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Holman DB, Gzyl KE, Kommadath A. The gut microbiome and resistome of conventionally vs. pasture-raised pigs. Microb Genom 2023; 9:mgen001061. [PMID: 37439777 PMCID: PMC10438820 DOI: 10.1099/mgen.0.001061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 06/12/2023] [Indexed: 07/14/2023] Open
Abstract
Conventional swine production typically houses pigs indoors and in large groups, whereas pasture-raised pigs are reared outdoors at lower stocking densities. Antimicrobial use also differs, with conventionally raised pigs often being exposed to antimicrobials directly or indirectly to control and prevent infectious disease. However, antimicrobial use can be associated with the development and persistence of antimicrobial resistance. In this study, we used shotgun metagenomic sequencing to compare the gut microbiomes and resistomes of pigs raised indoors on a conventional farm with those raised outdoors on pasture. The microbial compositions as well as the resistomes of both groups of pigs were significantly different from each other. Bacterial species such as Intestinibaculum porci, Pseudoscardovia radai and Sharpea azabuensis were relatively more abundant in the gut microbiomes of pasture-raised pigs and Hallella faecis and Limosilactobacillus reuteri in the conventionally raised swine. The abundance of antimicrobial resistance genes (ARGs) was significantly higher in the conventionally raised pigs for nearly all antimicrobial classes, including aminoglycosides, beta-lactams, macrolides-lincosamides-streptogramin B, and tetracyclines. Functionally, the gut microbiomes of the two group of pigs also differed significantly based on their carbohydrate-active enzyme (CAZyme) profiles, with certain CAZyme families associated with host mucin degradation enriched in the conventional pig microbiomes. We also recovered 1043 dereplicated strain-level metagenome-assembled genomes (≥90 % completeness and <5 % contamination) to provide taxonomic context for specific ARGs and metabolic functions. Overall, the study provides insights into the differences between the gut microbiomes and resistomes of pigs raised under two very different production systems.
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Affiliation(s)
- Devin B. Holman
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, 6000 C&E Trail, Lacombe, AB, T4L1W1, Canada
| | - Katherine E. Gzyl
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, 6000 C&E Trail, Lacombe, AB, T4L1W1, Canada
| | - Arun Kommadath
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, 6000 C&E Trail, Lacombe, AB, T4L1W1, Canada
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2
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Bajagai YS, Petranyi F, J Yu S, Lobo E, Batacan R, Kayal A, Horyanto D, Ren X, M Whitton M, Stanley D. Phytogenic supplement containing menthol, carvacrol and carvone ameliorates gut microbiota and production performance of commercial layers. Sci Rep 2022; 12:11033. [PMID: 35773309 PMCID: PMC9246849 DOI: 10.1038/s41598-022-14925-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 06/15/2022] [Indexed: 11/17/2022] Open
Abstract
Consumer push towards open and free-range production systems makes biosecurity on farms challenging, leading to increased disease and animal welfare issues. Phytogenic products are increasingly becoming a viable alternative for the use of antibiotics in livestock production. Here we present a study of the effects of commercial phytogenic supplement containing menthol, carvacrol and carvone on intestinal microbiota of layer hens, microbial functional capacity, and intestinal morphology. A total of 40,000 pullets were randomly assigned to two sides of the experimental shed. Growth performance, mortality, egg production and egg quality parameters were recorded throughout the trial period (18–30 weeks of age). Microbial community was investigated using 16S amplicon sequencing and functional difference using metagenomic sequencing. Phytogen supplemented birds had lower mortality and number of dirty eggs, and their microbial communities showed reduced richness. Although phytogen showed the ability to control the range of poultry pathogens, its action was not restricted to pathogenic taxa, and it involved functional remodelling the intestinal community towards increased cofactor production, heterolactic fermentation and salvage and recycling of metabolites. The phytogen did not alter the antimicrobial resistance profile or the number of antibiotic resistance genes. The study indicates that phytogenic supplementation can mimic the action of antibiotics in altering the gut microbiota and be used as their alternative in industry-scale layer production.
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Affiliation(s)
- Yadav S Bajagai
- Institute for Future Farming Systems, Central Queensland University, Rockhampton, QLD, 4702, Australia
| | - Friedrich Petranyi
- Institute for Future Farming Systems, Central Queensland University, Rockhampton, QLD, 4702, Australia
| | - Sung J Yu
- Institute for Future Farming Systems, Central Queensland University, Rockhampton, QLD, 4702, Australia
| | - Edina Lobo
- Institute for Future Farming Systems, Central Queensland University, Rockhampton, QLD, 4702, Australia
| | - Romeo Batacan
- Institute for Future Farming Systems, Central Queensland University, Rockhampton, QLD, 4702, Australia
| | - Advait Kayal
- Institute for Future Farming Systems, Central Queensland University, Rockhampton, QLD, 4702, Australia
| | - Darwin Horyanto
- Institute for Future Farming Systems, Central Queensland University, Rockhampton, QLD, 4702, Australia
| | - Xipeng Ren
- Institute for Future Farming Systems, Central Queensland University, Rockhampton, QLD, 4702, Australia
| | - Maria M Whitton
- Institute for Future Farming Systems, Central Queensland University, Rockhampton, QLD, 4702, Australia
| | - Dragana Stanley
- Institute for Future Farming Systems, Central Queensland University, Rockhampton, QLD, 4702, Australia.
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Ren Z, Fang H, Zhang J, Wang R, Xiao W, Zheng K, Yu H, Zhao Y. Dietary Aronia melanocarpa Pomace Supplementation Enhances the Expression of ZO-1 and Occludin and Promotes Intestinal Development in Pigs. Front Vet Sci 2022; 9:904667. [PMID: 35711808 PMCID: PMC9196908 DOI: 10.3389/fvets.2022.904667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 05/04/2022] [Indexed: 11/21/2022] Open
Abstract
A fruit juice production byproduct, Aronia melanocarpa pomace (AMP) is rich in natural polyphenol antioxidant components. The objectives of this study were to study the effects of dietary AMP supplementation on the feeding outcome and intestinal barrier function of pigs. In total, 27 growing pigs (Duroc × Landrace × Yorkshire, ~60 days, average weight of 27.77 ± 2.87 kg, males and females included at random) were randomly allotted to 3 treatment groups, with 3 repetitions per group and 3 pigs per repetition. At the experiment completion, 2 pigs (close to the average body weight of all experimental pigs) per replicate were slaughtered. The control group (CON group) was fed a basic diet, and the experimental groups were fed 4% (4% AMP group) and 8% (8% AMP group) AMP in the basic diet. These pigs were prefed for 3 days, and the formal experiments were performed for 7 weeks. The results showed that compared with the CON diet, the 4% AMP supplementation significantly increased the average daily gain of pigs (P < 0.05). Regarding intestinal development, 4% AMP significantly increased the jejunal villus height/crypt depth ratio (P < 0.05), and different AMP levels had no significant effect on the pig cecum morphology. Different AMP levels significantly decreased the relative abundance of Proteobacteria (P < 0.05). Regarding other microbial genera, 4% AMP supplementation significantly increased the levels of Lachnospira, Solobacterium, Romboutsia and other beneficial microorganisms (P < 0.05). Different AMP levels significantly decreased the relative abundances of the opportunistic pathogens Escherichia-Shigella and Pseudoscardovia (P < 0.05) and increased the contents of acetic acid and butyric acid in the pig cecal contents (P < 0.05). Compared with the CON treatment, 4% AMP supplementation significantly downregulated the jejunal gene expression of porcine proinflammatory factors (IL-1β, IL-6, IL-8 and TNF-α) and significantly upregulated the jejunal gene expression of ZO-1, Occludin and Claudin-1 (P < 0.05). In conclusion, 4% AMP supplementation in feed is beneficial to overall pig health and growth.
