International Journal of Systematic and Evolutionary Microbiology (2015), 65, 2769– 2773 DOI 10.1099/ijs.0.000336 Reclassification of Bacillus invictae as a later heterotypic synonym of Bacillus altitudinis Yang Liu, Qiliang Lai, Juan Du and Zongze Shao Correspondence Zongze Shao [email protected] State Key Laboratory Breeding Base of Marine Genetic Resources; Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, SOA; Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources; Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, PR China The aim of this study was to reclarify the taxonomic status of strain Bacillus invictae Bi.FFUP1T by performing comparative analyses with the other four type strains within the Bacillus pumilus group. The digital DNA–DNA hybridization (dDDH) and average nucleotide identity (ANI) values between strains B. invictae Bi.FFUP1 T (5DSMZ 26896T5MCCC 1A07089T), B. altitudinis 41KF2bT (5DSMZ 21631T5MCCC 1A06452T), B. safensis FO-36bT (5DSMZ 19292T5MCCC 1A6451T), B. pumilus ATCC 7061T (5DSMZ 27T5MCCC 1A06453T) and B. xiamenensis HYC-10T (5MCCC 1A00008T) were, respectively, 82.90 % and 98.10 %, which are greater than the thresholds for bacterial species delineation, suggesting that they should belong to the same species, while the dDDH and ANI values between strain B. invictae DSMZ 26896T and the other three type strains within the B. pumilus group were below the respective thresholds of 70 % and 95 %. Meanwhile, B. invictae DSMZ 26896T and B. altitudinis 41KF2bT shared 98.7 % gyrB gene sequence similarity based on resequencing, whereas strain B. invictae DSMZ 26896T shared low similarities (,95 %) with the other three type strains. In addition, in comparison with those from the other three type strains, phenotypic data of B. invictae DSMZ 26896T and B. altitudinis 41KF2bT, including API 20NE, API ZYM, Biolog GN2 and API 50CHB tests, showed slight differences. The data from these combined genotypic and phenotypic analyses suggest that Bacillus invictae Branquinho et al. 2014 should be regarded as a later heterotypic synonym of Bacillus altitudinis Shivaji et al. 2006. Bacillus invictae was isolated from a contaminated health product in Portugal and then proposed, on the basis of data from a polyphasic taxonomic approach, to represent a novel species of the Bacillus pumilus group with a sole strain (Branquinho et al., 2014a). Therefore, the B. pumilus group comprises five species at the time of writing, including B. pumilus, B. safensis (Satomi et al., 2006), B. altitudinis (Shivaji et al., 2006), B. xiamenensis (Lai et al., 2014) and B. invictae (Branquinho et al., 2014a). However, these closely related species were not discriminated accurately on the basis of 16S rRNA gene sequence. Several reliable and generally accepted typing methods, such as single housekeeping gene sequence analysis (i.e. gyrB, rpoB) (Branquinho et al., 2014b), multilocus sequence analysis (Liu et al., 2013) and matrix-assisted laser desorption/ionization time-of-flight MS (Branquinho et al., Abbreviations: ANI, average nucleotide identity; dDDH; digital DNA– DNA hybridization; DDH, DNA–DNA hybridization. The GenBank/EMBL/DDBJ accession number for the draft genome sequence of Bacillus invictae DSMZ 26896T is JXAI00000000. 