J Food Microbiol 294:18–26. https://doi.org/10.1016/j.ijfoodmicro.2019.01.010
Yu NY, Wagner JR, Laird MR, Melli G, Rey S, Lo R, Dao P et al (2010) PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes. Bioinformatics 26:1608–1615. https://doi.org/10.1093/bioinformatics/btq249
Funding
Part of this work was supported by by the German Ministry of Economics and Technology (via AiF) and Wifoe (Wissenschaftsförderung der Deutschen Brauwirtschaft e.V., Berlin) project AiF 19180N.
Author information
Authors and Affiliations
Contributions
VPLE and RFV conceived the idea and designed the study, VPLE performed all benchtop and bioinformatics work, data analysis, and wrote the first draft of the manuscript. Both authors contributed to and approved the final version.
Corresponding author
Ethics declarations
Conflict of interest
The authors declare that they have no conflicts of interest.
Human and animal rights statement
This article does not contain any studies with human participants or animals performed by any of the authors.
Additional information
Communicated by Erko Stackebrandt.
Publisher's Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Electronic supplementary material
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Eckel, V.P.L., Vogel, R.F. Genomic and physiological insights into the lifestyle of Bifidobacterium species from water kefir. Arch Microbiol 202, 1627–1637 (2020). https://doi.org/10.1007/s00203-020-01870-7
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00203-020-01870-7