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Splichalova A, Donovan SM, Tlaskalova-Hogenova H, Stranak Z, Splichalova Z, Splichal I. Monoassociation of Preterm Germ-Free Piglets with Bifidobacterium animalis Subsp. lactis BB-12 and Its Impact on Infection with Salmonella Typhimurium. Biomedicines 2021; 9:biomedicines9020183. [PMID: 33670419 PMCID: PMC7917597 DOI: 10.3390/biomedicines9020183] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 02/05/2021] [Accepted: 02/06/2021] [Indexed: 02/06/2023] Open
Abstract
Preterm germ-free piglets were monoassociated with probiotic Bifidobacterium animalis subsp. lactis BB-12 (BB12) to verify its safety and to investigate possible protection against subsequent infection with Salmonella Typhimurium strain LT2 (LT2). Clinical signs of salmonellosis, bacterial colonization in the intestine, bacterial translocation to mesenteric lymph nodes (MLN), blood, liver, spleen, and lungs, histopathological changes in the ileum, claudin-1 and occludin mRNA expression in the ileum and colon, intestinal and plasma concentrations of IL-8, TNF-α, and IL-10 were evaluated. Both BB12 and LT2 colonized the intestine of the monoassociated piglets. BB12 did not translocate in the BB12-monoassociated piglets. BB12 was detected in some cases in the MLN of piglets, consequently infected with LT2, but reduced LT2 counts in the ileum and liver of these piglets. LT2 damaged the luminal structure of the ileum, but a previous association with BB12 mildly alleviated these changes. LT2 infection upregulated claudin-1 mRNA in the ileum and colon and downregulated occludin mRNA in the colon. Infection with LT2 increased levels of IL-8, TNF-α, and IL-10 in the intestine and plasma, and BB12 mildly downregulated them compared to LT2 alone. Despite reductions in bacterial translocation and inflammatory cytokines, clinical signs of LT2 infection were not significantly affected by the probiotic BB12. Thus, we hypothesize that multistrain bacterial colonization of preterm gnotobiotic piglets may be needed to enhance the protective effect against the infection with S. Typhimurium LT2.
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Affiliation(s)
- Alla Splichalova
- Laboratory of Gnotobiology, Institute of Microbiology, Czech Academy of Sciences, 549 22 Novy Hradek, Czech Republic; (A.S.); (Z.S.)
| | - Sharon M. Donovan
- Department of Food Science and Human Nutrition, University of Illinois, Urbana, IL 61801, USA;
| | - Helena Tlaskalova-Hogenova
- Laboratory of Cellular and Molecular Immunology, Institute of Microbiology, Czech Academy of Sciences, 142 20 Prague, Czech Republic;
| | - Zbynek Stranak
- Department of Neonatology, Institute for the Care of Mother and Child, 147 00 Prague, Czech Republic;
| | - Zdislava Splichalova
- Laboratory of Gnotobiology, Institute of Microbiology, Czech Academy of Sciences, 549 22 Novy Hradek, Czech Republic; (A.S.); (Z.S.)
| | - Igor Splichal
- Laboratory of Gnotobiology, Institute of Microbiology, Czech Academy of Sciences, 549 22 Novy Hradek, Czech Republic; (A.S.); (Z.S.)
- Correspondence: ; Tel.: +420-491-418-539
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Splichalova A, Pechar R, Killer J, Splichalova Z, Bunesova VN, Vlkova E, Salmonova HS, Splichal I. Colonization of Germ-Free Piglets with Mucinolytic and Non-Mucinolytic Bifidobacterium boum Strains Isolated from the Intestine of Wild Boar and Their Interference with Salmonella Typhimurium. Microorganisms 2020; 8:microorganisms8122002. [PMID: 33333934 PMCID: PMC7765441 DOI: 10.3390/microorganisms8122002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 12/12/2020] [Accepted: 12/13/2020] [Indexed: 02/06/2023] Open
Abstract
Non-typhoidal Salmonella serovars are worldwide spread foodborne pathogens that cause diarrhea in humans and animals. Colonization of gnotobiotic piglet intestine with porcine indigenous mucinolytic Bifidobacterium boum RP36 strain and non-mucinolytic strain RP37 and their interference with Salmonella Typhimurium infection were compared. Bacterial interferences and impact on the host were evaluated by clinical signs of salmonellosis, bacterial translocation, goblet cell count, mRNA expression of mucin 2, villin, claudin-1, claudin-2, and occludin in the ileum and colon, and plasmatic levels of inflammatory cytokines IL-8, TNF-α, and IL-10. Both bifidobacterial strains colonized the intestine comparably. Neither RP36 nor RP37 B. boum strains effectively suppressed signs of salmonellosis. Both B. boum strains suppressed the growth of S. Typhimurium in the ileum and colon. The mucinolytic RP36 strain increased the translocation of S. Typhimurium into the blood, liver, and spleen.
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Affiliation(s)
- Alla Splichalova
- Laboratory of Gnotobiology, Institute of Microbiology, Czech Academy of Sciences, 549 22 Novy Hradek, Czech Republic; (A.S.); (Z.S.)
| | - Radko Pechar
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, 165 00 Prague, Czech Republic; (R.P.); (J.K.); (V.N.B.); (E.V.); (H.S.S.)
- Department of Research, Food Research Institute Prague, 102 00 Prague, Czech Republic
| | - Jiri Killer
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, 165 00 Prague, Czech Republic; (R.P.); (J.K.); (V.N.B.); (E.V.); (H.S.S.)
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, 142 20 Prague, Czech Republic
| | - Zdislava Splichalova
- Laboratory of Gnotobiology, Institute of Microbiology, Czech Academy of Sciences, 549 22 Novy Hradek, Czech Republic; (A.S.); (Z.S.)
| | - Vera Neuzil Bunesova
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, 165 00 Prague, Czech Republic; (R.P.); (J.K.); (V.N.B.); (E.V.); (H.S.S.)
| | - Eva Vlkova
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, 165 00 Prague, Czech Republic; (R.P.); (J.K.); (V.N.B.); (E.V.); (H.S.S.)
| | - Hana Subrtova Salmonova
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, 165 00 Prague, Czech Republic; (R.P.); (J.K.); (V.N.B.); (E.V.); (H.S.S.)
| | - Igor Splichal
- Laboratory of Gnotobiology, Institute of Microbiology, Czech Academy of Sciences, 549 22 Novy Hradek, Czech Republic; (A.S.); (Z.S.)
