Characterization of the Genus <i>Bifidobacterium</i> by Automated Ribotyping and 16S rRNA Gene Sequences

Sakata, Shinji; Ryu, Chun Sun; Kitahara, Maki; Sakamoto, Mitsuo; Hayashi, Hidenori; Fukuyama, Masafumi; Benno, Yoshimi

doi:10.1111/j.1348-0421.2006.tb03762.x

Cited by 28 publications

(16 citation statements)

References 39 publications

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“…The overall phylogenetic tree topology was in agreement with previous studies with cultured strains (23,39). For instance, sequences having Ͼ97% sequence similarity with cultured strains indeed formed specific clusters with species such as the B. catenulatum, B. pseudocatenulatum, B. longum, B. coryneforme, B. asteroides, and B. pseudolongum groups (23,31,39).…”

Section: ϫ14supporting

confidence: 89%

Bifidobacteria in Feces and Environmental Waters

Lamendella

Domingo

Kelty

et al. 2008

Appl Environ Microbiol

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Bifidobacteria have been recommended as potential indicators of human fecal pollution in surface waters even though very little is known about their presence in nonhuman fecal sources. The objective of this research was to shed light on the occurrence and molecular diversity of this fecal indicator group in different animals and environmental waters. Genus-and species-specific 16S rRNA gene PCR assays were used to study the presence of bifidobacteria among 269 fecal DNA extracts from 32 different animals. Twelve samples from three wastewater treatment plants and 34 water samples from two fecally impacted watersheds were also tested. The species-specific assays showed that Bifidobacterium adolescentis, B. bifidum, B. dentium, and B. catenulatum had the broadest host distribution (11.9 to 17.4%), whereas B. breve, B. infantis, and B. longum were detected in fewer than 3% of all fecal samples. Phylogenetic analysis of 356 bifidobacterial clones obtained from different animal feces showed that ca. 67% of all of the sequences clustered with cultured bifidobacteria, while the rest formed a supercluster with low sequence identity (i.e., <94%) to previously described Bifidobacterium spp. The B. pseudolongum subcluster (>97% similarity) contained 53 fecal sequences from seven different animal hosts, suggesting the cosmopolitan distribution of members of this clade. In contrast, two clades containing B. thermophilum and B. boum clustered exclusively with 37 and 18 pig fecal clones, respectively, suggesting host specificity. Using species-specific assays, bifidobacteria were detected in only two of the surface water DNA extracts, although other fecal anaerobic bacteria were detected in these waters. Overall, the results suggest that the use of bifidobacterial species as potential markers to monitor human fecal pollution in natural waters may be questionable.

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Section: ϫ14supporting

confidence: 89%

Bifidobacteria in Feces and Environmental Waters

Lamendella

Domingo

Kelty

et al. 2008

Appl Environ Microbiol

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“…The trees were rooted using the gene sequence of Mycobacterium tuberculosis H37Rv T , which is well known as the causative agent of tuberculosis. The topology of the rpoB gene tree was similar to the topologies of the hsp60 and 16S rRNA gene trees and to previously published reports (Jian et al, 2001;Sakata et al, 2006;Ventura et al, 2008) (Fig. 1).…”

supporting

confidence: 88%

Differentiation of Bifidobacterium species using partial RNA polymerase β-subunit (rpoB) gene sequences

