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Journal articles on the topic 'Fructose-6-phosphate phosphoketolase'

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Published: 4 June 2021
Last updated: 1 February 2022

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1

Glenn, Katie, and Kerry S. Smith. "Allosteric Regulation of Lactobacillus plantarum Xylulose 5-Phosphate/Fructose 6-Phosphate Phosphoketolase (Xfp)." Journal of Bacteriology 197, no. 7 (January 20, 2015): 1157–63. http://dx.doi.org/10.1128/jb.02380-14.

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ABSTRACTXylulose 5-phosphate/fructose 6-phosphate phosphoketolase (Xfp), which catalyzes the conversion of xylulose 5-phosphate (X5P) or fructose 6-phosphate (F6P) to acetyl phosphate, plays a key role in carbohydrate metabolism in a number of bacteria. Recently, we demonstrated that the fungalCryptococcus neoformansXfp2 exhibits both substrate cooperativity for all substrates (X5P, F6P, and Pi) and allosteric regulation in the forms of inhibition by phosphoenolpyruvate (PEP), oxaloacetic acid (OAA), and ATP and activation by AMP (K. Glenn, C. Ingram-Smith, and K. S. Smith. Eukaryot Cell13:657–663, 2014). Allosteric regulation has not been reported previously for the characterized bacterial Xfps. Here, we report the discovery of substrate cooperativity and allosteric regulation among bacterial Xfps, specifically theLactobacillus plantarumXfp.L. plantarumXfp is an allosteric enzyme inhibited by PEP, OAA, and glyoxylate but unaffected by the presence of ATP or AMP. Glyoxylate is an additional inhibitor to those previously reported forC. neoformansXfp2. As withC. neoformansXfp2, PEP and OAA share the same or possess overlapping sites onL. plantarumXfp. Glyoxylate, which had the lowest half-maximal inhibitory concentration of the three inhibitors, binds at a separate site. This study demonstrates that substrate cooperativity and allosteric regulation may be common properties among bacterial and eukaryotic Xfp enzymes, yet important differences exist between the enzymes in these two domains.IMPORTANCEXylulose 5-phosphate/fructose 6-phosphate phosphoketolase (Xfp) plays a key role in carbohydrate metabolism in a number of bacteria. Although we recently demonstrated that the fungalCryptococcusXfp is subject to substrate cooperativity and allosteric regulation, neither phenomenon has been reported for a bacterial Xfp. Here, we report that theLactobacillus plantarumXfp displays substrate cooperativity and is allosterically inhibited by phosphoenolpyruvate and oxaloacetate, as is the case forCryptococcusXfp. The bacterial enzyme is unaffected by the presence of AMP or ATP, which act as a potent activator and inhibitor of the fungal Xfp, respectively. Our results demonstrate that substrate cooperativity and allosteric regulation may be common properties among bacterial and eukaryotic Xfps, yet important differences exist between the enzymes in these two domains.
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2

Sánchez, Borja, Luis Noriega, Patricia Ruas-Madiedo, Clara G. Reyes-Gavilán, and Abelardo Margolles. "Acquired resistance to bile increases fructose-6-phosphate phosphoketolase activity inBifidobacterium." FEMS Microbiology Letters 235, no. 1 (June 2004): 35–41. http://dx.doi.org/10.1111/j.1574-6968.2004.tb09564.x.

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3

Meile, Leo, Lukas M. Rohr, Thomas A. Geissmann, Monique Herensperger, and Michael Teuber. "Characterization of the d-Xylulose 5-Phosphate/d-Fructose 6-Phosphate Phosphoketolase Gene (xfp) from Bifidobacterium lactis." Journal of Bacteriology 183, no. 9 (May 1, 2001): 2929–36. http://dx.doi.org/10.1128/jb.183.9.2929-2936.2001.

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ABSTRACT A d-xylulose 5-phosphate/d-fructose 6-phosphate phosphoketolase (Xfp) from the probioticBifidobacterium lactis was purified to homogeneity. The specific activity of the purified enzyme with d-fructose 6-phosphate as a substrate is 4.28 Units per mg of enzyme.Km values for d-xylulose 5-phosphate and d-fructose 6-phosphate are 45 and 10 mM, respectively. The native enzyme has a molecular mass of 550,000 Da. The subunit size upon sodium dodecyl sulfate-polyacrylamide gel electrophoresis (90,000 Da) corresponds with the size (92,529 Da) calculated from the amino acid sequence of the isolated gene (namedxfp) encoding 825 amino acids. The xfp gene was identified on the chromosome of B. lactis with the help of degenerated nucleotide probes deduced from the common N-terminal amino acid sequence of both the native and denatured enzyme. Comparison of the deduced amino acid sequence of the cloned gene with sequences in public databases revealed high homologies with hypothetical proteins (26 to 55% identity) in 20 microbial genomes. The amino acid sequence derived from the xfp gene contains typical thiamine diphosphate (ThDP) binding sites reported for other ThDP-dependent enzymes. Two truncated putative genes, pta andguaA, were localized adjacent to xfp on theB. lactis chromosome coding for a phosphotransacetylase and a guanosine monophosphate synthetase homologous to products of genes inMycobacterium tuberculosis. However, xfp is transcribed in B. lactis as a monocistronic operon. It is the first reported and sequenced gene of a phosphoketolase.
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4

BIBILONI, RODRIGO, PABLO F. PÉREZ, and GRACIELA L. DE ANTONI. "An Enzymatic–Colorimetric Assay for the Quantification of Bifidobacterium." Journal of Food Protection 63, no. 3 (March 1, 2000): 322–26. http://dx.doi.org/10.4315/0362-028x-63.3.322.

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An enzymatic–colorimetric assay for the quantification of Bifidobacterium was developed. The method, based upon the standard detection of fructose-6-phosphate phosphoketolase activity, was optimized with respect to bacterial cell pretreatment, time of incubation, and substrate concentration. The relationship between bacterial biomass and phosphoketolase activity was linear in a wide spectrum of bacterial densities. Higher sensitivity over the standard method was achieved by using 0.25% Triton X-100 in the reaction mixture to pretreat the bacterial cells. Because autoaggregation is a frequent feature among Bifidobacterium strains, this simple and reproducible method offers good advantage over viable plate count and turbidimetric techniques. The methodology can also be applied to the assessment of adherent Bifidobacterium strains to human epithelial cells.
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5

Kang, Tae Sun, Darren R. Korber, and Takuji Tanaka. "Regulation of Dual Glycolytic Pathways for Fructose Metabolism in Heterofermentative Lactobacillus panis PM1." Applied and Environmental Microbiology 79, no. 24 (October 4, 2013): 7818–26. http://dx.doi.org/10.1128/aem.02377-13.