- Correspondence: ; Tel.: +420-491-418-539; Fax: +420-491-478-264
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Modesto M, Satti M, Watanabe K, Sciavilla P, Felis GE, Sandri C, Spiezio C, Arita M, Mattarelli P. Alloscardovia theropitheci sp. nov., isolated from the faeces of gelada baboon, the 'bleeding heart' monkey (Theropithecus gelada). Int J Syst Evol Microbiol 2019; 69:3041-3048. [DOI: 10.1099/ijsem.0.003584] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Affiliation(s)
- Monica Modesto
- Department of Agricultural and Food Sciences, University of Bologna, Italy
| | - Maria Satti
- Department of Genetics, SOKENDAI University, Shizuoka 411-8540, Japan
| | - Koichi Watanabe
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu, Taiwan ROC
- Department of Animal Science and Technology, National Taiwan University, Taipei, Taiwan ROC
| | - Piero Sciavilla
- Department of Agricultural and Food Sciences, University of Bologna, Italy
| | | | - Camillo Sandri
- Department of Animal Health Care and Management, Parco Natura Viva - Garda Zoological Park (Bussolengo), Verona, Italy
| | - Caterina Spiezio
- Department of Animal Health Care and Management, Parco Natura Viva - Garda Zoological Park (Bussolengo), Verona, Italy
| | - Masanori Arita
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
- Bioinformation and DDBJ Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
- Department of Genetics, SOKENDAI University, Shizuoka 411-8540, Japan
| | - Paola Mattarelli
- Department of Agricultural and Food Sciences, University of Bologna, Italy
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Mekadim C, Bunešová V, Vlková E, Hroncová Z, Killer J. Genetic marker-based multi-locus sequence analysis for classification, genotyping, and phylogenetics of the family Bifidobacteriaceae as an alternative approach to phylogenomics. Antonie Van Leeuwenhoek 2019; 112:1785-1800. [PMID: 31368048 DOI: 10.1007/s10482-019-01307-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 07/24/2019] [Indexed: 02/07/2023]
Abstract
Bifidobacteria are widely known for their probiotic potential; however, little is known regarding the ecological significance and potential probiotic effects of the phylogenetically related 'scardovial' genera (Aeriscardovia, Alloscardovia, Bombiscardovia, Galliscardovia, Neoscardovia, Parascardovia, Pseudoscardovia and Scardovia) and Gardnerella classified with bifidobacteria within the Bifidobacteriaceae family. Accurate classification and genotyping of bacteria using certain housekeeping genes is possible, whilst current phylogenomic analyses allow for extremely precise classification. Studies of applicable genetic markers may provide results comparable to those obtained from phylogenomic analyses of the family Bifidobacteriaceae. Segments of the glyS (624 nucleotides), pheS (555 nucleotides), rpsA (630 nucleotides), and rpsB (432 nucleotides) genes and their concatenated sequence were explored. The mean glyS, pheS, rpsB and rpsA gene sequence similarities calculated for Bifidobacterium taxa were 84.8, 85.2, 90.2 and 86.8%, respectively. Interestingly, the average value of the Average Nucleotide Identity among 67 type strains of the family Bifidobacteriaceae (84.70%) calculated based on values published recently was in agreement with the average pairwise similarity (84.6%) among 75 type strains of Bifidobacteriaceae family computed in this study using the concatenated sequences of four gene fragments. Similar to phylogenomic analyses, several gene sequence and phylogenetic analyses revealed that concatenated gene regions allow for classification of Bifidobacteriaceae strains into particular phylogenetic clusters and groups. Phylogeny reconstructed from the concatenated sequences assisted in defining two novel phylogenetic groups, the Bifidobacterium psychraerophilum group consisting of B. psychraerophilum, Bifidobacterium crudilactis and Bifidobacterium aquikefiri species and the Bifidobacterium bombi group consisting of B. bombi, Bifidobacterium bohemicum and Bifidobacterium commune.
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Affiliation(s)
- Chahrazed Mekadim
- Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Vídeňská 1083, Prague 4, 142 20, Krč, Czech Republic.,Department of Microbiology, Nutrition and Dietetics, Food and Natural Resources, Faculty of Agrobiology, Czech University of Life Sciences, Kamýcká 129, Prague 6, 165 00, Suchdol, Czech Republic
| | - Věra Bunešová
- Department of Microbiology, Nutrition and Dietetics, Food and Natural Resources, Faculty of Agrobiology, Czech University of Life Sciences, Kamýcká 129, Prague 6, 165 00, Suchdol, Czech Republic
| | - Eva Vlková
- Department of Microbiology, Nutrition and Dietetics, Food and Natural Resources, Faculty of Agrobiology, Czech University of Life Sciences, Kamýcká 129, Prague 6, 165 00, Suchdol, Czech Republic
| | - Zuzana Hroncová
- Department of Microbiology, Nutrition and Dietetics, Food and Natural Resources, Faculty of Agrobiology, Czech University of Life Sciences, Kamýcká 129, Prague 6, 165 00, Suchdol, Czech Republic
| | - Jiří Killer
- Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Vídeňská 1083, Prague 4, 142 20, Krč, Czech Republic. .,Department of Microbiology, Nutrition and Dietetics, Food and Natural Resources, Faculty of Agrobiology, Czech University of Life Sciences, Kamýcká 129, Prague 6, 165 00, Suchdol, Czech Republic.
