Sporolactobacillus mangiferae sp. nov., a spore-forming lactic acid bacterium isolated from tree bark in Thailand.

A Gram-stain-positive, facultatively anaerobic and endospore-forming rod-shaped bacterium, designed strain CPB3-1T, was isolated from tree bark. This homofermentative strain produced dl-lactic acid from glucose. It grew at 20-45 °C, pH 4.0-9.5 and in 0-3.0 % (w/v) NaCl. It contained meso-diaminopimelic acid in cell-wall peptidoglycan and had menaquinone with seven isoprene units (MK-7) as the predominant component. The major fatty acid was anteiso-C17 : 0. The polar lipids were phosphatidylglycerol, diphosphatidylglycerol, an unknown phospholipid and an unknown lipid. Based on the results of 16S rRNA gene sequence analysis, strain CPB3-1T belonged to the genus Sporolactobacillus and was closely related to Sporolactobacillus kofuensis DSM 11701T and Sporolactobacillus spathodeae BK117-1T (both 96.7 % similarity), Sporolactobacillus inulinus NRIC 1133T and Sporolactobacillus terrae DSM 11697T (both 96.6 % similarity), and Sporolactobacillus shoreicorticis MK21-7T, Sporolactobacillus laevolacticus DSM 442T, Sporolactobacillus shoreae BK92T and Sporolactobacillus pectinivorans GD201205T (all 95.8-96.5 % similarity). The draft genome of strain CPB3-1T contained 2 930 919 bps with 3117 coding genes. The DNA G+C content was 45.1 mol%. The digital DNA-DNA hybridization values between strain CPB3-1T and closely related type strains were 19.2-24.0 %. The average nucleotide identity (84.0-87.6 %) and average amino acid identity (66.5-76.3 %) values were lower than the cut-off values for species delineation. Strain CPB3-1T was clearly distinguished from related Sporolactobacillus species based on its phenotypic and chemotaxonomic characteristics, 16S rRNA gene sequence similarity and the results of draft genome analysis. Therefore, the strain represents a novel species of the genus Sporolactobacillus, for which the name Sporolactobacillus mangiferae sp. nov. is proposed. The type strain is CPB3-1T (=JCM 35082T=TISTR 10004T).

[1]  Mohammad Alanjary,et al.  AutoMLST: an automated web server for generating multi-locus species trees highlighting natural product potential , 2019, Nucleic Acids Res..

[2]  Sudhir Kumar,et al.  MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms. , 2018, Molecular biology and evolution.

[3]  A. Parte.  LPSN - List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on. , 2018, International journal of systematic and evolutionary microbiology.

[4]  Jia Gu,et al.  fastp: an ultra-fast all-in-one FASTQ preprocessor , 2018, bioRxiv.

[5]  N. Thongchul,et al.  Sporolactobacillus shoreicorticis sp.nov., a lactic acid-producing bacterium isolated from tree bark. , 2017, International journal of systematic and evolutionary microbiology.

[6]  Quanxue Lan,et al.  Sporolactobacillus pectinivorans sp. nov., an anaerobic bacterium isolated from spoiled jelly. , 2016, International journal of systematic and evolutionary microbiology.

[7]  Jörg Peplies,et al.  JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison , 2015, Bioinform..

[8]  M. Ohkuma,et al.  Sporolactobacillus shoreae sp. nov. and Sporolactobacillus spathodeae sp. nov., two spore-forming lactic acid bacteria isolated from tree barks in Thailand. , 2015, International journal of systematic and evolutionary microbiology.

[9]  Alexander F. Auch,et al.  Genome sequence-based species delimitation with confidence intervals and improved distance functions , 2013, BMC Bioinformatics.

[10]  N. Thongchul,et al.  Characterization of lactic acid producing bacteria from Thai sources , 2013 .

[11]  Sergey I. Nikolenko,et al.  SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing , 2012, J. Comput. Biol..

[12]  J. Chun,et al.  Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. , 2012, International journal of systematic and evolutionary microbiology.

[13]  K. Goto,et al.  Sporolactobacillus putidus sp. nov., an endospore-forming lactic acid bacterium isolated from spoiled orange juice. , 2010, International journal of systematic and evolutionary microbiology.

[14]  R. Rosselló-Móra,et al.  Shifting the genomic gold standard for the prokaryotic species definition , 2009, Proceedings of the National Academy of Sciences.

[15]  H. Oh,et al.  Sporolactobacillus vineae sp. nov., a spore-forming lactic acid bacterium isolated from vineyard soil. , 2008, International journal of systematic and evolutionary microbiology.