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ABSTRACTLactobacillus panisPM1 belongs to the group III heterofermentative lactobacilli that use the 6-phosphogluconate/phosphoketolase (6-PG/PK) pathway as their central metabolic pathway and are reportedly unable to grow on fructose as a sole carbon source. We isolated a variant PM1 strain capable of sporadic growth on fructose medium and observed its distinctive characteristics of fructose metabolism. The end product pattern was different from what is expected in typical group III lactobacilli using the 6-PG/PK pathway (i.e., more lactate, less acetate, and no mannitol). In addition,in silicoanalysis revealed the presence of genes encoding most of critical enzymes in the Embden-Meyerhof (EM) pathway. These observations indicated that fructose was metabolized via two pathways. Fructose metabolism in the PM1 strain was influenced by the activities of two enzymes, triosephosphate isomerase (TPI) and glucose 6-phosphate isomerase (PGI). A lack of TPI resulted in the intracellular accumulation of dihydroxyacetone phosphate (DHAP) in PM1, the toxicity of which caused early growth cessation during fructose fermentation. The activity of PGI was enhanced by the presence of glyceraldehyde 3-phosphate (GAP), which allowed additional fructose to enter into the 6-PG/PK pathway to avoid toxicity by DHAP. Exogenous TPI gene expression shifted fructose metabolism from heterolactic to homolactic fermentation, indicating that TPI enabled the PM1 strain to mainly use the EM pathway for fructose fermentation. These findings clearly demonstrate that the balance in the accumulation of GAP and DHAP determines the fate of fructose metabolism and the activity of TPI plays a critical role during fructose fermentation via the EM pathway inL. panisPM1.
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6

Glenn, Katie, Cheryl Ingram-Smith, and Kerry S. Smith. "Biochemical and Kinetic Characterization of Xylulose 5-Phosphate/Fructose 6-Phosphate Phosphoketolase 2 (Xfp2) from Cryptococcus neoformans." Eukaryotic Cell 13, no. 5 (March 21, 2014): 657–63. http://dx.doi.org/10.1128/ec.00055-14.

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ABSTRACTXylulose 5-phosphate/fructose 6-phosphate phosphoketolase (Xfp), previously thought to be present only in bacteria but recently found in fungi, catalyzes the formation of acetyl phosphate from xylulose 5-phosphate or fructose 6-phosphate. Here, we describe the first biochemical and kinetic characterization of a eukaryotic Xfp, from the opportunistic fungal pathogenCryptococcus neoformans, which has twoXFPgenes (designatedXFP1andXFP2). Our kinetic characterization ofC. neoformansXfp2 indicated the existence of both substrate cooperativity for all three substrates and allosteric regulation through the binding of effector molecules at sites separate from the active site. Prior to this study, Xfp enzymes from two bacterial genera had been characterized and were determined to follow Michaelis-Menten kinetics.C. neoformansXfp2 is inhibited by ATP, phosphoenolpyruvate (PEP), and oxaloacetic acid (OAA) and activated by AMP. ATP is the strongest inhibitor, with a half-maximal inhibitory concentration (IC50) of 0.6 mM. PEP and OAA were found to share the same or have overlapping allosteric binding sites, while ATP binds at a separate site. AMP acts as a very potent activator; as little as 20 μM AMP is capable of increasing Xfp2 activity by 24.8% ± 1.0% (mean ± standard error of the mean), while 50 μM prevented inhibition caused by 0.6 mM ATP. AMP and PEP/OAA operated independently, with AMP activating Xfp2 and PEP/OAA inhibiting the activated enzyme. This study provides valuable insight into the metabolic role of Xfp within fungi, specifically the fungal pathogenCryptococcus neoformans, and suggests that at least some Xfps display substrate cooperative binding and allosteric regulation.
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7

Suzuki, Ryuichiro, Byung-Jun Kim, Tsuyoshi Shibata, Yuki Iwamoto, Takane Katayama, Hisashi Ashida, Takayoshi Wakagi, Hirofumi Shoun, Shinya Fushinobu, and Kenji Yamamoto. "Overexpression, crystallization and preliminary X-ray analysis of xylulose-5-phosphate/fructose-6-phosphate phosphoketolase fromBifidobacterium breve." Acta Crystallographica Section F Structural Biology and Crystallization Communications 66, no. 8 (July 29, 2010): 941–43. http://dx.doi.org/10.1107/s1744309110023845.

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8

Fandi, K. G., H. M. Ghazali, A. M. Yazid, and A. R. Raha. "Purification and N-terminal amino acid sequence of fructose-6-phosphate phosphoketolase from Bifidobacterium longum BB536." Letters in Applied Microbiology 32, no. 4 (April 11, 2001): 235–39. http://dx.doi.org/10.1046/j.1472-765x.2001.00895.x.

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9

Gavini, F., M. Van Esbroeck, J. P. Touzel, A. Fourment, and H. Goossens. "Detection of Fructose-6-phosphate Phosphoketolase (F6PPK), a Key Enzyme of the Bifid-Shunt, inGardnerella vaginalis." Anaerobe 2, no. 3 (June 1996): 191–93. http://dx.doi.org/10.1006/anae.1996.0025.

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10

Bolado-Martínez, E., E. Acedo-Félix, A. B. Peregrino-Uriarte, and G. Yepiz-Plascencia. "Fructose 6-phosphate phosphoketolase activity in wild-type strains of Lactobacillus, isolated from the intestinal tract of pigs." Applied Biochemistry and Microbiology 48, no. 5 (September 2012): 444–51. http://dx.doi.org/10.1134/s000368381205002x.

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11

Sánchez, Borja, Marie-Christine Champomier-Vergès, Patricia Anglade, Fabienne Baraige, Clara G. de los Reyes-Gavilán, Abelardo Margolles, and Monique Zagorec. "Proteomic Analysis of Global Changes in Protein Expression during Bile Salt Exposure of Bifidobacterium longum NCIMB 8809." Journal of Bacteriology 187, no. 16 (August 15, 2005): 5799–808. http://dx.doi.org/10.1128/jb.187.16.5799-5808.2005.

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ABSTRACT Adaptation to and tolerance of bile stress are among the main limiting factors to ensure survival of bifidobacteria in the intestinal environment of humans. The effect of bile salts on protein expression patterns of Bifidobacterium longum was examined. Protein pattern comparison of strains grown with or without bile extract allowed us to identify 34 different proteins whose expression was regulated. The majority of these proteins were induced after both a minor (0.6 g liter−1) and a major (1.2 g liter−1) exposure to bile. These include general stress response chaperones, proteins involved in transcription and translation and in the metabolism of amino acids and nucleotides, and several enzymes of glycolysis and pyruvate catabolism. Remarkably, xylulose 5-phosphate/fructose 6-phosphate phosphoketolase, the key enzyme of the so-called bifidobacterial shunt, was found to be upregulated, and the activity on fructose 6-phosphate was significantly higher for protein extracts of cells grown in the presence of bile. Changes in the levels of metabolic end products (acetate and lactate) were also detected. These results suggest that bile salts, to which bifidobacteria are naturally exposed, induce a complex physiological response rather than a single event in which proteins from many different functional categories take part. This study has extended our understanding of the molecular mechanism underlying the capacity of intestinal bifidobacteria to tolerate bile.
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12

Watanabe, Seiji, Mutsunori Shirai, Mikiya Kishi, and Yasuo Ohnishi. "Involvement of an FNR-like oxygen sensor in Komagataeibacter medellinensis for survival under oxygen depletion." Bioscience, Biotechnology, and Biochemistry 85, no. 9 (June 30, 2021): 2065–75. http://dx.doi.org/10.1093/bbb/zbab121.