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Liu Y, Chen X, Zhao W, Lang M, Zhang X, Wang T, Farouk MH, Zhen Y, Qin G. Effects of yeast culture supplementation and the ratio of non-structural carbohydrate to fat on rumen fermentation parameters and bacterial-community composition in sheep. Anim Feed Sci Technol 2019; 249:62-75. [DOI: 10.1016/j.anifeedsci.2019.02.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Killer J, Mekadim C, Pechar R, Bunešová V, Vlková E. The threonine-tRNA ligase gene region is applicable in classification, typing, and phylogenetic analysis of bifidobacteria. J Microbiol 2018; 56:713-721. [DOI: 10.1007/s12275-018-8167-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 06/26/2018] [Accepted: 06/27/2018] [Indexed: 11/27/2022]
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Sechovcová H, Killer J, Pechar R, Geigerová M, Švejstil R, Salmonová H, Mekadim C, Rada V, Vlková E, Kofroňová O, Benada O. Alloscardovia venturai sp. nov., a fructose 6-phosphate phosphoketolase-positive species isolated from the oral cavity of a guinea-pig (Cavia aperea f. porcellus). Int J Syst Evol Microbiol 2017; 67:2842-2847. [PMID: 28820091 DOI: 10.1099/ijsem.0.002031] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A slightly irregular, short rod-shaped bacterial strain, MOZIV/2T, showing activity of fructose 6-phosphate phosphoketolase was isolated from the oral cavity of a home-bred guinea-pig. Based on comparative 16S rRNA gene sequence analyses, its closest relatives were Alloscardovia omnicolens DSM 21503T and Alloscardovia criceti DSM 17774T with 96.0 and 95.6 % pairwise similarities, respectively. Completeness of the compared sequences was 97.3 and 96.9 %, respectively. Growth was found only under anaerobic conditions. Activities of α- and β-gluco(galacto)sidases were detected in strain MOZIV/2T, which is characteristic for almost all members of the family Bifidobacteriaceae. Sequencing of other molecular markers (fusA, gyrB and xfp) revealed low gene sequence similarities to A. omnicolens DSM 21503T ranging from 72.7 to 87.5 %. Strain MOZIV/2T differed from other species within the genus Alloscardovia by the presence of C18 : 1ω9t. In addition, much higher proportions of C8 : 0, C11 : 0, C12 : 0, C14 : 1, C16 : 1 and C17 : 0 fatty acids were found in cells of strain MOZIV/2T. The peptidoglycan structure was of type A4α [l-Lys(l-Orn)-d-Asp], which is consistent with its classification within the genus Alloscardovia. The DNA G+C content (45.8 mol%) was lower than those found in other alloscardovia. Phylogenetic studies and evaluation of phenotypic characteristics including the results of biochemical, physiological and chemotaxonomic analyses confirmed the novel species status for strain MOZIV/2T, for which the name Alloscardovia venturai sp. nov. is proposed. The type strain is MOZIV/2T (=DSM 100237T=CCM 8604T=LMG 28781T).
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Affiliation(s)
- Hana Sechovcová
- Institute of Animal Physiology and Genetics v.v.i., Czech Academy of Sciences, v.v.i., Vídeňská 1083, Prague 4 - Krč, 142 20, Czech Republic
| | - Jiri Killer
- Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Faculty of Agrobiology, Food and Natural Resources, Kamýcká 129, Prague 6 - Suchdol, 16500, Czech Republic.,Institute of Animal Physiology and Genetics v.v.i., Czech Academy of Sciences, v.v.i., Vídeňská 1083, Prague 4 - Krč, 142 20, Czech Republic
| | - Radko Pechar
- Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Faculty of Agrobiology, Food and Natural Resources, Kamýcká 129, Prague 6 - Suchdol, 16500, Czech Republic
| | - Martina Geigerová
- Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Faculty of Agrobiology, Food and Natural Resources, Kamýcká 129, Prague 6 - Suchdol, 16500, Czech Republic
| | - Roman Švejstil
- Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Faculty of Agrobiology, Food and Natural Resources, Kamýcká 129, Prague 6 - Suchdol, 16500, Czech Republic
| | - Hana Salmonová
- Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Faculty of Agrobiology, Food and Natural Resources, Kamýcká 129, Prague 6 - Suchdol, 16500, Czech Republic
| | - Chahrazed Mekadim
- Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Faculty of Agrobiology, Food and Natural Resources, Kamýcká 129, Prague 6 - Suchdol, 16500, Czech Republic
| | - Vojtěch Rada
- Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Faculty of Agrobiology, Food and Natural Resources, Kamýcká 129, Prague 6 - Suchdol, 16500, Czech Republic
| | - Eva Vlková
- Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Faculty of Agrobiology, Food and Natural Resources, Kamýcká 129, Prague 6 - Suchdol, 16500, Czech Republic
| | - Olga Kofroňová
- Institute of Microbiology of the Czech Academy of Sciences, v.v.i., Vídeňská 1083, 142 20 Prague 4, Czech Republic
| | - Oldřich Benada
- Institute of Microbiology of the Czech Academy of Sciences, v.v.i., Vídeňská 1083, 142 20 Prague 4, Czech Republic.,Department of Biology, Faculty of Science, J. E. Purkyně University in Ústí nad Labem, Za Válcovnou 1000/8, 400 96 Ústí nad Labem, Czech Republic
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Pechar R, Killer J, Mekadim C, Geigerová M, Rada V. Classification of Culturable Bifidobacterial Population from Colonic Samples of Wild Pigs (Sus scrofa) Based on Three Molecular Genetic Methods. Curr Microbiol 2017; 74:1324-1331. [PMID: 28756573 DOI: 10.1007/s00284-017-1320-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 07/25/2017] [Indexed: 12/24/2022]
Abstract
Occurrence of bifidobacteria, known as health-promoting probiotic microorganisms, in the digestive tract of wild pigs (Sus scrofa) has not been examined yet. One hundred forty-nine fructose-6-phosphate phosphoketolase positive bacterial strains were isolated from colonic content of twenty-two individuals of wild pigs originated from four localities in the Czechia. Based on PCR-DGGE technique targeting the variable V3 region of the 16S rRNA genes, strains were initially differentiated into four groups represented by: (i) probably a new Bifidobacterium species (89 strains), (ii) B. boum/B. thermophilum/B. thermacidophilum subsp. porcinum/B. thermacidophilum subsp. thermacidophilum (sub)species (49 strains), (iii) Pseudoscardovia suis (7 strains), and (iv) B. pseudolongum subsp. globosum/B. pseudolongum subsp. pseudolongum (4 strains), respectively. Given the fact that DGGE technique did not allow to differentiate the representatives of thermophilic bifidobacteria and B. pseudolongum subspecies, strains were further classified by the 16S rRNA and thrS gene sequences. Primers targeting the variable regions of the latter gene were designed to be applicable in identification and phylogeny of Bifidobacteriaceae family. The 16S rRNA-derived phylogenetic study classified members of the first group into five subgroups in a separated cluster of thermophilic bifidobacteria. Comparable results were obtained by the thrS-derived phylogenetic analysis. Remarkably, variability among thrS sequences was higher compared with 16S rRNA gene sequences. Overall, molecular genetic techniques application allowed to identify a new Bifidobacterium phylotype which is predominant in the digestive tract of examined wild pigs.
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Affiliation(s)
- Radko Pechar
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, Kamýcká 129, Suchdol, 165 00, Prague 6, Czech Republic.,Food Research Institute Prague, Radiová 1285/7, Hostivař, 102 00, Prague 10, Czech Republic
| | - Jiří Killer
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, Kamýcká 129, Suchdol, 165 00, Prague 6, Czech Republic. .,Institute of Animal Physiology and Genetics v.v.i, Czech Academy of Sciences, Vídeňská 1083, Krč, 142 20, Prague 4, Czech Republic.