000336 G 2015 IUMS 2014c), provide a promising avenue for identification of strains within the B. pumilus group. According to Branquinho et al. (2014a), two type strains, B. invictae Bi.FFUP1T and B. altitudinis 41KF2bT, shared a DNA–DNA hybridization (DDH) value of 61.7 % and 98.7 % gyrB gene sequence similarity. But, in the study of Liu et al. (2013), the range of 95–96 % gyrB gene sequence similarity was proposed as an interspecies gap for the B. pumilus group. Therefore, in order to address this contradiction, it was necessary to redetermine the taxonomic status of the type strain B. invictae Bi.FFUP1T using a variety of genotypic and phenotypic criteria. Four type strains, B. invictae DSMZ 26896T (5Bi.FFUP1T5 MCCC 1A07089T), B. altitudinis DSMZ 21631T (541KF2bT5 MCCC 1A06452T), B. safensis DSMZ 19292T (5FO-36bT 5MCCC 1A6451T) and B. pumilus DSMZ 27T (5ATCC 7061T 5 MCCC 1A06453T) originated from the Deutsche Sammlung von Mikroorganismen und Zellkulturen (DSMZ) and were accessioned into the Marine Culture Collection of China (MCCC). The type strain B. xiamenensis MCCC 1A00008T (5HYC-10T) was obtained from the MCCC. The resequenced 16S rRNA and gyrB genes of strain Downloaded from www.microbiologyresearch.org by IP: 88.99.165.207 On: Sun, 18 Jun 2017 23:31:58 Printed in Great Britain 2769 Y. Liu and others B. invictae DSMZ 26896T were identical with previous results (Branquinho et al., 2014a), suggesting reliability of this strain in this study. In this study, the draft genome sequence of strain B. invictae Bi.FFUP1T was determined by Shanghai Majorbio Bio-pharm Technology (Shanghai, China), using Solexa paired-end (500 bp library) sequencing technology. A total of 500 Mbp clean data were generated to reach about 100-fold depth of coverage with an Illumina/Solexa Genome Analyser IIx. The clean data were assembled by SOAPdenovo2 (Luo et al., 2012). Subsequently the digital DNA–DNA hybridization (dDDH) and average nucleotide identity (ANI) values between strain B. invictae DSMZ 26896T and the other four type strains, B. altitudinis 41KF2bT, B. xiamenensis HYC-10T, B. safensis FO-36bT and B. pumilus ATCC 7061T, were respectively calculated using a web tool of the genome-to-genome distance calculator (GGDC2.0) (Meier-Kolthoff et al., 2013) and an EzGenome web service based on the algorithm of Goris et al. (2007). Meanwhile, similarities of gyrB gene sequence between strain B. invictae DSMZ 26896T and the other four type strains were determined using DNAMAN version 8 (Lynnon). In addition, phenotypic comparisons were carried out with API 20NE, API ZYM, API 50CHB (bioMérieux) and Biolog GN2 systems according to the manufacturers’ instructions. The 70 % DDH value has served as a gold standard for species delineation in the classification of prokaryotes (Wayne et al., 1987). Consequently, the draft genome sequence of strain B. invictae DSMZ 26896T was obtained (GenBank accession number: JXAI00000000). As shown in Table 1, the dDDH values between strain B. invictae DSMZ 26896T and B. altitudinis 41KF2bT, B. xiamenensis HYC-10T, B. safensis FO-36bT and B. pumilus ATCC 7061T were, respectively, 82.9 %, 43.8 %, 36.5 % and 36.2 %, suggesting that strain B. invictae DSMZ 26896T should belong to the species B. altitudinis. However, the dDDH value between strain B. invictae DSMZ 26896T and these four type strains were, respectively, 61.9 %, 61.7 %, 49.9 % and 39.6 % in the original study (Branquinho et al., 2014a). Generally, such discrepancy may be caused by use of the different methods. In contrast to the dDDH, wet-lab DDH is much more likely to