DOI: https://doi.org/10.1099/ijsem.0.006517
Recognition of two subspecies of Lactobacillus amylovorus, with proposal of Lactobacillus amylovorus subsp. animalis subsp. nov. isolated from bovine feces and Lactobacillus amylovorus subsp. amylovorus, and an emended description of Lactobacillus amylovorus
##article.authors##
- Kenji Yamane Innovative Animal Production System, University of Tsukuba,Nihon Shokuhin Kako Co., LTD, Research Institute https://orcid.org/0009-0000-8330-7734
-
Yasuhiro Tanizawa
Department of Informatics, National Institute of Genetics
https://researchmap.jp/ytani
-
Hisami Kobayashi
Institute of Livestock and Grassland Science, National Agriculture and Food Research Organization
https://researchmap.jp/hisamiK
-
Tomomi Kamizono
Institute of Livestock and Grassland Science, National Agriculture and Food Research Organization
https://researchmap.jp/t-kamizono
- Yoichiro Kojima Institute of Livestock and Grassland Science, National Agriculture and Food Research Organization
- Hiroki Takagi Nihon Shokuhin Kako Co., LTD, Research Institute
-
Masanori Tohno
Innovative Animal Production System, University of Tsukuba, Institute of Livestock and Grassland Science, National Agriculture and Food Research Organization, Research Center of Genetic Resources, National Agriculture and Food Research Organization
https://researchmap.jp/mtohno
DOI:
https://doi.org/10.51094/jxiv.521Keywords:
lactic acid bacteria, bacillota, lactobacillus amylovorus subsp. animalis, bovine fevesAbstract
Five novel lactic acid bacterial strains (BF125T, BF186, YK3, YK6, and YK10) were isolated from the fresh feces of Japanese black beef cattle or spent mushroom substrates and characterized using a polyphasic taxonomy method. These strains are rod-shaped, Gram-stain-positive, nonmotile, non-spore-forming, catalase-negative, cytochrome oxidase-negative, facultatively anaerobic, and homofermentative. The cells of BF125T were 0.5–0.7 µm in width and 3.0–7.0 µm in length. Strain BF125T did not produce any gas from glucose; both D- and L-lactate were produced as end products of glucose (D/L, 40:60). Growth occurred at a temperature of 30–45°C (optimum, 37°C), pH of 5.0–8.0 (optimum, pH 6.0), and NaCl concentration of 1.0–3.0% (w/v). The GC content of genomic DNA of strain BF125T was 37.8% (whole-genome analysis). The major fatty acids were C16:0, C18:1 w9c, C19:0 cyclo w8c, and summed feature 10. Strain BF125T retained high similarity of the 16S rRNA gene to the type strain of Lactobacillus amylovorus (99.93%), and the other isolates were also identified as L. amylovorus based on high 16S rRNA gene similarities. Comparison of the core genomes of L. amylovorus strains, including the five isolates, showed that they could be divided into two clusters, and phenotypic differences in fermentability were observed for D-lactose, salicin, and gentiobiose between these two groups. Digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) analyses showed that both categories were below the thresholds for defining subspecies (maximum dDDH value, 77.2%; maximum ANI value, 96.50%). In light of the physiological, genotypic, and phylogenetic evidence, we propose a novel subspecies of L. amylovorus, L. amylovorus subsp. animalis subsp. nov. Type strain: BF125T (= MAFF 212522T = DSM 115528T). Our results also led to the automatic creation of L. amylovorus subsp. amylovorus subsp. nov. and an emended description of the species L. amylovorus.
Conflicts of Interest Disclosure
K. Y. and H. T. are employees of Nihon Shokuhin Kako Co., Ltd.. H. K., T. K., and M. T. received research grants from Nihon Shokuhin Kako Co., Ltd.. The authors declare no conflicts of interest.Downloads *Displays the aggregated results up to the previous day.