| | - Chahrazed Mekadim
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, Kamýcká 129, Suchdol, 165 00, Prague 6, Czech Republic
| | - Martina Geigerová
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, Kamýcká 129, Suchdol, 165 00, Prague 6, Czech Republic
| | - Vojtěch Rada
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, Kamýcká 129, Suchdol, 165 00, Prague 6, Czech Republic
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Pechar R, Killer J, Švejstil R, Salmonová H, Geigerová M, Bunešová V, Rada V, Benada O. Galliscardovia ingluviei gen. nov., sp. nov., a thermophilic bacterium of the family Bifidobacteriaceae isolated from the crop of a laying hen (Gallus gallus f. domestica). Int J Syst Evol Microbiol 2017; 67:2403-2411. [DOI: 10.1099/ijsem.0.001972] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Affiliation(s)
- R. Pechar
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, Kamýcká 129, Prague 6 – Suchdol, 165 00, Czech Republic
| | - J. Killer
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, Kamýcká 129, Prague 6 – Suchdol, 165 00, Czech Republic
- Institute of Animal Physiology and Genetics v.v.i., Academy of Sciences of the Czech Republic, Vídeňská 1083, Prague 4 – Krč, 142 20, Czech Republic
| | - R. Švejstil
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, Kamýcká 129, Prague 6 – Suchdol, 165 00, Czech Republic
| | - H. Salmonová
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, Kamýcká 129, Prague 6 – Suchdol, 165 00, Czech Republic
| | - M. Geigerová
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, Kamýcká 129, Prague 6 – Suchdol, 165 00, Czech Republic
| | - V. Bunešová
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, Kamýcká 129, Prague 6 – Suchdol, 165 00, Czech Republic
| | - V. Rada
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, Kamýcká 129, Prague 6 – Suchdol, 165 00, Czech Republic
| | - O. Benada
- Institute of Microbiology of the Czech Academy of Sciences, v.v.i., Vídeňská 1083, 142 20, Prague 4, Czech Republic
- Department of Biology, Faculty of Science, J. E. Purkyně University in Ústí nad Labem, Za Válcovnou 1000/8, 400 96 Ústí nad Labem, Czech Republic
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Pechar R, Killer J, Salmonová H, Geigerová M, Švejstil R, Švec P, Sedláček I, Rada V, Benada O. Bifidobacterium apri sp. nov., a thermophilic actinobacterium isolated from the digestive tract of wild pigs (Sus scrofa). Int J Syst Evol Microbiol 2017; 67:2349-2356. [DOI: 10.1099/ijsem.0.001956] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- R. Pechar
- Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Faculty of Agrobiology, Food and Natural Resources, Kamýcká 129, Prague 6 – Suchdol, 165 21, Czech Republic
| | - J. Killer
- Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Faculty of Agrobiology, Food and Natural Resources, Kamýcká 129, Prague 6 – Suchdol, 165 21, Czech Republic
- Institute of Animal Physiology and Genetics v.v.i., Academy of Sciences of the Czech Republic, Vídeňská 1083, Prague 4 – Krč, 142 20, Czech Republic
| | - H. Salmonová
- Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Faculty of Agrobiology, Food and Natural Resources, Kamýcká 129, Prague 6 – Suchdol, 165 21, Czech Republic
| | - M. Geigerová
- Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Faculty of Agrobiology, Food and Natural Resources, Kamýcká 129, Prague 6 – Suchdol, 165 21, Czech Republic
| | - R. Švejstil
- Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Faculty of Agrobiology, Food and Natural Resources, Kamýcká 129, Prague 6 – Suchdol, 165 21, Czech Republic
| | - P. Švec
- Czech Collection of Microorganisms, Masaryk University, Faculty of Science, Kamenice 5, building A25, 625 00, Brno, Czech Republic
| | - I. Sedláček
- Czech Collection of Microorganisms, Masaryk University, Faculty of Science, Kamenice 5, building A25, 625 00, Brno, Czech Republic
| | - V. Rada
- Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Faculty of Agrobiology, Food and Natural Resources, Kamýcká 129, Prague 6 – Suchdol, 165 21, Czech Republic
| | - O. Benada
- Institute of Microbiology of the Czech Academy of Sciences, v.v.i., Vídeňská 1083, 142 20, Prague 4, Czech Republic
- Department of Biology, Faculty of Science, J. E. Purkyně University in Ústi nad Labem, Za Válcovnou 1000/8, 400 96 Ústí nad Labem, Czech Republic
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Zhang G, Gao B, Adeolu M, Khadka B, Gupta RS. Phylogenomic Analyses and Comparative Studies on Genomes of the Bifidobacteriales: Identification of Molecular Signatures Specific for the Order Bifidobacteriales and Its Different Subclades. Front Microbiol 2016; 7:978. [PMID: 27446019 PMCID: PMC4921777 DOI: 10.3389/fmicb.2016.00978] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 06/07/2016] [Indexed: 11/24/2022] Open
Abstract
The order Bifidobacteriales comprises a diverse variety of species found in the gastrointestinal tract of humans and other animals, some of which are opportunistic pathogens, whereas a number of others exhibit health-promoting effects. However, currently very few biochemical or molecular characteristics are known which are specific for the order Bifidobacteriales, or specific clades within this order, which distinguish them from other bacteria. This study reports the results of detailed comparative genomic and phylogenetic studies on 62 genome-sequenced species/strains from the order Bifidobacteriales. In a robust phylogenetic tree for the Bifidobacteriales constructed based on 614 core proteins, a number of well-resolved clades were observed including a clade separating the Scarodvia-related genera (Scardovia clade) from the genera Bifidobacterium and Gardnerella, as well as a number of previously reported clusters of Bifidobacterium spp. In parallel, our comparative analyses of protein sequences from the Bifidobacteriales genomes have identified numerous molecular markers that are specific for this group of bacteria. Of these markers, 32 conserved signature indels (CSIs) in widely distributed proteins and 10 signature proteins are distinctive characteristics of all sequenced Bifidobacteriales species and provide novel and highly specific means for distinguishing these bacteria. In addition, multiple other molecular signatures are specific for the following clades of Bifidobacteriales: (i) 5 CSIs specific for a clade comprising of the Scardovia-related genera; (ii) 3 CSIs and 2 CSPs specific for a clade consisting of the Bifidobacterium and Gardnerella spp.; (iii) multiple other signatures demarcating a number of clusters of the B. asteroides-and B. longum- related species. The described molecular markers provide novel and reliable means for distinguishing the Bifidobacteriales and a number of their clades in molecular terms and for the classification of these bacteria. The Bifidobacteriales-specific CSIs, found in important proteins, are predicted to play important roles in modifying the cellular functions of the affected proteins. Hence, biochemical studies on the cellular functions of these CSIs could lead to discovery of novel characteristics of either all Bifidobacteriales, or specific groups of bacteria within this order. Some of the functions affected/modified by these genetic changes could also be important for the probiotic/pathogenic activities of the bifidobacteria.