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ABSTRACT During acetic acid fermentation, acetic acid bacteria face oxygen depletion stress caused by the vigorous oxidation of ethanol to acetic acid. However, the molecular mechanisms underlying the response to oxygen depletion stress remain largely unknown. Here, we focused on an oxygen-sensing FNR homolog, FnrG, in Komagataeibacter medellinensis. Comparative transcriptomic analysis between the wild-type and fnrG-disrupted strains revealed that FnrG upregulated 8 genes (fold change >3). Recombinant FnrG bound to a specific DNA sequence only when FnrG was reconstituted anaerobically. An operon consisting of acetate kinase and xylulose-5-phosphate/fructose-6-phosphate phosphoketolase genes was found to be an FnrG regulon involved in cell survival under oxygen-limiting conditions. Moreover, a strain that overexpressed these 2 genes accumulated more acetic acid than the wild-type strain harboring an empty vector. Thus, these 2 genes could be new targets for the molecular breeding of acetic acid bacteria with high acetic acid productivity.
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13

BIBILONI, RODRIGO, ANDREA GÓMEZ ZAVAGLIA, and GRACIELA DE ANTONI. "Enzyme-Based Most Probable Number Method for the Enumeration of Bifidobacterium in Dairy Products." Journal of Food Protection 64, no. 12 (December 1, 2001): 2001–6. http://dx.doi.org/10.4315/0362-028x-64.12.2001.

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An enzyme-based assay in combination with the most probable number (MPN) technique was developed for the enumeration of bifidobacteria. The assay employs the detection of fructose-6-phosphate phosphoketolase (F6PPK) activity as an indicator of the presence of bifidobacteria. The method was validated against viable counts and optimized with respect to selective media in order to quantitatively assess bifidobacteria in dairy products and other probiotic preparations. Several commercial products and homemade fermented milks were analyzed. Counts of bifidobacteria ranged from 107 to 108 MPN/ml in commercial products and homemade fermented milks. Commercial starters provided by Argentinean industries had between 107 and 1011 MPN/ml. The results obtained in this study suggest that the combination of F6PPK activity determination and the MPN methodology allows an accurate determination of Bifidobacterium in pure cultures, dairy products, and other probiotic preparations.
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14

Vlková, E., J. Medková, and V. Rada. "Comparison of four methods for identification of bifidobacteria to the genus level." Czech Journal of Food Sciences 20, No. 5 (November 19, 2011): 171–74. http://dx.doi.org/10.17221/3528-cjfs.

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The identification of bifidobacteria to the genus level is important for the differentiation of these bacteria from other bacteria occurring in the animal and human intestine. The detection of fructose-6-phosphate phosphoketolase (F6PPK-test) is used traditionally for the identification of Bifidobacterium sp. The original procedure is time consuming and therefore it was modified several times recently. The aim of the present work was to compare the following methods for the genus identification of bifidobacteria: F6PPK-test, F6PPK-test modified by the addition of triton X-100, F6PPK-test modified by the addition of cetridium bromide (F6PPK-CTAB-test), and PCR using genus specific primers. Bifidobacteria isolated from fermented milk products (3 strains), human faeces (6 strains), and animal intestinal tract (2 strains) were tested. All the methods tested proved to be reliable tests for the genus identification of bifidobacteria. The F6PPK-CTAB-test gave the best results. This procedure is quick and does not require any special laboratory equipment.  
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Duranti, Sabrina, Gabriele Andrea Lugli, Alice Viappiani, Leonardo Mancabelli, Giulia Alessandri, Rosaria Anzalone, Giulia Longhi, et al. "Characterization of the phylogenetic diversity of two novel species belonging to the genus Bifidobacterium: Bifidobacterium cebidarum sp. nov. and Bifidobacterium leontopitheci sp. nov." International Journal of Systematic and Evolutionary Microbiology 70, no. 4 (April 1, 2020): 2288–97. http://dx.doi.org/10.1099/ijsem.0.004032.

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Two Bifidobacterium strains, i.e., 2176BT and 2177BT, were isolated from Golden-Headed Lion Tamarin (Leontopithecus chrysomelas) and Goeldi's monkey (Callimico goeldii). Isolates were shown to be Gram-positive, non-motile, non-sporulating, facultative anaerobic and d-fructose 6-phosphate phosphoketolase-positive. Phylogenetic analyses based on 16S rRNA sequences, multilocus sequences (including hsp60, rpoB, dnaJ, dnaG and clpC genes) and the core genome revealed that bifidobacterial strains 2176BT and 2177BT exhibit close phylogenetic relatedness to Bifidobacterium felsineum DSM 103139T and Bifidobacterium bifidum LMG 11041T, respectively. Further genotyping based on the genome sequence of the isolated strains combined with phenotypic analyses, clearly show that these strains are distinct from each of the type strains of the so far recognized Bifidobacterium species. Thus, Bifidobacterium cebidarum sp. nov. (2176BT=LMG 31469T=CCUG 73785T) and Bifidobacterium leontopitheci sp. nov. (2177BT=LMG 31471T=CCUG 73786T are proposed as novel Bifidobacterium species.
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Killer, J., J. Havlík, V. Bunešová, E. Vlková, and O. Benada. "Pseudoscardovia radai sp. nov., a representative of the family Bifidobacteriaceae isolated from the digestive tract of a wild pig (Sus scrofa scrofa)." International Journal of Systematic and Evolutionary Microbiology 64, Pt_9 (September 1, 2014): 2932–38. http://dx.doi.org/10.1099/ijs.0.063230-0.

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The presence of bifidobacteria and representatives of the new genus Pseudoscardovia within the family Bifidobacteriaceae in the digestive tract of wild pigs was reported recently. Results based on comparative 16S rRNA gene sequence analysis of a new fructose-6-phosphate phosphoketolase-positive bacterial isolate, strain DPVI-TET3T, originating from the small intestine of a wild pig revealed a relationship to Pseudoscardovia suis DPTE4T (96.8 % sequence similarity). Phylogenetic and comparative analyses based on 16S rRNA, hsp60, xfp, fusA, tuf and rpoC partial gene sequences confirmed the relationship of the novel bacterial strain to P. suis DPTE4T in comparison with other bifidobacterial species occurring in the digestive tract of domestic and wild pigs. Differences in utilization of various substrates, production of enzymes, cell morphology, peptidoglycan structure and profiles of cellular fatty acids and polar lipids between strain DPVI-TET3T and P. suis DPTE4T allow the establishment of a novel species, for which the name Pseudoscardovia radai sp. nov. is proposed. The type strain is strain DPVI-TET3T ( = CCM 7943T = DSM 24742T).
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17

Sechovcová, Hana, Jiri Killer, Radko Pechar, Martina Geigerová, Roman Švejstil, Hana Salmonová, Chahrazed Mekadim, et al. "Alloscardovia venturai sp. nov., a fructose 6-phosphate phosphoketolase-positive species isolated from the oral cavity of a guinea-pig (Cavia aperea f. porcellus)." International Journal of Systematic and Evolutionary Microbiology 67, no. 8 (August 1, 2017): 2842–47. http://dx.doi.org/10.1099/ijsem.0.002031.

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Killer, J., I. Sedláček, V. Rada, J. Havlík, and J. Kopečný. "Reclassification of Bifidobacterium stercoris Kim et al. 2010 as a later heterotypic synonym of Bifidobacterium adolescentis." International Journal of Systematic and Evolutionary Microbiology 63, Pt_11 (November 1, 2013): 4350–53. http://dx.doi.org/10.1099/ijs.0.054957-0.