yield imprecise and error-prone results owing to dependency on the reannealing temperature used or the particular method employed by a laboratory (Gevers et al., 2005). Therefore, genome sequence-based dDDH has been proposed to replace wet-lab DDH to be used in microbial taxonomy (Auch et al., 2010; Meier-Kolthoff et al., 2013). Meanwhile, the ANI values between strain B. invictae DSMZ 26896T and B. altitudinis 41KF2bT, B. xiamenensis HYC-10T, B. safensis FO-36bT and B. pumilus ATCC 7061T were 98.1 %, 91.2 %, 88.9 % and 88.6 %, respectively. According to the standard ANI criteria for species definition (95–96 %) (Richter & Rosselló-Móra, 2009), two type strains, B. invictae DSMZ 26896T and B. altitudinis 41KF2bT, should be attributed to the same species. In addition, the similarity of gyrB gene sequences between strains B. invictae DSMZ 26896T and B. altitudinis 41KF2bT was 98.7 %, while similarities of the gyrB gene sequence between strain B. invictae DSMZ 26896T and the other three type strains were below 95 %. As a result, in the light of the proposals of 95 % gyrB gene sequence similarity corresponding to 70 % DNA–DNA relatedness among species of the Bacillus subtilis group (Wang et al., 2007) and an interspecies gap of 95–96 % gyrB gene sequence similarity within the B. pumilus group (Liu et al., 2013), strain B. invictae DSMZ 26896T fell into the species B. altitudinis. The genomic DNA G+C content of strain B. invictae DSMZ 26896T was 41.1 mol% based on its draft genome sequence and accordant with the previously reported value of 41 mol% (Branquinho et al., 2014a). In comparison with genotype, phenotype has played a vital role in identification and classification of bacteria and archaea (Kämpfer, 2014). Therefore, phenotypic characteristics of all type strains within the B. pumilus group were analysed. The results are shown in Tables 2 and 3. In API 20NE and API ZYM tests, the results of our study are almost consistent with those of Branquinho et al. (2014a). Two type strains, B. invictae DSMZ 26896T and B. altitudinis 41KF2bT, revealed more consistent phenotypic features relative to the other three type strains. In Biolog tests, similar cases were also encountered. In contrast, more differences between our results and those of Branquinho et al. (2014a) were exhibited in API 50CHB tests. To our knowledge, inconsistent results from the same strains used in different studies are normal and understandable. We believed that some reasons may explain these discrepancies. On the one hand, several results of API 50CHB in the study Table 1. dDDH and ANI values, and gyrB gene sequence similarities between strain B. invictae DSMZ 26896T and reference strains Strain B. B. B. B. B. T invictae DSMZ 26896 altitudinis DSMZ 21631T pumilus ATCC 7061T xiamenensis HYC-10T safensis FO-36bT 2770 Accession no. dDDH ANIm gyrB JXAI00000000 ASJC00000000 ABRX01000000 AMSH00000000 ASJD00000000 100 % 82.9 % 36.2 % 43.8 % 36.5 % 100 % 98.1 % 88.6 % 91.2 % 88.9 % 100 % 98.7 % 94.3 % 91.7 % 90.8 % Downloaded from www.microbiologyresearch.org by International Journal of Systematic and Evolutionary Microbiology 65 IP: 88.99.165.207 On: Sun, 18 Jun 2017 23:31:58 Bacillus invictae is a later synonym of B. altitudinis Table 2. Characteristics of the five type strains within the B. pumilus group Strains: 1, B. invictae DSMZ 26896T; 2, B. altitudinis DSMZ 21631T; 3, B. xiamenensis HYC-10T; 4, B. safensis FO-36bT; 