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Affiliation(s)
- Grace Zhang
- Department of Biochemistry and Biomedical Sciences, McMaster University Hamilton, ON, Canada
| | - Beile Gao
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences Guangzhou, China
| | - Mobolaji Adeolu
- Department of Biochemistry and Biomedical Sciences, McMaster University Hamilton, ON, Canada
| | - Bijendra Khadka
- Department of Biochemistry and Biomedical Sciences, McMaster University Hamilton, ON, Canada
| | - Radhey S Gupta
- Department of Biochemistry and Biomedical Sciences, McMaster University Hamilton, ON, Canada
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Michelini S, Oki K, Yanokura E, Shimakawa Y, Modesto M, Mattarelli P, Biavati B, Watanabe K. Bifidobacterium myosotis sp. nov., Bifidobacterium tissieri sp. nov. and Bifidobacterium hapali sp. nov., isolated from faeces of baby common marmosets (Callithrix jacchus L.). Int J Syst Evol Microbiol 2015; 66:255-265. [PMID: 26515885 DOI: 10.1099/ijsem.0.000708] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In a previous study on bifidobacterial distribution in New World monkeys, six strains belonging to the Bifidobacteriaceae were isolated from faecal samples of baby common marmosets (Callithrix jacchus L.). All the isolates were Gram-positive-staining, anaerobic, asporogenous and fructose-6-phosphate phosphoketolase-positive. Comparative analysis of 16S rRNA gene sequences revealed relatively low levels of similarity (maximum identity 96 %) to members of the genus Bifidobacterium, and placed the isolates in three independent clusters: strains of cluster I (MRM_5.9T and MRM_5.10) and cluster III (MRM_5.18T and MRM_9.02) respectively showed 96.4 and 96.7 % 16S rRNA gene sequence similarity to Bifidobacterium callitrichos DSM 23973T, while strains of cluster II (MRM_8.14T and MRM_9.14) showed 95.4 % similarity to Bifidobacterium stellenboschense DSM 23968T. Phylogenetic analysis of partial hsp60 and clpC gene sequences supported an independent phylogenetic position of each cluster from each other and from the related type strains B. callitrichos DSM 23973T and B. stellenboschense DSM 23968T. Clusters I, II and III respectively showed DNA G+C contents of 64.9-65.1, 56.4-56.7 and 63.1-63.7 mol%. The major cellular fatty acids of MRM_5.9T were C14 : 0, C16 : 0 and C18 : 1ω9c dimethylacetal, while C16 : 0 was prominent in strains MRM_5.18T and MRM_8.14T, followed by C18 : 1ω9c and C14 : 0. Biochemical profiles and growth parameters were recorded for all the isolates. Based on the data provided, the clusters represent three novel species, for which the names Bifidobacterium myosotis sp. nov. (type strain MRM_5.9T = DSM 100196T = JCM 30796T), Bifidobacterium hapali sp. nov. (type strain MRM_8.14T = DSM 100202T = JCM 30799T) and Bifidobacterium tissieri sp. nov. (type strain MRM_5.18T = DSM 100201T = JCM 30798T) are proposed.
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Affiliation(s)
- Samanta Michelini
- Department of Agricultural Sciences, University of Bologna, Bologna, Italy
| | - Kaihei Oki
- Yakult Honsha European Research Center for Microbiology ESV, Technologie Park 4, 9052 Zwijnaarde, Belgium
| | - Emiko Yanokura
- Yakult Central Institute, 5-11 Izumi, Kunitachi, Tokyo 186-8650, Japan
| | | | - Monica Modesto
- Department of Agricultural Sciences, University of Bologna, Bologna, Italy
| | - Paola Mattarelli
- Department of Agricultural Sciences, University of Bologna, Bologna, Italy
| | - Bruno Biavati
- Institute of Earth Systems, Division of Rural Sciences & Food Systems, University of Malta, Msida, Malta
| | - Koichi Watanabe
- Department of Animal Science and Technology, National Taiwan University, No. 50, Lane 155, Sec. 3, Keelung Rd, Taipei 10673, Taiwan ROC
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Bunesova V, Vlkova E, Rada V, Killer J, Musilova S. Bifidobacteria from the gastrointestinal tract of animals: differences and similarities. Benef Microbes 2015; 5:377-88. [PMID: 24889892 DOI: 10.3920/bm2013.0081] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
At present, the genus Bifidobacterium includes 48 species and subspecies, and this number is expected to increase. Bifidobacteria are found in different ecological niches. However, most were originally isolated from animals, mainly mammals, especially during the milk feeding period of life. Their presence in high numbers is associated with good health of the host. Moreover, bifidobacteria are often found in poultry and insects that exhibit a social mode of life (honeybees and bumblebees). This review is designed as a summary of currently known species of the genus Bifidobacterium, especially focused on their difference and similarities. The primary focus is on their occurrence in the digestive tract of animals, as well as the specificities of animal strains, with regard to their potential use as probiotics.
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Affiliation(s)
- V Bunesova
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 16521 Prague 6-Suchdol, Czech Republic
| | - E Vlkova
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 16521 Prague 6-Suchdol, Czech Republic
| | - V Rada
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 16521 Prague 6-Suchdol, Czech Republic
| | - J Killer
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 16521 Prague 6-Suchdol, Czech Republic Institute of Animal Physiology and Genetics, Academy of Sciences of the Czech Republic, Vídeňská 1083, 14200 Prague 4-Krč, Czech Republic
| | - S Musilova
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 16521 Prague 6-Suchdol, Czech Republic
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Hroncova Z, Havlik J, Killer J, Doskocil I, Tyl J, Kamler M, Titera D, Hakl J, Mrazek J, Bunesova V, Rada V. Variation in honey bee gut microbial diversity affected by ontogenetic stage, age and geographic location. PLoS One 2015; 10:e0118707. [PMID: 25768309 PMCID: PMC4358834 DOI: 10.1371/journal.pone.0118707] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 01/22/2015] [Indexed: 02/07/2023] Open
Abstract
Social honey bees, Apis mellifera, host a set of distinct microbiota, which is similar across the continents and various honey bee species. Some of these bacteria, such as lactobacilli, have been linked to immunity and defence against pathogens. Pathogen defence is crucial, particularly in larval stages, as many pathogens affect the brood. However, information on larval microbiota is conflicting. Seven developmental stages and drones were sampled from 3 colonies at each of the 4 geographic locations of A. mellifera carnica, and the samples were maintained separately for analysis. We analysed the variation and abundance of important bacterial groups and taxa in the collected bees. Major bacterial groups were evaluated over the entire life of honey bee individuals, where digestive tracts of same aged bees were sampled in the course of time. The results showed that the microbial tract of 6-day-old 5th instar larvae were nearly equally rich in total microbial counts per total digestive tract weight as foraging bees, showing a high percentage of various lactobacilli (Firmicutes) and Gilliamella apicola (Gammaproteobacteria 1). However, during pupation, microbial counts were significantly reduced but recovered quickly by 6 days post-emergence. Between emergence and day 6, imago reached the highest counts of Firmicutes and Gammaproteobacteria, which then gradually declined with bee age. Redundancy analysis conducted using denaturing gradient gel electrophoresis identified bacterial species that were characteristic of each developmental stage. The results suggest that 3-day 4th instar larvae contain low microbial counts that increase 2-fold by day 6 and then decrease during pupation. Microbial succession of the imago begins soon after emergence. We found that bacterial counts do not show only yearly cycles within a colony, but vary on the individual level. Sampling and pooling adult bees or 6th day larvae may lead to high errors and variability, as both of these stages may be undergoing dynamic succession.