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The taxonomic position of Bifidobacterium stercoris Eg1T ( = JCM 15918T) based on comparative 16S rRNA gene and hsp60 sequence analyses was found to be controversial, as the strain showed high similarity to the type strain of Bifidobacterium adolescentis , CCUG 18363T. Therefore, the relationship between the two species was investigated by a taxonomic study that included, in addition to re-evaluation of the 16S rRNA gene sequence, determination of DNA–DNA binding and multilocus sequence analysis (MLSA) of housekeeping genes encoding the DNA-directed RNA polymerase B subunit (rpoC), putative xylulose-5-phosphate/fructose-6-phosphate phosphoketolase (xfp), elongation factor EF-G (fusA), 50S ribosomal protein L2 (rplB) and DNA gyrase B subunit (gyrB). Comparative 16S rRNA gene sequence analysis showed relatively high similarity (98.9 %) between B. stercoris KCTC 5756T and B. adolescentis ATCC 15703T. MLSA revealed close relatedness between B. stercoris KCTC 5756T and B. adolescentis CCUG 18363T, with 99.3–100 % similarity between the rpoC, xfp, fusA, rplB and gyrB gene sequences. In addition, relatively high dnaJ1 gene sequence similarity of 97.7 % was found between the strains. Similar phenotypes and a high DNA–DNA binding value (78.9 %) confirmed that B. stercoris and B. adolescentis are synonymous. Based on these results, it is proposed that the species Bifidobacterium stercoris Kim et al. 2010 should be reclassified as a later heterotypic synonym of Bifidobacterium adolescentis Reuter 1963 (Approved Lists 1980).
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Yin, Xianhua, James R. Chambers, Kathleen Barlow, Aaron S. Park, and Roger Wheatcroft. "The gene encoding xylulose-5-phosphate/fructose-6-phosphate phosphoketolase (xfp) is conserved amongBifidobacteriumspecies within a more variable region of the genome and both are useful for strain identification." FEMS Microbiology Letters 246, no. 2 (May 2005): 251–57. http://dx.doi.org/10.1016/j.femsle.2005.04.013.

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20

VELAZQUEZ, MADELINE, and JOELLEN M. FEIRTAG. "Isolation and Partial Physiological Characterization of Commercial Strains of Bifidobacteria." Journal of Food Protection 60, no. 5 (May 1, 1997): 537–43. http://dx.doi.org/10.4315/0362-028x-60.5.537.

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The genus Bifidobacterium has been suggested to be capable of performing gastrointestinal modifications, providing nutritional value when added to the diet as a probiotic and having an inducing effect on the immune system by enhancing cytokine production. As a consequence, the dairy food industry is introducing bifidobacteria to such products as yogurt, flavored milk, and cottage cheese. The objectives of this project were to characterize isolates of bifidobacteria from commercial suppliers, to isolate and characterize bifidobacteria from dairy products, and to establish and compare their physiological characteristics. Physiological characterization was performed based on phenotypic characteristics, carbohydrate fermentation patterns, enzyme profiles, fructose-6-phosphate phosphoketolase (F6PPK) assays, and antibiotic sensitivities. The results demonstrated that commercial bifidobacteria strains and those strains isolated from dairy products were physiologically different. This demonstrates that some bifidobacteria present in dairy products may be mischaracterized when identifying their presence based solely on phenotypic characteristics. The difficulty in growth, rapid assessment, and isolation of bifidobacteria from a mixed culture in dairy products was evaluated in this study. X-α-Gal medium was selected as the most suitable for isolation of bifidobacteria from mixed culture products and modified lactobacilli MRS medium for growing pure isolates of bifidobacteria.
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Choi, Jung-Hye, Kyung Min Lee, Myung-Ki Lee, Chang-Jun Cha, and Geun-Bae Kim. "Bifidobacterium faecale sp. nov., isolated from human faeces." International Journal of Systematic and Evolutionary Microbiology 64, Pt_9 (September 1, 2014): 3134–39. http://dx.doi.org/10.1099/ijs.0.063479-0.

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A novel strain, designated strain CU3-7T, was isolated from faeces of a two-week-old baby. The isolate was Gram-staining-positive, anaerobic and rod-shaped. Results from 16S rRNA gene sequence analysis revealed that strain CU3-7T was phylogenetically affiliated with members of the genus Bifidobacterium . Strain CU3-7T showed the highest level of sequence similarity with Bifidobacterium adolescentis KCTC 3216T (98.4 %), followed by Bifidobacterium ruminantium KCTC 3425T (97.9 %). Analysis of hsp60 sequences showed that strain CU3-7T was closely related to B. adolescentis KCTC 3216T (94.0 %) and B. ruminantium KCTC 3425T (92.5 %). The DNA–DNA hybridization values with the closely related strains were all below the cut-off value for species delineation, 17.0 % with B. ruminantium KCTC 3425T and 14.9 % with B. adolescentis KCTC 3216T. Fructose-6-phosphate phosphoketolase activity was detected. The predominant cellular fatty acids were C16 : 0 (27.7 %), C18 : 1ω9c (27.4 %) and C18 : 1ω9c dimethylacetate (15.5 %). The DNA G+C content was 58.6 mol%. On the basis of polyphasic taxonomy, strain CU3-7T should be classified as the type strain of a novel species within the genus Bifidobacterium , for which the name Bifidobacterium faecale sp. nov. is proposed ( = KACC 17904T = JCM 19861T).
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Eckel, Viktor P. L., Lisa-Marie Ziegler, Rudi F. Vogel, and Matthias Ehrmann. "Bifidobacterium tibiigranuli sp. nov. isolated from homemade water kefir." International Journal of Systematic and Evolutionary Microbiology 70, no. 3 (March 1, 2020): 1562–70. http://dx.doi.org/10.1099/ijsem.0.003936.

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Two Bifidobacterium strains, TMW 2.2057T and TMW 2.1764 were isolated from two different homemade water kefirs from Germany. Both strains were oxidase- and catalase-negative and Gram-staining-positive. Cells were non-motile, irregular rods that were aerotolerant anaerobes. On basis of fructose 6-phosphate phosphoketolase activity, they were assigned to the family Bifidobacteriaceae. Comparative analysis of 16S rRNA and concatenated housekeeping genes (clpC, dnaB, dnaG, dnaJ, hsp60 and rpoB) demonstrated that both strains represented a member of the genus Bifidobacterium , with Bifidobacterium subtile DSM 20096T as the closest phylogenetic relative (98.35 % identity). Both strains can be distinguished using randomly amplified polymorphic DNA fingerprinting. Analysis of concatenated marker gene sequences as well as average nucleotide identity by blast (ANIb) and in silico DNA–DNA hybridization (isDDH) calculations of their genome sequences confirmed Bifidobacterium subtile DSM 20096T as the closest relative (87.91 and 35.80 % respectively). All phylogenetic analyses allow differentiation of strains TMW 2.2057T and TMW 2.1764 from all hitherto described species of the genus Bifidobacterium with validly published names. We therefore propose a novel species with the name Bifidobacterium tibiigranuli, for which TMW 2.2057T (=DSM 108414T=LMG 31086T) is the type strain.
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Neuzil-Bunesova, Vera, Gabriele Andrea Lugli, Nikol Modrackova, Marie Makovska, Jakub Mrazek, Chahrazed Mekadim, Sarka Musilova, et al. "Bifidobacterium canis sp. nov., a novel member of the Bifidobacterium pseudolongum phylogenetic group isolated from faeces of a dog (Canis lupus f. familiaris)." International Journal of Systematic and Evolutionary Microbiology 70, no. 9 (September 1, 2020): 5040–47. http://dx.doi.org/10.1099/ijsem.0.004378.