Kim

Yun

et al. 2010

International Journal of Systematic and Evolutionary Microbiology

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Partial RNA polymerase b-subunit gene (rpoB) sequences (315 bp) were determined and used to differentiate the type strains of 23 species of the genus Bifidobacterium. The sequences were compared with those of the partial hsp60 (604 bp) and 16S rRNA genes (1475 or 1495 bp). The rpoB gene sequences showed nucleotide sequence similarities ranging from 84.1 % to 99.0 %, while the similarities of the hsp60 sequences ranged from 78.5 % to 99.7 % and the 16S rRNA gene sequence similarities ranged from 89.4 % to 99.2 %. The phylogenetic trees constructed from the sequences of these three genes showed similar clustering patterns, with the exception of several species. The Bifidobacterium catenulatum-Bifidobacterium pseudocatenulatum, Bifidobacterium pseudolongum subsp. pseudolongum-Bifidobacterium pseudolongum subsp. globosum and Bifidobacterium gallinarum-Bifidobacterium pullorum-Bifidobacterium saeculare groups were more clearly differentiated in the partial rpoB and hsp60 gene sequence trees than they were in the 16S rRNA gene tree. Based on sequence similarities and tree topologies, the newly determined rpoB gene sequences are suitable molecular markers for the differentiation of species of the genus Bifidobacterium and support various other molecular tools used to determine the relationships among species of this genus.Bifidobacteria are Gram-positive, non-spore-forming, nonmotile, non-gas-producing, anaerobic, bifid-shaped rods that colonize the gastrointestinal tracts of humans, as well as other mammals and some insects. There has been increased interest in these organisms recently due to their beneficial effects on gastrointestinal health. Indeed, they have been used as probiotics and evaluated for their ability to reduce several gastrointestinal tract diseases and protect against pathogens (Guarner & Malagelada, 2003;Mitsuoka & Kaneuchi, 1977;Ventura et al., 2008).Bacillus bifidus was first isolated from a healthy breast-fed infant by Tissier in 1899. The genus Bifidobacterium was later designated as an independent taxon by Orla-Jensen (1924) (Ventura et al., 2008), after which many species belonging to this genus were identified and classified. Traditionally, phenotypic analyses based on morphology and the patterns of various carbohydrate fermentation tests have been used to differentiate species of the genus Bifidobacterium. However, it has been suggested that these classification criteria may be unclear and may provide questionable results (Mitsuoka & Kaneuchi, 1977). Therefore, improved methods of identification and differentiation are necessary. Accordingly, various molecular tools that are currently available may be useful for the reliable identification of such organisms.The recent rapid developments in molecular biology have resulted in the use of various new methods for the identification and differentiation of species of the genus Bifidobacterium. These include PCR-linked methods such as nucleotide-dependent phylogenetic analysis targeting housekeeping genes (Jian et al., 2001;Ventura et al., 2004aVent...

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“…16S rRNA gene sequences have been the primary resource for phylogenetic studies and sequence-based taxonomy (20,23,32,33). In recent years, several house keeping genes, such as genes encoding transaldolase, ATPase (atpBEFHAGDC), elongation factor Tu (tuf), and xylulose-5-phosphate/fructose-6-phosphate phosphoketolase (xfp), and recombination protein A (recA) have been used for taxonomical studies of bifidobacterial species (15,18,29,30,34).…”

Section: Discussionmentioning

confidence: 99%

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

Okamoto

Benno

Leung³

et al. 2007

Microbiology and Immunology

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A novel microorganism, Metascardovia criceti gen. nov., sp. nov., was isolated from dental plaque of golden hamsters fed with a high‐carbohydrate diet. The three isolated strains, OMB104, OMB105, and OMB107, were Gram‐positive, facultative anaerobic rods that lacked catalase activity. Analyses of the partial 16S rRNA and heat‐shock protein 60 (HSP60) gene sequences of these isolates indicated that they belonged to the family Bifidobacteriaceae. However, in contrast to Bifidobacterium, one of the genera under this family, these isolates grew under aerobic conditions, and the DNA G + C contents were lower (53 mol%) than those of Bifidobacterium. On the basis of phylogenetic analyses using phenotypic characterization, and partial 16S rRNA and HSP60 gene sequences data, we propose a novel taxa, Metascardovia criceti for OMB105T (type strain=JCM 13493T=DSM 17774T) for this newly described isolate.

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Characterization of the Genus Bifidobacterium by Automated Ribotyping and 16S rRNA Gene Sequences

Cited by 28 publications

References 39 publications

Bifidobacteria in Feces and Environmental Waters

Bifidobacteria in Feces and Environmental Waters

Differentiation of Bifidobacterium species using partial RNA polymerase β-subunit (rpoB) gene sequences

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

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