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Affiliation(s)
- Zuzana Hroncova
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Jaroslav Havlik
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Prague, Czech Republic
- * E-mail:
| | - Jiri Killer
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Prague, Czech Republic
- Institute of Animal Physiology and Genetics v.v.i., Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Ivo Doskocil
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Jan Tyl
- Bee Research Institute at Dol, Libcice nad Vltavou, Czech Republic
| | - Martin Kamler
- Bee Research Institute at Dol, Libcice nad Vltavou, Czech Republic
| | - Dalibor Titera
- Bee Research Institute at Dol, Libcice nad Vltavou, Czech Republic
- Department of Zoology and Fisheries, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Josef Hakl
- Department of Forage Crops and Grassland Management, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Jakub Mrazek
- Institute of Animal Physiology and Genetics v.v.i., Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Vera Bunesova
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Vojtech Rada
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Prague, Czech Republic
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Abstract
The purpose of this announcement is to effect the valid publication of the following effectively published new names and new combinations under the procedure described in the Bacteriological Code (1990 Revision). Authors and other individuals wishing to have new names and/or combinations included in future lists should send three copies of the pertinent reprint or photocopies thereof, or an electronic copy of the published paper to the IJSEM Editorial Office for confirmation that all of the other requirements for valid publication have been met. It is also a requirement of IJSEM and the ICSP that authors of new species, new subspecies and new combinations provide evidence that types are deposited in two recognized culture collections in two different countries. It should be noted that the date of valid publication of these new names and combinations is the date of publication of this list, not the date of the original publication of the names and combinations. The authors of the new names and combinations are as given below. Inclusion of a name on these lists validates the publication of the name and thereby makes it available in the nomenclature of prokaryotes. The inclusion of a name on this list is not to be construed as taxonomic acceptance of the taxon to which the name is applied. Indeed, some of these names may, in time, be shown to be synonyms, or the organisms may be transferred to another genus, thus necessitating the creation of a new combination.
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Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, Givat Ram, 91904 Jerusalem, Israel
| | - George M. Garrity
- Department of Microbiology & Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA
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Killer J, Votavová A, Valterová I, Vlková E, Rada V, Hroncová Z. Lactobacillus bombi sp. nov., from the digestive tract of laboratory-reared bumblebee queens (Bombus terrestris). Int J Syst Evol Microbiol 2014; 64:2611-7. [DOI: 10.1099/ijs.0.063602-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three bacterial strains belonging to the genus
Lactobacillus
were isolated from the digestive tracts of laboratory-reared bumblebee queens (Bombus terrestris) using MRS agar under anaerobic conditions. The isolates were identified according to 16S rRNA gene sequence analysis as undescribed members of the genus
Lactobacillus
, with the highest 16S rRNA gene sequence similarity (96.9 %) to the uncharacterized bacterial strain Lactobacillus sp. Mboho2r2 isolated from the stomach of a European honeybee (Apis mellifera).
Lactobacillus tucceti
was found to be the closest related species with a validly published name, with 92.9 % 16S rRNA gene sequence similarity to the type strain. However, phylogenetic analyses based on different markers revealed that this species is phylogenetically very distant from the novel strains. The DNA G+C content of the proposed type strain BTLCH M1/2T is 37.8 mol%. The fatty acids C19 : 1ω6c and/or C19 : 0 cyclo ω10c/19ω6, C18 : 1ω9c and C16 : 0 were predominant in all strains. Diphosphatidylglycerol, phosphatidylglycerol, a phospholipid, seven glycolipids and two phosphoglycolipids were detected in the novel strains. Growth was observed at 47 °C. The peptidoglycan type A4α l-Lys–d-Asp was determined for strain BTLCH M1/2T. Genotypic characteristics and phylogenetic analyses based on the phylogenetic markers hsp60, pheS, rpoA and tuf as well as phenotypic characteristics and the results of chemotaxonomic analyses confirmed that the new isolates belong to a novel species of the genus
Lactobacillus
, for which the name Lactobacillus bombi sp. nov. is proposed. The type strain is BTLCH M1/2T ( = DSM 26517T = CCM 8440T).
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Bunesova V, Killer J, Vlkova E, Musilova S, Tomaska M, Rada V, Kmet V. Isolation and characterization of bifidobacteria from ovine cheese. Int J Food Microbiol 2014; 188:26-30. [PMID: 25086349 DOI: 10.1016/j.ijfoodmicro.2014.07.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2014] [Revised: 06/21/2014] [Accepted: 07/01/2014] [Indexed: 11/18/2022]
Abstract
Animal products are one of the niches of bifidobacteria, a fact probably attributable to secondary contamination. In this study, 2 species of the genus Bifidobacterium were isolated by culture-dependent methods from ovine cheeses that were made from unpasteurized milk without addition of starter cultures. The isolates were identified as Bifidobacterium crudilactis and Bifidobacterium animalis subsp. lactis using matrix-assisted laser desorption/ionization time-of-flight analysis and sequencing of phylogenetic markers (16S rRNA, hsp60, and fusA).
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Affiliation(s)
- Vera Bunesova
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, Prague 6-Suchdol 165 21, Czech Republic.
| | - Jiri Killer
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, Prague 6-Suchdol 165 21, Czech Republic; Institute of Animal Physiology and Genetics, Academy of Sciences of the Czech Republic, Vídeňská 1083, Prague 4-Krč 14 200, Czech Republic
| | - Eva Vlkova
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, Prague 6-Suchdol 165 21, Czech Republic
| | - Sarka Musilova
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, Prague 6-Suchdol 165 21, Czech Republic
| | - Martin Tomaska
- Dairy Research Institute, Dlhá 95, 010 01 Žilina, Slovakia
| | - Vojtech Rada
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, Prague 6-Suchdol 165 21, Czech Republic
| | - Vladimir Kmet
- Institute of Animal Physiology of Slovak Academy of Sciences, Soltesovej 4, 040 01 Kosice, Slovakia
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Killer J, Havlik J, Bunesova V, Vlkova E, Benada O. Pseudoscardovia radai sp. nov., another representative of a new genus within the family Bifidobacteriaceae isolated from the digestive tract of a wild pig ( Sus scrofa scrofa ). Int J Syst Evol Microbiol 2014; 64:2932-2938. [PMID: 24867175 DOI: 10.1099/ijs.0.063230-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Presence of bifidobacteria and representatives of the new genus Pseudoscardovia within the family Bifidobacteriaceae in the digestive tract of wild pigs has been reported recently. Results based on comparative 16S rRNA gene sequence analysis of a new fructose-6-phosphate phosphoketolase-positive bacterial isolate originated 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 relationship of the new bacterial strain to Pseudoscardovia suis compared with bifidobacteria species occurring in the digestive tract of domestic and wild pigs. Differences in utilization of various substrates, production of enzymes, cell morphology, peptidoglycan structure, profile of cellular fatty acids and polar lipids between the new bacterial isolate designated as DPVI-TET3T and P. suis DPTE4T allow to establish a new bacterial taxon for which the name Pseudoscardovia radai sp. nov. (= DPVI/TET3T = CCM 7943T = DSM 24742T) was proposed.