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A fructose-6-phosphate phosphoketolase-positive strain (GSD1FST) was isolated from a faecal sample of a 3 weeks old German Shepherd dog. The closest related taxa to isolate GSD1FST based on results from the EZBioCloud database were Bifidobacterium animalis subsp. animalis ATCC 25527T, Bifidobacterium animalis subsp. lactis DSM 10140T and Bifidobacterium anseris LMG 30189T, belonging to the Bifidobacterium pseudolongum phylogenetic group. The resulting 16S rRNA gene identities (compared length of 1454 nucleotides) towards these taxa were 97.30, 97.23 and 97.09 %, respectively. The pairwise similarities of strain GSD1FST using argS, atpA, fusA, hsp60, pyrG, rpsC, thrS and xfp gene fragments to all valid representatives of the B. pseudolongum phylogenetic group were in the concatenated range of 83.08–88.34 %. Phylogenomic analysis based on whole-genome methods such as average nucleotide identity revealed that bifidobacterial strain GSD1FST exhibits close phylogenetic relatedness (88.17 %) to Bifidobacetrium cuniculi LMG 10738T. Genotypic characteristics and phylogenetic analyses based on nine molecular markers, as well as genomic and comparative phenotypic analyses, clearly proved that the evaluated strain should be considered as representing a novel species within the B. pseudolongum phylogenetic group named as Bifidobacterium canis sp. nov. (GSD1FST=DSM 105923T=LMG 30345T=CCM 8806T).
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González-Rodríguez, Irene, Paula Gaspar, Borja Sánchez, Miguel Gueimonde, Abelardo Margolles, and Ana Rute Neves. "Catabolism of Glucose and Lactose in Bifidobacterium animalis subsp. lactis, Studied by13C Nuclear Magnetic Resonance." Applied and Environmental Microbiology 79, no. 24 (September 27, 2013): 7628–38. http://dx.doi.org/10.1128/aem.02529-13.

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ABSTRACTBifidobacteria are widely used as probiotics in several commercial products; however, to date there is little knowledge about their carbohydrate metabolic pathways. In this work, we studied the metabolism of glucose and lactose in the widely used probiotic strainBifidobacterium animalissubsp.lactisBB-12 byin vivo13C nuclear magnetic resonance (NMR) spectroscopy. The metabolism of [1-13C]glucose was characterized in cells grown in glucose as the sole carbon source. Moreover, the metabolism of lactose specifically labeled with13C on carbon 1 of the glucose or the galactose moiety was determined in suspensions of cells grown in lactose. These experiments allowed the quantification of some intermediate and end products of the metabolic pathways, as well as determination of the consumption rate of carbon sources. Additionally, the labeling patterns in metabolites derived from the metabolism of glucose specifically labeled with13C on carbon 1, 2, or 3 in cells grown in glucose or lactose specifically labeled in carbon 1 of the glucose moiety ([1-13Cglucose]lactose), lactose specifically labeled in carbon 1 of the galactose moiety ([1-13Cgalactose]lactose), and [1-13C]glucose in lactose-grown cells were determined in cell extracts by13C NMR. The NMR analysis showed that the recovery of carbon was fully compatible with the fructose 6-phosphate, or bifid, shunt. The activity of lactate dehydrogenase, acetate kinase, fructose 6-phosphate phosphoketolase, and pyruvate formate lyase differed significantly between glucose and lactose cultures. The transcriptional analysis of several putative glucose and lactose transporters showed a significant induction of Balat_0475 in the presence of lactose, suggesting a role for this protein as a lactose permease. This report provides the firstin vivoexperimental evidence of the metabolic flux distribution in the catabolic pathway of glucose and lactose in bifidobacteria and shows that the bifid shunt is the only pathway involved in energy recruitment from these two sugars. On the basis of our experimental results, a model of sugar metabolism inB. animalissubsp.lactisis proposed.
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Modesto, Monica, Samanta Michelini, Ilaria Stefanini, Camillo Sandri, Caterina Spiezio, Annamaria Pisi, Gianfranco Filippini, Bruno Biavati, and Paola Mattarelli. "Bifidobacterium lemurum sp. nov., from faeces of the ring-tailed lemur (Lemur catta)." International Journal of Systematic and Evolutionary Microbiology 65, Pt_6 (June 1, 2015): 1726–34. http://dx.doi.org/10.1099/ijs.0.000162.

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Four Gram-positive-staining, microaerophilic, non-spore-forming, fructose-6-phosphate phosphoketolase-positive bacterial strains were isolated from a faecal sample of a 5-year-old ring-tailed lemur (Lemur catta). The strains showed a peculiar morphology, resembling a small coiled snake, a ring shape, or forming a little ‘Y’ shape. The isolated strains appeared identical, and LMC 13T was chosen as a representative strain and characterized further. Strain LMC 13T showed an A3β peptidoglycan type, similar to that found in Bifidobacterium longum . The DNA base composition was 57.2 mol% G+C. Almost-complete 16S rRNA, hsp60, rpoB, dnaJ, dnaG, purF, clpC and rpoC gene sequences were obtained, and phylogenetic relationships were determined. Comparative analysis of 16S rRNA gene sequences showed that strain LMC 13T showed the highest similarity to B. longum subsp. suis ATCC 27533T (96.65 %) and Bifidobacterium saguini DSM 23967T (96.64 %). Strain LMC 13T was located in an actinobacterial cluster and was more closely related to the genus Bifidobacterium than to other genera in the Bifidobacteriaceae . On the basis of these results, strain LMC 13T represents a novel species within the genus Bifidobacterium , for which the name Bifidobacterium lemurum sp. nov. is proposed; the type strain is LMC 13T ( = DSM 28807T = JCM 30168T).
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Cleusix, V., C. Lacroix, G. Dasen, M. Leo, and G. Le Blay. "Comparative study of a new quantitative real-time PCR targeting the xylulose-5-phosphate/fructose-6-phosphate phosphoketolase bifidobacterial gene (xfp) in faecal samples with two fluorescence in situ hybridization methods." Journal of Applied Microbiology 108, no. 1 (January 2010): 181–93. http://dx.doi.org/10.1111/j.1365-2672.2009.04408.x.

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Mart�n, Roc�o, Esther Jim�nez, Hans Heilig, Leonides Fern�ndez, Mar�a L. Mar�n, Erwin G. Zoetendal, and Juan M. Rodr�guez. "Isolation of Bifidobacteria from Breast Milk and Assessment of the Bifidobacterial Population by PCR-Denaturing Gradient Gel Electrophoresis and Quantitative Real-Time PCR." Applied and Environmental Microbiology 75, no. 4 (December 16, 2008): 965–69. http://dx.doi.org/10.1128/aem.02063-08.

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ABSTRACT The objective of this work was to elucidate if breast milk contains bifidobacteria and whether they can be transmitted to the infant gut through breastfeeding. Twenty-three women and their respective infants provided samples of breast milk and feces, respectively, at days 4 to 7 after birth. Gram-positive and catalase-negative isolates from specific media with typical bifidobacterial shapes were identified to the genus level by F6PPK (fructose-6-phosphate phosphoketolase) assays and to the species level by 16S rRNA gene sequencing. Bifidobacterial communities in breast milk were assessed by PCR-denaturing gradient gel electrophoresis (PCR-DGGE), and their levels were estimated by quantitative real-time PCR (qRTi-PCR). Bifidobacteria were present in 8 milk samples and 21 fecal samples. Bifidobacterium breve, B. adolescentis, and B. bifidum were isolated from milk samples, while infant feces also contained B. longum and B. pseudocatenulatum. PCR-DGGE revealed the presence of one to four dominant bifidobacterial bands in 22 milk samples. Sequences with similarities above 98% were identified as Bifidobacterium breve, B. adolescentis, B. longum, B. bifidum, and B. dentium. Bifidobacterial DNA was detected by qRTi-PCR in the same 22 milk samples at a range between 40 and 10,000 16S rRNA gene copies per ml. In conclusion, human milk seems to be a source of living bifidobacteria for the infant gut.
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GOLFETTO, Lisléia, Fernanda Duarte de SENNA, Julia HERMES, Bruna Teles Soares BESERRA, Franciane da Silva FRANÇA, and Flávia MARTINELLO. "LOWER BIFIDOBACTERIA COUNTS IN ADULT PATIENTS WITH CELIAC DISEASE ON A GLUTEN-FREE DIET." Arquivos de Gastroenterologia 51, no. 2 (June 2014): 139–43. http://dx.doi.org/10.1590/s0004-28032014000200013.