[16]  Rick L. Stevens,et al.  The RAST Server: Rapid Annotations using Subsystems Technology , 2008, BMC Genomics.

[17]  A. Nakamura,et al.  Tuberibacillus calidus gen. nov., sp. nov., isolated from a compost pile and reclassification of Bacillus naganoensis Tomimura et al. 1990 as Pullulanibacillus naganoensis gen. nov., comb. nov. and Bacillus laevolacticus Andersch et al. 1994 as Sporolactobacillus laevolacticus comb. nov. , 2006, International journal of systematic and evolutionary microbiology.

[18]  D. Sorokin.  Is there a limit for high-pH life? , 2005, International journal of systematic and evolutionary microbiology.

[19]  K. Komagata,et al.  Lactic acid bacteria isolated from soy sauce mash in Thailand. , 2002, The Journal of general and applied microbiology.

[20]  K. Komagata,et al.  Lactic acid bacteria found in fermented fish in Thailand. , 1998, The Journal of general and applied microbiology.

[21]  J. Thompson,et al.  The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. , 1997, Nucleic acids research.

[22]  K. Komagata,et al.  Proposal of Sporolactobacillus nakayamae subsp. nakayamae sp. nov., subsp. nov., Sporolactobacillus nakayamae subsp. racemicus subsp. nov., Sporolactobacillus terrae sp. nov., Sporolactobacillus kofuensis sp. nov., and Sporolactobacillus lactosus sp. nov. , 1997 .

[23]  D. Claus,et al.  Description of Bacillus laevolacticus (ex Nakayama and Yanoshi 1967) sp. nov., nom. rev. , 1994 .

[24]  William R. Taylor,et al.  The rapid generation of mutation data matrices from protein sequences , 1992, Comput. Appl. Biosci..

[25]  N. Saitou,et al.  The neighbor-joining method: a new method for reconstructing phylogenetic trees. , 1987, Molecular biology and evolution.

[26]  J. Felsenstein.  CONFIDENCE LIMITS ON PHYLOGENIES: AN APPROACH USING THE BOOTSTRAP , 1985, Evolution; international journal of organic evolution.

[27]  D. Minnikin,et al.  AN INTEGRATED PROCEDURE FOR THE EXTRACTION OF BACTERIAL ISOPRENOID QUINONES AND POLAR LIPIDS , 1984 .

[28]  J. Felsenstein,et al.  EVOLUTIONARY TREES FROM GENE FREQUENCIES AND QUANTITATIVE CHARACTERS: FINDING MAXIMUM LIKELIHOOD ESTIMATES , 1981, Evolution; international journal of organic evolution.

[29]  L. Forbes.  Rapid Flagella Stain , 1981, Journal of clinical microbiology.

[30]  M. Collins,et al.  Distribution of menaquinones in actinomycetes and corynebacteria. , 1977, Journal of general microbiology.

[31]  J. Staneck,et al.  Simplified Approach to Identification of Aerobic Actinomycetes by Thin-Layer Chromatography , 1974 .

[32]  J. Farris,et al.  Quantitative Phyletics and the Evolution of Anurans , 1969 .

[33]  J. Suzuki,et al.  SPOROLACTOBACILLUS NOV. SUBGEN. , 1963 .

[34]  R. Slepecky,et al.  ALTERATIONS IN METAL CONTENT OF SPORES OF BACILLUS MEGATERIUM AND THE EFFECT ON SOME SPORE PROPERTIES , 1959, Journal of bacteriology.

[35]  H. J. Conn,et al.  Methods Of Gram Staining , 1923 .

[36]  P. Vandamme,et al.  DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. , 2007, International journal of systematic and evolutionary microbiology.

[37]  Marguerita Sasser,et al.  Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids Technical Note # 101 , 2001 .

[38]  Chia-Liang Lai,et al.  ON THE SPORE FORMATION OF SPOROLACTOBACILLUS INULINUS , 1967 .

[39]  O. Nakayama,et al.  SPORE-BEARING LACTIC ACID BACTERIA ISOLATED FROM RHIZOSPHERE:I. TAXONOMIC STUDIES ON BACILLUS LAEVOLACTICUS NOV. SP. AND BACILLUS RACEMILACTICUS NOV. SP. , 1967 .

[40]  K. Miura,et al.  PREPARATION OF TRANSFORMING DEOXYRIBONUCLEIC ACID BY PHENOL TREATMENT. , 1963, Biochimica et biophysica acta.