References
Hatti-Kaul R, Chen L, Dishisha T, Enshasy HE. Lactic acid bacteria: from starter cultures to producers of chemicals. FEMS Microbiol Lett 2018;365(20). doi:10.1093/femsle/fny213
Gilliland SE. Health and nutritional benefits from lactic acid bacteria. FEMS Microbiol Rev 1990;7(1-2):175-188. doi:10.1111/j.1574-6968.1990.tb04887.x
Zheng J, Wittouck S, Salvetti E, Franz C, Harris HMB et al. A taxonomic note on the genus Lactobacillus: Description of 23 novel genera, emended description of the genus Lactobacillus Beijerinck 1901, and union of Lactobacillaceae and Leuconostocaceae. Int J Syst Evol Microbiol 2020;70(4):2782-2858. doi:10.1099/ijsem.0.004107
Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P et al. DNA–DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007;57(1):81-91. doi:10.1099/ijs.0.64483-0
Stackebrandt E, Goebel BM. Taxonomic note: n place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Evol Microbiol 1994;44(4):846-849. doi:10.1099/00207713-44-4-846
Tohno M, Tanizawa Y, Kojima Y, Sakamoto M, Ohkuma M et al. Lactobacillus corticis sp. nov., isolated from hardwood bark. Int J Syst Evol Microbiol 2021;71(7). doi:10.1099/ijsem.0.004882
Parte AC, Sardà Carbasse J, Meier-Kolthoff JP, Reimer LC, Göker M. List of prokaryotic names with standing in nomenclature (LPSN) moves to the DSMZ. Int J Syst Evol Microbiol 2020;70(11):5607-5612. doi:10.1099/ijsem.0.004332
Nakamura LK. Lactobacillus amylovorus, a new starch-hydrolyzing species from cattle waste-corn fermentations. Int J Syst Evol Microbiol 1981;31(1):56-63. doi:10.1099/00207713-31-1-56
De Vuyst L, Callewaert R, Crabbé K. Primary metabolite kinetics of bacteriocin biosynthesis by Lactobacillus amylovorus and evidence for stimulation of bacteriocin production under unfavourable growth conditions. Microbiology 1996;142(4):817-827. doi:10.1099/00221287-142-4-817
Contreras BG, De Vuyst L, Devreese B, Busanyova K, Raymaeckers J et al. Isolation, purification, and amino acid sequence of lactobin A, one of the two bacteriocins produced by Lactobacillus amylovorus LMG P-13139. Appl Environ Microbiol 1997;63(1):13-20. doi:doi:10.1128/aem.63.1.13-20.1997
Romain M, Patrick D, Christine Z, Anne MP. Evaluation of Lactobacillus sobrius/L. amylovorus as a new microbial marker of pig manure. Appl Environ Microbiol 2010;76(5):1456-1461. doi:doi:10.1128/AEM.01895-09
Nakamura F, Ishida Y, Aihara K, Sawada D, Ashida N et al. Effect of fragmented Lactobacillus amylovorus CP1563 on lipid metabolism in overweight and mildly obese individuals: a randomized controlled trial. Microb Ecol Health Dis 2016;27:30312. doi:10.3402/mehd.v27.30312
Peyer LC, Bellut K, Lynch KM, Zarnkow M, Jacob F et al. Impact of buffering capacity on the acidification of wort by brewing-relevant lactic acid bacteria. J Inst Brew 2017;123(4):497-505. doi:10.1002/jib.447
Xu Z, He H, Zhang S, Guo T, Kong J. Characterization of feruloyl esterases produced by the Four Lactobacillus species: L. amylovorus, L. acidophilus, L. farciminis and L. fermentum, Isolated from ensiled corn stover. Front Microbiol 2017;8. doi:10.3389/fmicb.2017.00941
Tohno M, Tanizawa Y, Kojima Y, Sakamoto M, Nakamura Y et al. Lactobacillus salitolerans sp. nov., a novel lactic acid bacterium isolated from spent mushroom substrates. Int J Syst Evol Microbiol 2019;69(4):964-969. doi:10.1099/ijsem.0.003224
Tohno M, Tanizawa Y, Kojima Y, Sakamoto M, Ohkuma M, et al. Lentilactobacillus fungorum sp. nov., isolated from spent mushroom substrates. Int J Syst Evol Microbiol 2021;71(12). doi:10.1099/ijsem.0.005184
Lane DJ. 16S/23S rRNA sequencing. In Stackebrandt E, Goodfellow M. (editors). Nucleic Acid Techniques in Bacterial Systematics 175 Chichester, UK: John Wiley and Sons 1991:115.