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Affiliation(s)
- Jiri Killer
- Institute of Animal Physiology and Genetics AS CR Prague;
| | - Jaroslav Havlik
- Czech University of Life Sciences, Faculty of Agrobiology, Food and Natural Resources
| | - Vera Bunesova
- Czech University of Life Sciences, Faculty of Agrobiology, Food and Natural Resources
| | - Eva Vlkova
- Czech University of Life Sciences, Faculty of Agrobiology, Food and Natural Resources
| | - Oldrich Benada
- Institute of Microbiology v.v.i., Academy of Sciences of the Czech Republic
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Killer J, Havlík J, Vlková E, Rada V, Pechar R, Benada O, Kopečný J, Kofroňová O, Sechovcová H. Lactobacillus rodentium sp. nov., from the digestive tract of wild rodents. Int J Syst Evol Microbiol 2014; 64:1526-1533. [DOI: 10.1099/ijs.0.054924-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three strains of regular, long, Gram-stain-positive bacterial rods were isolated using TPY, M.R.S. and Rogosa agar under anaerobic conditions from the digestive tract of wild mice (Mus musculus). All 16S rRNA gene sequences of these isolates were most similar to sequences of
Lactobacillus gasseri
ATCC 33323T and
Lactobacillus johnsonii
ATCC 33200T (97.3 % and 97.2 % sequence similarities, respectively). The novel strains shared 99.2–99.6 % 16S rRNA gene sequence similarities. Type strains of
L. gasseri
and
L. johnsonii
were also most related to the newly isolated strains according to rpoA (83.9–84.0 % similarities), pheS (84.6–87.8 %), atpA (86.2–87.7 %), hsp60 (89.4–90.4 %) and tuf (92.7–93.6 %) gene sequence similarities. Phylogenetic studies based on 16S rRNA, hsp60, rpoA, atpA and pheS gene sequences, other genotypic and many phenotypic characteristics (results of API 50 CHL, Rapid ID 32A and API ZYM biochemical tests; cellular fatty acid profiles; cellular polar lipid profiles; end products of glucose fermentation) showed that these bacterial strains represent a novel species within the genus
Lactobacillus
. The name Lactobacillus rodentium sp. nov. is proposed to accommodate this group of new isolates. The type strain is MYMRS/TLU1T ( = DSM 24759T = CCM 7945T).
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Affiliation(s)
- J. Killer
- Czech University of Life Sciences, Faculty of Agrobiology, Food and Natural Resources, Department of Microbiology, Nutrition and Dietetics, Kamýcká 129, Prague 6 – Suchdol 165 21, Czech Republic
- Institute of Animal Physiology and Genetics v.v.i., Academy of Sciences of the Czech Republic, Vídeňská 1083, Prague 4 – Krč 142 20, Czech Republic
| | - J. Havlík
- Czech University of Life Sciences, Faculty of Agrobiology, Food and Natural Resources, Department of Microbiology, Nutrition and Dietetics, Kamýcká 129, Prague 6 – Suchdol 165 21, Czech Republic
| | - E. Vlková
- Czech University of Life Sciences, Faculty of Agrobiology, Food and Natural Resources, Department of Microbiology, Nutrition and Dietetics, Kamýcká 129, Prague 6 – Suchdol 165 21, Czech Republic
| | - V. Rada
- Czech University of Life Sciences, Faculty of Agrobiology, Food and Natural Resources, Department of Microbiology, Nutrition and Dietetics, Kamýcká 129, Prague 6 – Suchdol 165 21, Czech Republic
| | - R. Pechar
- Czech University of Life Sciences, Faculty of Agrobiology, Food and Natural Resources, Department of Microbiology, Nutrition and Dietetics, Kamýcká 129, Prague 6 – Suchdol 165 21, Czech Republic
| | - O. Benada
- Department of Biology, Faculty of Science, J. E. Purkyně University in Ustí nad Labem, Za Válcovnou 1000/8, 400 96 Ústí nad Labem, Czech Republic
- Laboratory of Molecular Structure Characterization, Institute of Microbiology, Institute of Microbiology, v.v.i., Academy of Sciences of the Czech Republic, Vídeňská 1083, Prague 4 – Krč 142 20, Czech Republic
| | - J. Kopečný
- Institute of Animal Physiology and Genetics v.v.i., Academy of Sciences of the Czech Republic, Vídeňská 1083, Prague 4 – Krč 142 20, Czech Republic
| | - O. Kofroňová
- Laboratory of Molecular Structure Characterization, Institute of Microbiology, Institute of Microbiology, v.v.i., Academy of Sciences of the Czech Republic, Vídeňská 1083, Prague 4 – Krč 142 20, Czech Republic
| | - H. Sechovcová
- Institute of Animal Physiology and Genetics v.v.i., Academy of Sciences of the Czech Republic, Vídeňská 1083, Prague 4 – Krč 142 20, Czech Republic
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Killer J, Švec P, Sedláček I, Černohlávková J, Benada O, Hroncová Z, Havlík J, Vlková E, Rada V, Kopečný J, Kofroňová O. Vagococcus entomophilus sp. nov., from the digestive tract of a wasp (Vespula vulgaris). Int J Syst Evol Microbiol 2014; 64:731-7. [DOI: 10.1099/ijs.0.054940-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three unknown Gram-stain-positive, catalase-negative, facultatively anaerobic and coccus-shaped strains of bacteria were isolated from the digestive tracts of wasps (Vespula vulgaris). Analysis of 16S rRNA gene sequences revealed that these strains had identical sequences and showed that
Vagococcus salmoninarum
, with 96.2 % sequence similarity, was the closest phylogenetic neighbour. Further analyses based on hsp60 and pheS gene sequences of representatives of the family Enteroccocaceae and genotypic and phenotypic characterization using (GTG)5-PCR fingerprintings, EcoRI ribotyping, DNA G+C content, whole-cell protein profiling, cellular fatty acid profiles analysis and extensive biotyping confirmed that the investigated strains were representatives of a novel bacterial species within the genus Vagoccocus for which the name Vagoccocus entomophilus sp. nov. is proposed. The type strain is VOSTP2T ( = DSM 24756T = CCM 7946T).
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Killer J, Ročková Š, Vlková E, Rada V, Havlík J, Kopečný J, Bunešová V, Benada O, Kofroňová O, Pechar R, Profousová I. 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. Int J Syst Evol Microbiol 2013; 63:4439-46. [DOI: 10.1099/ijs.0.051326-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
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, Sedláček I, Rada V, Havlík J, Kopečný J. Reclassification of Bifidobacterium stercoris Kim et al. 2010 as a later heterotypic synonym of Bifidobacterium adolescentis. Int J Syst Evol Microbiol 2013; 63:4350-3. [DOI: 10.1099/ijs.0.054957-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
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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