<i>Metascardovia criceti</i> Gen. Nov., Sp. Nov., from Hamster Dental Plaque

Okamoto, Masaaki; Benno, Yoshimi; Leung, K.-P.; Maeda, Nobuyo

doi:10.1111/j.1348-0421.2007.tb03964.x

Cited by 32 publications

(14 citation statements)

References 38 publications

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“…In agreement with previous culture-based studies, Bifidobacterium species are underabundant in T-bet -/- × Rag2 -/- mice [68], and LEfSe highlights several additional genus-level clades, including the specifically depleted Roseburia and Papillibacter within the otherwise overabundant Firmicutes.…”

Section: Resultssupporting

confidence: 91%

“…At the family level, the Rag2 -/- enrichment of Bifidobacteriaceae, Porphyromonadaceae, Staphylococcaceae and the T-bet -/- × Rag2 -/- enrichment of Lachnospiraceae confirm our reports in [68] using culture-based and quantitative real time PCR techniques. LEfSe's LDA score more informatively reorders these taxa relative to the P -values found for these families in our previous work, highlighting the Bifidobacteria and, interestingly, several clades within the Clostridia.…”

Section: Resultssupporting

confidence: 91%

“…These include the Rag2 -/- -specific Roseburia and Papillibacter genera belonging to T-bet -/- × Rag2 -/- -specific families (Lachnospiraceae and Ruminococcaceae). The significant presence of Metascardovia (Bifidobacteriaceae) in Rag2 -/- mice is also interesting, as it may have a role similar to Bifidobacterium and because Metascardovia has been previously observed primarily in the oral cavity [68]. This analysis both highlights the agreement of LEfSe's effect size estimation with respect to low-throughput confirmations and suggests additional clades to be further investigated experimentally.…”

Section: Resultsmentioning

confidence: 66%

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Metagenomic biomarker discovery and explanation

et al. 2011

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This study describes and validates a new method for metagenomic biomarker discovery by way of class comparison, tests of biological consistency and effect size estimation. This addresses the challenge of finding organisms, genes, or pathways that consistently explain the differences between two or more microbial communities, which is a central problem to the study of metagenomics. We extensively validate our method on several microbiomes and a convenient online interface for the method is provided at http://huttenhower.sph.harvard.edu/lefse/.

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Section: Resultssupporting

confidence: 91%

Section: Resultssupporting

confidence: 91%

Section: Resultsmentioning

confidence: 66%

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Metagenomic biomarker discovery and explanation

et al. 2011

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“…Phylogenetic markers useful in the taxonomy of the family Bifidobacteriaceae, partial sequences of the hsp60, fusA, xfp, tuf, rpoC, rplB, gyrB and dnaK genes, were considered. A fragment of the hsp60 gene was amplified from the studied strain using primers MO-157 and MO-158 under PCR conditions described previously (Okamoto et al, 2007). PCR conditions and primers for amplification of fusA, rplB and gyrB gene sequences were taken from Delétoile et al (2010).…”

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confidence: 99%

Pseudoscardovia radai sp. nov., a representative of the family Bifidobacteriaceae isolated from the digestive tract of a wild pig (Sus scrofa scrofa)

Killer

Havlík

Bunešová

et al. 2014

International Journal of Systematic and Evolutionary Microbiology

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Pseudoscardovia radai sp. nov., a representative of the family Bifidobacteriaceae isolated from the digestive tract of a wild pig (Sus scrofa scrofa) 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-TET3 T , originating from the small intestine of a wild pig revealed a relationship to Pseudoscardovia suis DPTE4 T (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 DPTE4 T 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-TET3 T and P. suis DPTE4 T allow the establishment of a novel species, for which the name Pseudoscardovia radai sp. nov. is proposed. The type strain is strain DPVI-TET3 T (5CCM 7943 T 5DSM 24742 T ).Bacterial diversity in the gastrointestinal tract of wild mammals is still not adequately explored (Nelson et al., 2003; Xu et al., 2010) and is influenced by many factors such as food composition, age, health, individual variation, environment, geographical distribution and physiological state of the host (Thompson-Chagoyán et al., 2007; Ochman et al., 2010). Isolation and characterization of representatives of novel bacterial taxa within these specific ecological niches is inter alia important from the viewpoint of usage of their potentially beneficial properties in humans and economically important animals (Walter, 2008;Trebichavsky et al., 2009;Rossi et al., 2011). The most studied groups of bacteria by the scientific community with the potential for positive effects on host health are the bifidobacteria and lactobacilli (Tejero-Sariñena et al., 2013;Sikorska & Smoragiewicz, 2013;Vlasova et al., 2013).Species of bifidobacteria from animals are found in the digestive tracts of primates (Endo et al., 2012;Tsuchida et al., 2014), domesticated pigs, rabbits, cattle, poultry, honeybees (Biavati & Mattarelli, 2012) and bumblebees (Killer et al., 2009(Killer et al., , 2011. In recent years, some fructose-6-phosphate phosphoketolase-positive bacteria have been classified into new scardovial genera phylogenetically different from members of the genus Bifidobacterium (Jian & Dong, 2002;Killer et al., 2010Killer et al., , 2013b.The presence of a differential bifidobacterial population in the digestive tract of wild pigs has been reported recently. A representative of a new genus, Pseudoscardovia, was described in that study (Killer et al., 2013a). This study comprises the detailed characterization of a novel bacterial species most clo...

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“…The hsp60 gene has been proposed as an alternative phylogenetic marker for the family Bifidobacteriaceae (Jian et al, 2001;Huys et al, 2007). Hence, partial sequences (~590 bp) of the hsp60 gene were determined as described by Okamoto et al (2007). Fragments were then sequenced on a 3100-Avant Genetic Analyzer with a BigDye Terminator version 3.1 cycle sequencing kit (both from Applied Biosystems).…”

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confidence: 99%

Bifidobacterium actinocoloniiforme sp. nov. and Bifidobacterium bohemicum sp. nov., from the bumblebee digestive tract

Killer

Kopečný

Mrázek

et al. 2011

International Journal of Systematic and Evolutionary Microbiology

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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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Metascardovia criceti Gen. Nov., Sp. Nov., from Hamster Dental Plaque

Cited by 32 publications

References 38 publications

Metagenomic biomarker discovery and explanation

Metagenomic biomarker discovery and explanation

Pseudoscardovia radai sp. nov., a representative of the family Bifidobacteriaceae isolated from the digestive tract of a wild pig (Sus scrofa scrofa)

Bifidobacterium actinocoloniiforme sp. nov. and Bifidobacterium bohemicum sp. nov., from the bumblebee digestive tract

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