5, B. pumilus ATCC 7061T. Data for strains 1 and 2 were from this study, while data for strains 3, 4 and 5 were from the study by Lai et al. (2014). In API 20NE tests, all strains were positive for b-glucosidase (aesculin hydrolysis), gelatin hydrolysis, b-galactosidase, and utilization of D -glucose, D -mannitol, D -mannose, malic acid, N-acetylglucosamine, potassium gluconate and trisodium citrate; all strains were negative for reduction of nitrate, denitrification, indole production, arginine dihydrolase, urease, and utilization of adipic acid and capric acid. In API ZYM tests, all strains were positive for alkaline phosphatase, acid phosphatase, esterase (C4), esterase lipase (C8), naphthol-AS-BI-phosphoamidase and b-glucosidase; all strains were negative for N-acetyl-b-glucosaminidase, a-fucosidase, a-galactosidase and b-glucuronidase. In Biolog tests, all strains were able to utilize acetic acid, itaconic acid, N-acetyl-D -glucosamine, adonitol, cellobiose, L -fucose, gentiobiose, lactulose, D -mannitol, L -rhamnose, D -sorbitol, formic acid, D -glucosaminic acid, c-hydroxybutyric acid, D -alanine, c-aminobutyric acid, inosine, uridine, thymidine and phenylethylamine; none of the strains could utilize a-cyclodextrin, D -fructose, dextrin, D -mannose, Tween 80, N-acetyl-D -galactosamine, a-D -glucose, melibiose, methyl b-D -glucoside, sucrose, turanose, xylitol, D -galacturonic acid, D -glucuronic acid, b-hydroxybutyric acid, a-ketoglutaric acid, a-ketovaleric acid, malonic acid, D -saccharic acid, bromosuccinic acid, succinamic acid, glucuronamide, L -alaninamide, L -glutamic acid, glycyl-L -aspartic acid, L -histidine, L -threonine, glycerol, DL a-glycerol phosphate or glucose 1-phosphate. +, Positive; 2, negative; W , weakly positive. Characteristic API 20NE D -Glucose fermentation, maltose L -Arabinose API ZYM Cystine aminopeptidase, trypsin a-Mannosidase Leucine aminopeptidase Lipase (C14) Valine aminopeptidase a-Chymotrypsin a-Glucosidase b-Galactosidase Biolog cis-Aconitic acid, putrescine i-Erythritol, L -alanine, hydroxy-L -proline D -Psicose, citric acid Monomethyl succinate a-Lactose Quinic acid Succinic acid, D -serine Glycogen, L -arabinose D -Galactonic acid lactone a-Hydroxybutyric acid Urocanic acid D -Arabitol Methyl pyruvate D,L -Lactic acid Tween 40 Maltose L -Alanyl glycine D -Trehalose, a-ketobutyric acid, L -pyroglutamic acid D -Gluconic acid, L -leucine, 2-aminoethanol Propionic acid L -Proline p-Hydroxyphenylacetic acid D -Raffinose, glucose 6-phosphate L -Phenylalanine L -Aspartic acid L -Serine D -Galactose Sebacic acid, L -asparagine myo-inositol http://ijs.sgmjournals.org 1 2 3 4 5 2 + 2 + 2 2 + + 2 + 2 2 2 2 2 W W + 2 + W W W W W W W W + + + + + + + W W W W W W 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 + + + + + + 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 + + + 2 2 2 2 2 2 2 + + + + + + + W W 2 + W W W W W Downloaded from www.microbiologyresearch.org by IP: 88.99.165.207 On: Sun, 18 Jun 2017 23:31:58 W W W W W W 2 W 2 + W + + + 2 2 W W 2 + 2 + 2 + + + W W W + + + + W + + + 2 W 2 W + + 2 W + W W W + W W 2 2 2 + + 2 + + + + + + + 2 + W 2 + 2 + 2 + + W + + + + 2 W 2771 Y. Liu and others Table 2. cont. Characteristic 1 2 3 4 5 2,3-Butanediol Glycyl-L -glutamic acid L -Ornithine D,L -Carnitine DNA G+C content (mol%) W W W 2 2 + + W W W W W W + 2 + 41.7 W W W W 41.4 41.3 41.3 41.6 Nevertheless, in comparison with the