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ContextThe ingestion of gluten is responsible for the symptoms of Celiac disease, but other environmental factors can also influence. Strains of theBifidobacterium genus have been shown to afford protection against the inflammatory response and mucosal damage caused by gliadin peptides in vitro.ObjectivesThis study was designed to compare the concentration of fecal bifidobacteria and pH of patients with celiac disease on gluten-free diet and control subjects in order to identify if the imbalance on fecal microbiota still remain during the treatment of celiac disease and identify the necessity of dietary supplementation with pre- or probiotics.MethodsIt was analyzed the feces of 42 healthy subjects and 14 celiac patients. The bifidobacteria count in feces was done in selective medium BIM-25. Microscopic analysis of the colonies was performed by Gram stain. The identification of the genus Bifidobacterium was performed by determination of fructose-6-phosphate phosphoketolase. Fecal pH was measured using a pH meter.ResultsThe concentration of bifidobacteria per gram of feces was significantly higher in healthy subjects (controls) (1.5 ± 0.63 x108 CFU/g) when compared to celiac patients (2.5 ± 1.5 x107 CFU/g). The fecal pH was not different between celiac patients (7.19 ± 0.521) and controls (7.18 ± 0.522).ConclusionsThese results suggest that with lower levels of bifidobacteria, celiac patients have an imbalance in the intestinal microbiota, regardless of pH, even while on a gluten-free diet. This fact could favor the pathological process of the disorder.
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Kim, Min-Soo, Seong Woon Roh, and Jin-Woo Bae. "Bifidobacterium stercoris sp. nov., isolated from human faeces." International Journal of Systematic and Evolutionary Microbiology 60, no. 12 (December 1, 2010): 2823–27. http://dx.doi.org/10.1099/ijs.0.019943-0.

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Strain Eg1T, an anaerobic, Gram-stain-positive, non-motile and non-spore-forming bacterium, was isolated from human faeces. The optimal temperature for growth was 37 °C and tests for oxidase and catalase activities gave negative results. Fructose-6-phosphate phosphoketolase activity was detected. Acid was produced during fermentation of several substrates, including glucose. The end products of glucose fermentation were acetic acid and lactic acid, which were produced in a molar ratio of 1.76 : 1 (approximately 3 : 2). The G+C content was 57.8 mol%. Comparative analysis of 16S rRNA gene sequences showed that strain Eg1T was closely related to Bifidobacterium adolescentis YIT 4011T (98.36 % 16S rRNA gene sequence similarity) and Bifidobacterium ruminantium JCM 8222T (97.93 %) and analysis of hsp60 sequences showed that strain Eg1T was closely related to B. adolescentis JCM 1275T (99.35 % hsp60 sequence similarity) and B. ruminantium JCM 8222T (92.13 %). However, despite these degrees of similarity being high enough for strain Eg1T to be included at the same species level as B. adolescentis and B. ruminantium (96.5–100 % for the genus Bifidobacterium), the isolate could be distinguished from B. adolescentis KCTC 3216T and B. ruminantium KCTC 3425T by low levels of DNA–DNA relatedness (41 and 17 %, respectively). Based on phenotypic, genotypic and phylogenetic analyses, we propose that strain Eg1T is classified in a novel species, Bifidobacterium stercoris sp. nov. The type strain is Eg1T (=KCTC 5756T =JCM 15918T).
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Simpson, P. J., C. Stanton, G. F. Fitzgerald, and R. P. Ross. "Genomic Diversity and Relatedness of Bifidobacteria Isolated from a Porcine Cecum." Journal of Bacteriology 185, no. 8 (April 15, 2003): 2571–81. http://dx.doi.org/10.1128/jb.185.8.2571-2581.2003.

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ABSTRACT This study initially involved the isolation of a number of bifidobacteria from either the lumen or the epithelium of a porcine cecum. A total of 160 isolates were selected at random on MRS plates containing cysteine hydrochloride (0.5 g/liter) and mupirocin (50 mg/liter). All were identified as bifidobacteria based on fructose-6-phosphate phosphoketolase activity. Following genomic digestion with the restriction enzyme XbaI and pulsed-field gel electrophoresis (PFGE), the isolates produced 15 distinct macro-restriction patterns. Several of the PFGE patterns differed by only 1, 2, or 3 DNA fragments and were grouped as related patterns into seven PFGE types, termed A through G. The related patterns appeared to show genomic plasticity within the isolates arising from chromosomal mutations or possibly horizontal transfer of plasmids. The relative frequency of each PFGE type was maintained within each cecal sample, with PFGE type E representing approximately 50% of the isolates. Randomly amplified polymorphic DNA PCR, cell morphology, whole-cell protein profiling, 16S ribosomal DNA sequencing, and DNA-DNA hybridization were used to determine if the seven apparently unrelated PFGE types represented genetically distinct isolates. Four groups were identified: PFGE types A, C/D/G, B/E, and F, and these appeared to represent Bifidobacterium minimum, Bifidobacterium pseudolongum subsp. pseudolongum, and Bifidobacterium pseudolongum subsp. globosum and two new species, respectively. The data demonstrate the presence of considerable genomic diversity within a relatively simple bifidobacteria population, consisting of 15 distinct strains representing four groups, which was maintained throughout the porcine cecal contents and epithelial layer.
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Killer, J., Š. Ročková, E. Vlková, V. Rada, J. Havlík, J. Kopečný, V. Bunešová, et al. "Alloscardovia macacae sp. nov., isolated from the milk of a macaque (Macaca mulatta), emended description of the genus Alloscardovia and proposal of Alloscardovia criceti comb. nov." International Journal of Systematic and Evolutionary Microbiology 63, Pt_12 (December 1, 2013): 4439–46. http://dx.doi.org/10.1099/ijs.0.051326-0.

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A novel bacterial strain, designated M8T, was isolated from milk of a female macaque bred in captivity. The strain was Gram-stain-positive, anaerobic, irregular coccoid–rod-shaped without catalase activity. Analysis of 16S rRNA gene sequence similarity revealed that the isolate was most closely related to Alloscardovia omnicolens CCUG 31649T (96.4 %) and Metascardovia criceti OMB105T (96.6 %). Sequences of hsp60, fusA, and xfp genes also confirmed that the strain was most closely related to the type strains of A. omnicolens and M. criceti . The isolate produced fructose-6-phosphate phosphoketolase which is in agreement with classification within the family Bifidobacteriaceae . The major fatty acids were C18 : 1ω9c (35.8 %), C16 : 1 (6.2 %) and C14 : 0 (5.7 %). Polar lipid analysis revealed five different glycolipids, two unidentified phospholipids and diphosphatidylglycerol. The peptidoglycan was of the type A4α l-Lys–d-Asp with the presence of d(l)-alanine, d-glutamine, d-asparagine and l-lysine. The DNA G+C content of strain M8T was 50.1 mol%. On the basis of genetic, phylogenetic and phenotypic data, strain M8T represents a novel species of the genus Alloscardovia for which the name Alloscardovia macacae sp. nov. is proposed. The type strain is M8T ( = DSM 24762T = CCM 7944T). In addition, our results also revealed that Alloscardovia omnicolens DSM 21503T and Metascardovia criceti DSM 17774T do not belong to different genera within the family Bifidobacteriaceae . We therefore propose to reclassify Metascardovia criceti as Alloscardovia criceti comb. nov. An emended description of the genus Alloscardovia is also provided.
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Killer, J., J. Kopečný, J. Mrázek, I. Koppová, J. Havlík, O. Benada, and T. Kott. "Bifidobacterium actinocoloniiforme sp. nov. and Bifidobacterium bohemicum sp. nov., from the bumblebee digestive tract." International Journal of Systematic and Evolutionary Microbiology 61, no. 6 (June 1, 2011): 1315–21. http://dx.doi.org/10.1099/ijs.0.022525-0.