Tazawa J, Kobayashi H, Tanizawa Y, Uchino A, Tanaka F et al. Clostridium folliculivorans sp. nov., isolated from soil samples of an organic paddy in Japan. Int J Syst Evol Microbiol 2023;73(4). doi:10.1099/ijsem.0.005876
Yoon SH, Ha SM, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 2017;67(5):1613-1617. doi:10.1099/ijsem.0.001755
Kim M, Oh HS, Park SC, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 2014;64(Pt 2):346-351. doi:10.1099/ijs.0.059774-0
Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: Improvements in performance and usability. Mol Bio Evol 2013;30(4):772-780. doi:10.1093/molbev/mst010
Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 2009;25(15):1972-1973. doi:10.1093/bioinformatics/btp348
Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980;16(2):111-120. doi:10.1007/BF01731581
Simonsen M, Mailund T, Pedersen CNS. Rapid Neighbour-Joining. . In proceedings of the 8th Workshop in Algorithms in Bioinformatics (WABI):113-122: Springer Verlag, ; October 2008.doi:10.1007/978-3-540-87361-7_10
Nguyen LT, Schmidt HA, Von Haeseler A, Minh BQ. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol 2015;32(1):268-274. doi:10.1093/molbev/msu300
Kalyaanamoorthy S, Minh BQ, Wong TKF, von Haeseler A, Jermiin LS. ModelFinder: fast model selection for accurate phylogenetic estimates. Nat Methods 2017;14(6):587-589. doi:10.1038/nmeth.4285
Tamura K, Stecher G, Kumar S. MEGA11: molecular evolutionary genetics analysis version 11. Mol Biol Evol 2021;38(7):3022-3027. doi:10.1093/molbev/msab120
Letunic I, Bork P. Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Research 2021;49(W1):W293-W296. doi:10.1093/nar/gkab301
Tohno M, Tanizawa Y, Sawada H, Sakamoto M, Ohkuma M et al. A novel species of lactic acid bacteria, Ligilactobacillus pabuli sp. nov., isolated from alfalfa silage. Int J Syst Evol Microbiol 2022;72(10). doi:10.1099/ijsem.0.005587
Kobayashi H, Tanizawa Y, Yagura M, Sakamoto M, Ohkuma M et al. Clostridium zeae sp. nov., isolated from corn silage. Int J Syst Evol Microbiol 2021;71(11). doi:10.1099/ijsem.0.005088
Chen S, Zhou Y, Chen Y, Gu J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 2018;34(17):i884-i890. doi:10.1093/bioinformatics/bty560
Souvorov A, Agarwala R, Lipman DJ. SKESA: strategic k-mer extension for scrupulous assemblies. Genome Biol 2018;19(1):153. doi:10.1186/s13059-018-1540-z
Tanizawa Y, Fujisawa T, Nakamura Y. DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication. Bioinformatics 2018;34(6):1037-1039. doi:10.1093/bioinformatics/btx713
Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 2015;25(7):1043-1055. doi:10.1101/gr.186072.114
Dereeper A, Summo M, Meyer DF. PanExplorer: a web-based tool for exploratory analysis and visualization of bacterial pan-genomes. Bioinformatics 2022;38(18):4412-4414. doi:10.1093/bioinformatics/btac504
Perrin A, Rocha EPC. PanACoTA: a modular tool for massive microbial comparative genomics. NAR Genom Bioinform 2021;3(1):lqaa106. doi:10.1093/nargab/lqaa106
Amat S, Holman DB, Timsit E, Gzyl KE, Alexander TW. Draft genome sequences of 14 Lactobacillus, Enterococcus, and Staphylococcus isolates from the nasopharynx of healthy feedlot cattle. Microbiol Resour Announc 2019;8(34). doi:10.1128/mra.00534-19