results in Table 3, we discovered that our results agreed almost entirely with those from the literature, while the results of Branquinho et al. (2014a) did not. Therefore, our results of API 50 CHB tests of these strains are more reliable. In brief, the two strains, B. invictae DSMZ 26896T and B. altitudinis 41KF2bT, are difficult to distinguish in terms of a small number of differences of Branquinho et al. (2014a) are ambiguous, such as D xylose (+/2), D -galactose (+/2), methyl a-D -mannoside (+/2) and amygdalin (+/2). On the other hand, some strains being clones can lose some traits as a result of mutations during their storage and growth. In addition, it is possible to bring about some differences during manual operation in tests and determination of results. Table 3. Profiles of acid production from carbohydrates of the five type strains within the B. pumilus group Strains: 1, B. invictae DSMZ 26896T; 2, B. altitudinis DSMZ 21631T; 3, B. xiamenensis MCCC 1A00008T; 4, B. safensis DSMZ 19292T; 5, B. pumilus DSMZ 27T. Data from this study except where indicated otherwise. All strains can produce acid by use of glycerol, D -ribose, D -fructose, arbutin, aesculin, salicin, sucrose and trehalose; none of the strains produce acid using L -xylose, D -adonitol, methyl b-D -xyloside, L -sorbose, dulcitol, inulin, melezitose, glycogen, xylitol, D -lyxose, D -fucose, L -fucose, D -arabitol, L -arabitol, gluconate, 2-ketogluconate or 5-ketogluconate. +, Positive; 2, negative; W , weakly positive, V , variable. Carbohydrate D -Turanose Inositol Lactose Melibiose Erythritol Raffinose Methyl-D -glucopyranoside Maltose L -Rhamnose D -Sorbitol D -Arabinose Starch D -Mannitol N-Acetylglucosamine D -Glucose D -Tagatose L -Arabinose D -Mannose Cellobiose D -Ribose Gentiobiose D -Xylose Methyl a-D -mannoside D -Galactose Amygdalin 1* 1 2* 2 3* 3 4* 4 4D 5* 5 5d 2 2 2 2 2 2 2 2 2 2 2 2 2 2 + + + + + + + +/2 +/2 +/2 +/2 2 2 2 2 2 2 2 2 2 2 2 2 + 2 2 2 2 2 2 2 + + + + + + 2 2 + + + + + + + + + + 2 2 2 2 2 2 2 2 2 2 2 + 2 2 + + 2 + + 2 2 + + + + + + + + + + 2 2 2 2 2 2 2 2 2 2 2 2 + + + 2 2 + + + + 2 2 2 + 2 2 2 2 + 2 2 2 2 2 + 2 + 2 + + + 2 + + + + + + + + + 2 2 2 + + + 2 2 2 2 + + + + + + + + + + + + + + + 2 + 2 2 + + 2 + 2 2 + 2 + 2 2 + + + 2 + + + + + + + + 2 2 2 31 (+) 11 (2) 14 (2) 15 (2) 1 (2) 15 (2) 27 (+) 35 (+) 14 (2) 2 (2) 1 (2) 1 (2) 99 (+) 64 (+) 99 (+) 90 (+) 88 (+) 99 (+) 99 (+) 97 (+) 67 (+) 65 (+) 37 (+) 49 (+) 62 (+) W + + + + + + + 2 2 + + W 2 2 2 + + + + + + + + + + + W W + + V V 2 2 + + 2 2 2 2 + + + + + + + + V + + + + W + + 2 2 2 2 + + + + + + + + + + W + + *Data from earlier results by Branquinho et al. (2014a). DData from earlier results by Satomi et al. (2006). dData from http://www.biologiemarine.com/___fiches/APIpdf/api50%20CHBE%20Medium-_07964_-_F_-_50430.pdf (page 44). 2772 Downloaded from www.microbiologyresearch.org by International Journal of Systematic and Evolutionary Microbiology 65 IP: 88.99.165.207 On: Sun, 18 Jun 2017 23:31:58 Bacillus invictae is a later synonym of B. altitudinis in phenotypic characteristics relative to the other three type strains within the B. pumilus group (Tables 2 and 3). On the basis of the genotypic and phenotypic evidence described above, we propose that B. invictae (Branquinho et al., 2014a) should be regarded as a later heterotypic synonym of B. altitudinis (Shivaji et al., 2006). 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