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Our previous study, based primarily on PCR-denaturing gradient gel electrophoresis and 16S rRNA gene sequencing, focused on the isolation of four bifidobacterial groups from the digestive tract of three bumblebee species. In that study, we proposed that these isolated groups potentially represented novel species of the family Bifidobacteriaceae. One of the four, Bifidobacterium bombi, has been described recently. Strains representing two of the other groups have been classified as members of the genus Bifidobacterium on the basis of positive results for fructose-6-phosphate phosphoketolase activity and analysis of partial 16S rRNA and heat-shock protein 60 (hsp60) gene sequences. Analysis of 16S rRNA gene sequence similarities revealed that the isolates of the first group were affiliated to Bifidobacterium asteroides YIT 11866T, B. indicum JCM 1302T and B. coryneforme ATCC 25911T (96.2, 96.0 and 95.9 % sequence similarity, respectively), together with other bifidobacteria showing lower sequence similarity. Additional representatives of the second group were found to be affiliated to Bifidobacterium minimum YIT 4097T and B. coryneforme ATCC 25911T (96.0 and 96.3 % sequence similarity) and also to other bifidobacteria with lower sequence similarity. These results indicate that the isolates of the two groups belong to novel species within the genus Bifidobacterium. This observation was further substantiated by the results of partial sequencing of hsp60. On the basis of phylogenetic and phenotypic analyses and analysis of 16S rRNA and partial hsp60 gene sequences, we propose two novel species, Bifidobacterium actinocoloniiforme sp. nov. (type strain LISLUCIII-P2T = DSM 22766T = CCM 7728T) and Bifidobacterium bohemicum sp. nov. (type strain JEMLUCVIII-4T = DSM 22767T = CCM 7729T).
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MARTINELLO, Flávia, Camila Fontana ROMAN, and Paula Alves de SOUZA. "EFFECTS OF PROBIOTIC INTAKE ON INTESTINAL BIFIDOBACTERIA OF CELIAC PATIENTS." Arquivos de Gastroenterologia 54, no. 2 (February 23, 2017): 85–90. http://dx.doi.org/10.1590/s0004-2803.201700000-07.

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ABSTRACT BACKGROUND Healthy individuals exhibit a significantly higher concentration of faecal bifidobacteria in comparison to celiac patients. Even though there are potential benefits in probiotic usage, they have been little explored as an adjunctive therapy in celiac disease. OBJECTIVE This study aimed at the comparison of faecal bifidobacteria concentration and pH among celiac patients and healthy subjects before and after the daily intake of 100 g of yogurt containing probiotic for a thirty-day period. METHODS Feces from 17 healthy subjects and 14 celiac patients were analyzed, in which stool culture was performed for the isolation and quantification of faecal bifidobacteria. Furthermore, Gram’s method was employed for the microscopic analysis of the colonies, while the identification of the Bifidobacterium genus was made through determination of the fructose-6-phosphate phosphoketolase enzyme. Faecal pH was measured using a calibrated pHmeter. RESULTS Faecal bifidobacteria concentration before probiotic consumption was significantly higher in healthy individuals (2.3x108±6.3x107 CFU/g) when compared to celiac patients (1.0x107±1.7x107 CFU/g). Faecal pH values did not show a significant difference. After the daily consumption of probiotic-containing yogurt both groups showed a significant increase in the concentration of faecal bifidobacteria, but healthy subjects presented significantly higher bifidobacteria concentrations (14.7x108±0.2x108 CFU/g) than the celiac group (0.76x108±0.1x108 CFU/g). The obtained pH values from both groups were not significantly different, being 7.28±0.518 for the celiac patients and 7.07±0.570 for healthy individuals after the probiotic intake. CONCLUSION The probiotic supplementation significantly increased the number of bifidobacteria in the feces of celiac patients, although it was not sufficient to reach the concentration found in healthy individuals prior to its consumption.
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Modesto, M., S. Michelini, I. Stefanini, A. Ferrara, S. Tacconi, B. Biavati, and P. Mattarelli. "Bifidobacterium aesculapii sp. nov., from the faeces of the baby common marmoset (Callithrix jacchus)." International Journal of Systematic and Evolutionary Microbiology 64, Pt_8 (August 1, 2014): 2819–27. http://dx.doi.org/10.1099/ijs.0.056937-0.

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Six Gram-positive-staining, microaerophilic, non-spore-forming, fructose-6-phosphate phosphoketolase-positive bacterial strains with a peculiar morphology were isolated from faecal samples of baby common marmosets (Callithrix jacchus). Cells of these strains showed a morphology not reported previously for a bifidobacterial species, which resembled a coiled snake, always coiled or ring shaped or forming a ‘Y’ shape. Strains MRM 3/1T and MRM 4/2 were chosen as representative strains and characterized further. The bacteria utilized a wide range of carbohydrates and produced urease. Glucose was fermented to acetate and lactate. Strain MRM 3/1T showed a peptidoglycan type unique among members of the genus Bifidobacterium . The DNA base composition was 64.7 mol% G+C. Almost-complete 16S rRNA, hsp60, clpC and rpoB gene sequences were obtained and phylogenetic relationships were determined. Comparative analysis of 16S rRNA gene sequences showed that strains MRM 3/1T and MRM 4/2 had the highest similarities to Bifidobacterium scardovii DSM 13734T (94.6 %) and Bifidobacterium stellenboschense DSM 23968T (94.5 %). Analysis of hsp60 showed that both strains were closely related to B. stellenboschense DSM 23968T (97.5 % similarity); however, despite this high degree of similarity, our isolates could be distinguished from B. stellenboschense DSM 23968T by low levels of DNA–DNA relatedness (30.4 % with MRM 3/1T). Strains MRM 3/1T and MRM 4/2 were located in an actinobacterial cluster and were more closely related to the genus Bifidobacterium than to other genera in the family Bifidobacteriaceae . On the basis of these results, strains MRM 3/1T and MRM 4/2 represent a novel species within the genus Bifidobacterium , for which the name Bifidobacterium aesculapii sp. nov. is proposed; the type strain is MRM 3/1T ( = DSM 26737T = JCM 18761T).
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Morita, Hidetoshi, Akiyo Nakano, Hiromi Onoda, Hidehiro Toh, Kenshiro Oshima, Hideto Takami, Masaru Murakami, et al. "Bifidobacterium kashiwanohense sp. nov., isolated from healthy infant faeces." International Journal of Systematic and Evolutionary Microbiology 61, no. 11 (November 1, 2011): 2610–15. http://dx.doi.org/10.1099/ijs.0.024521-0.