Konstantinov SR, Poznanski E, Fuentes S, Akkermans AD, Smidt H et al. Lactobacillus sobrius sp. nov., abundant in the intestine of weaning piglets. Int J Syst Evol Microbiol 2006;56(Pt 1):29-32. doi:10.1099/ijs.0.63508-0
Jakava VM, Murros A, Palva A, Björkroth KJ. Lactobacillus sobrius Konstantinov et al. 2006 is a later synonym of Lactobacillus amylovorus Nakamura 1981. Int J Syst Evol Microbiol 2008;58(Pt 4):910-913. doi:10.1099/ijs.0.65432-0
Richter M, Rosselló-Móra R, Oliver Glöckner F, Peplies J. JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 2016;32(6):929-931. doi:10.1093/bioinformatics/btv681
Meier-Kolthoff JP, Carbasse JS, Peinado-Olarte RL, Göker M. TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes. Nucleic Acids Res 2022;50(D1):D801-d807. doi:10.1093/nar/gkab902
Sutton GG, Brinkac LM, Clarke TH, Fouts DE. Enterobacter hormaechei subsp. hoffmannii subsp. nov., Enterobacter hormaechei subsp. xiangfangensis comb. nov., Enterobacter roggenkampii sp. nov., and Enterobacter muelleri is a later heterotypic synonym of Enterobacter asburiae based on computational analysis of sequenced Enterobacter genomes. F1000Res 2018;7:521. doi:10.12688/f1000research.14566.2
Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 2009;106(45):19126-19131. doi:10.1073/pnas.0906412106
Tanizawa Y, Fujisawa T, Kaminuma E, Nakamura Y, Arita M. DFAST and DAGA: web-based integrated genome annotation tools and resources. Biosci Microbiota Food Health 2016;35(4):173-184. doi:10.12938/bmfh.16-003
Meier-Kolthoff JP, Hahnke RL, Petersen J, Scheuner C, Michael V et al. Complete genome sequence of DSM 30083(T), the type strain (U5/41(T)) of Escherichia coli, and a proposal for delineating subspecies in microbial taxonomy. Stand Genomic Sci 2014;9:2. doi:10.1186/1944-3277-9-2
Moldoveanu SC. Chapter 11 - Pyrolysis of Carbohydrates. In: Moldoveanu SC (editor). Pyrolysis of Organic Molecules (Second Edition): Elsevier; 2019. pp. 419-482.
Badenhuizen N, Bose RJ, Kirkwood S, Lewis BA, Smith F. Isolation of gentiobiose from gentian root. J Org Chem 1964;29(7):2079-2080. doi:10.1021/jo01030a548
Jenness R, Regehr EA, Sloan RE. Comparative biochemical studies of milks— II. Dialyzable carbohydrates. Comp Biochem Physiol 1964;13(4):339-352. doi:10.1016/0010-406X(64)90028-3
Leong-Morgenthaler P, Zwahlen MC, Hottinger H. Lactose metabolism in Lactobacillus bulgaricus: analysis of the primary structure and expression of the genes involved. J Bacteriol 1991;173(6):1951-1957. doi:doi:10.1128/jb.173.6.1951-1957.1991
Thomas DL, Joanna ZA, Tim KJ, Rikke HL, Mette B et al. Culture-independent analysis of gut bacteria: the pig gastrointestinal tract microbiota revisited. App Environ Microbiol 2002;68(2):673-690. doi:doi:10.1128/AEM.68.2.673-690.2002
Wang W, Hu H, Zijlstra RT, Zheng J, Gänzle MG. Metagenomic reconstructions of gut microbial metabolism in weanling pigs. Microbiome 2019;7(1):48. doi:10.1186/s40168-019-0662-1
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Kenji Yamane
Yasuhiro Tanizawa
Hisami Kobayashi
Tomomi Kamizono
Yoichiro Kojima
Hiroki Takagi
Masanori Tohno
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