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Strains HM2-1 and HM2-2T were isolated from the faeces of a healthy infant and were characterized by determining their phenotypic and biochemical features and phylogenetic positions based on partial 16S rRNA gene sequence analysis. They were Gram-positive, obligately anaerobic, non-spore-forming, non-gas-producing, and catalase-negative non-motile rods. They did not grow at 15 or 45 °C in anaerobic bacterial culture medium, and their DNA G+C content was in the range 56–59 mol%. In enzyme activity tests, strains HM2-1 and HM2-2T were positive for α/β-galactosidases and α/β-glucosidases but negative for β-glucuronidase and cystine arylamidase. An analysis of the cell-wall composition of strains HM2-1 and HM2-2T revealed the presence of glutamic acid, alanine and lysine. The presence of fructose-6-phosphate phosphoketolase shows that isolates HM2-1 and HM2-2T are members of the genus Bifidobacterium. These two isolates belong to the same species of the genus Bifidobacterium. Strain HM2-2T was found to be related to Bifidobacterium catenulatum JCM 1194T (97.4 % 16S rRNA gene sequence identity: 1480/1520 bp), Bifidobacterium pseudocatenulatum JCM 1200T (97.2 %: 1472/1514 bp), Bifidobacterium dentium ATCC 27534T (96.7 %: 1459/1509 bp) and Bifidobacterium angulatum ATCC 27535T (96.5 %: 1462/1515 bp). The predominant cellular fatty acids of strains HM2-1 and HM2-2T were 16 : 0 and 18 : 1ω9c, with proportions greater than 18 % of the total. Phylogenetic analyses involving phenotypic characterization, DNA–DNA hybridization and partial 16S rRNA gene sequencing proves that the strains represent a novel species of the genus Bifidobacterium, for which the name Bifidobacterium kashiwanohense sp. nov. is proposed. The type strain is HM2-2T ( = JCM 15439T = DSM 21854T).
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Rosberg-Cody, E., R. P. Ross, S. Hussey, C. A. Ryan, B. P. Murphy, G. F. Fitzgerald, R. Devery, and C. Stanton. "Mining the Microbiota of the Neonatal Gastrointestinal Tract for Conjugated Linoleic Acid-Producing Bifidobacteria." Applied and Environmental Microbiology 70, no. 8 (August 2004): 4635–41. http://dx.doi.org/10.1128/aem.70.8.4635-4641.2004.

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ABSTRACT This study was designed to isolate different strains of the genus Bifidobacterium from the fecal material of neonates and to assess their ability to produce the cis-9, trans-11 conjugated linoleic acid (CLA) isomer from free linoleic acid. Fecal material was collected from 24 neonates aged between 3 days and 2 months in a neonatal unit (Erinville Hospital, Cork, Ireland). A total of 46 isolates from six neonates were confirmed to be Bifidobacterium species based on a combination of the fructose-6-phosphate phosphoketolase assay, RAPD [random(ly) amplified polymorphic DNA] PCR, pulsed-field gel electrophoresis (PFGE), and partial 16S ribosomal DNA sequencing. Interestingly, only 1 of the 11 neonates that had received antibiotic treatment produced bifidobacteria. PFGE after genomic digestion with the restriction enzyme XbaI demonstrated that the bifidobacteria population displayed considerable genomic diversity among the neonates, with each containing between one and five dominant strains, whereas 11 different macro restriction patterns were obtained. In only one case did a single strain appear in two neonates. All genetically distinct strains were then screened for CLA production after 72 h of incubation with 0.5 mg of free linoleic acid ml−1 by using gas-liquid chromatography. The most efficient producers belonged to the species Bifidobacterium breve, of which two different strains converted 29 and 27% of the free linoleic acid to the cis-9, trans-11 isomer per microgram of dry cells, respectively. In addition, a strain of Bifidobacterium bifidum showed a conversion rate of 18%/μg dry cells. The ability of some Bifidobacterium strains to produce CLA could be another human health-promoting property linked to members of the genus, given that this metabolite has demonstrated anticarcinogenic activity in vitro and in vivo.
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Grill, Jean-Pierre, Joel Crociani, and Jean Ballongue. "Characterization of fructose 6 phosphate phosphoketolases purified from Bifidobacterium species." Current Microbiology 31, no. 1 (July 1995): 49–54. http://dx.doi.org/10.1007/bf00294634.

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Moriyama, Takashi, Naoyuki Tajima, Kohsuke Sekine, and Naoki Sato. "Characterization of three putative xylulose 5-phosphate/fructose 6-phosphate phosphoketolases in the cyanobacteriumAnabaenasp. PCC 7120." Bioscience, Biotechnology, and Biochemistry 79, no. 5 (December 20, 2014): 767–74. http://dx.doi.org/10.1080/09168451.2014.993357.

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Neuzil-Bunesova, Vera, Gabriele Andrea Lugli, Nikol Modrackova, Eva Vlkova, Petra Bolechova, Johanna Burtscher, Giulia Longhi, et al. "Five novel bifidobacterial species isolated from faeces of primates in two Czech zoos: Bifidobacterium erythrocebi sp. nov., Bifidobacterium moraviense sp. nov., Bifidobacterium oedipodis sp. nov., Bifidobacterium olomucense sp. nov. and Bifidobacterium panos sp. nov." International Journal of Systematic and Evolutionary Microbiology, November 23, 2020. http://dx.doi.org/10.1099/ijsem.0.004573.

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Abstract:
Five Bifidobacterium strains, VB23T, VB24T, VB25T, VB26T and VB31T, were isolated from chimpanzee (Pan troglodytes), cotton-top tamarin (Saguinus oedipus), Goeldi’s marmoset (Callimico goeldii), moustached tamarin (Saguinus mystax) and patas monkey (Erythrocebus patas), respectively, which were kept in two Czech zoos. These strains were isolated from faecal samples and were Gram-positive, non-motile, non-sporulating, anaerobic and fructose-6-phosphate phosphoketolase-positive. Phylogenetic analyses based on 16S rRNA revealed close relatedness between VB23T and Bifidobacterium angulatum LMG 11039T (96.0 %), VB24T and Bifidobacterium pullorum subsp. pullorum DSM 20433T (96.1 %), VB25T and Bifidobacterium goeldii LMG 30939T (96.5 %), VB26T and Bifidobacterium imperatoris LMG 30297T (98.1 %), and VB31T and B . angulatum LMG 11039T (99.40 %). Internal transcribed spacer profiling revealed that VB23T, VB24T, VB25T, VB26T and VB31T had highest similarity to Bifidobacterium breve LMG 13208T (77.2 %), Bifidobacterium longum subsp. infantis ATCC 15697T (85.8 %), Bifidobacterium biavatii DSM 23969T (76.9 %), B. breve LMG 13208T (81.2 %) and B. angulatum LMG 11039T (88.2 %), respectively. Average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) analyses with their closest neighbours supported the independent phylogenetic positions of the strains with values between 86.3 and 94.3 % for ANI and 25.8 and 54.9 % for dDDH. These genomic and phylogenetic analyses suggested that the evaluated strains were novel Bifidobacterium species named Bifidobacterium erythrocebi sp. nov. (VB31T=DSM 109960T=CCUG 73843T), Bifidobacterium moraviense sp. nov. (VB25T=DSM 109958T=CCUG 73842T), Bifidobacterium oedipodis sp. nov. (VB24T=DSM 109957T=CCUG 73932T), Bifidobacterium olomucense sp. nov. (VB26T=DSM 109959T=CCUG 73845T) and Bifidobacterium panos sp. nov. (VB23T=DSM 109963T=CCUG 73840T).
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