Phylogenetic Characterization of Clostridium Related Segmented Filamentous Bacteria in Mice Based on 16S Ribosomal RNA Analysis

Snel, J.; Blok, H.J.; Kengen, H.M.P.; Ludwig, Wolfgang; Poelma, F. G. J.; Koopman, J. P.; Akkermans, A.D.L.

doi:10.1016/s0723-2020(11)80004-4

Cited by 34 publications

(22 citation statements)

References 32 publications

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“…The phylogene tic analysis described above supplemented the previous analysis of Snel et al (19), and our results clearly demonstrated that SFB obtained from chickens, mice, and rats belong to a distinct lineage within the Clostn'dium subphylum at the rank of genus. Since these bacteria cannot be cultured in vitro, this genus can now be described mainly on the basis of its phylogeny and morphology.…”

Section: Discussionsupporting

confidence: 83%

“…A total of 35 rounds of temperaturc cycling (93°C for I min, 54°C for 2 min, and 72°C for 3 min) in a DNA thermal cycler (Perkin-Elmer, Nonvalk, Conn.) were followed by 7 min of incubation at 72°C. An aliquot of each PCR product was dot blotted with a mouse SFB-specific oligonucleotide probe, SFB1008 (5'-GCGAGCTTCCCTCATTACAAGG-3') (19), and a universal bacterial probe, EUB338 ( 2 ) , by using standard methods Blotting. DNA samples were spotted on a nylon membrane (Hybond N' ; Amersham International) by using a standard procedure and were covalently bound to the membrane by UV irradiation.…”

Section: Animalsmentioning

confidence: 99%

“…In a recent study, the 16s rRNA-encoding gene sequence of SFB obtained from mice was determined (19). This study was greatly facilitated by the use of a monoculture of these organisms in formerly germfree mice (12).…”

mentioning

confidence: 99%

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Comparison of 16S rRNA Sequences of Segmented Filamentous Bacteria Isolated from Mice, Rats, and Chickens and Proposal of "Candidatus Arthromitus"

Snel

Heinen²,

Blok³

et al. 1995

International Journal of Systematic Bacteriology

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153

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Segmented filamentous bacteria (SFB) are nonpathogenic bacteria that are commonly found attached to the intestinal walls of many animals. Until now, these bacteria have not been cultured in vitro. Recently, a 16s rRNA sequence analysis revealed that SFB isolated from mice represent a distinct subline within the Cfostridium subphylum of the gram-positive bacteria. Since SFB isolated from mice, rats, and chickens are known to be host specific, we investigated the phylogenetic relationships among SFB obtained from these three hosts.Total DNAs from the intestinal floras of chickens and rats were used as templates for PCR amplification of 16s rRNA genes. PCR products were cloned and screened by a dot blot hybridization procedure to identify homologous sequences that cross-reacted with mouse SFB-specific oligonucleotide probes. A phylogenetic analysis of these 16s ribosomal DNA sequences revealed that SFB isolated from these three hosts form a natural group, which is peripherally related to the genus Cfostridiurn sensu strict0 (group I Cfostridiurn). The SFB obtained from chickens, rats, and mice had closely related, albeit different, 16s rRNA gene sequences. The observed levels of 16s rRNA sequence divergence, ca. 1.5 to 3%, together with host specificity, suggest that SFB isolated from mice, rats, and chickens represent different species and that coevolution of the SFB and their hosts occurred. "Candidatus Arthromitus" is proposed as the provisional generic name for this group of organisms.The small intestines of many animals (e.g., mice, rats, pigs, and other mammals, as well as chickens, amphibians, and insects) are inhabited by segmented filamentous bacteria (SFB), which are also referred to as long segmented filamentous organisms (reviewed in reference 10). These bacteria cannot be cultured in vitro and do not have official taxonomic names. Until recently, SFB could be recognized only on the basis of their morphology and their ecological niches. In intestines, these gram-positive, endospore-forming organisms are attached via holdfasts to the epithelial walls. In rodents, colonization by SFB is restricted to the ileum (4). In birds, SFB are also found in the ceca (9). No pathologic effects of SFB have been found, even in immunodeficient animals. SFB found in different animal species are morphologically very similar. However, attempts to transfer bacteria from one host species to another have revealed that SFB found in mice, rats, and chickens exhibit host specificity (1, 13, 21). It is not known if SFB that inhabit different hosts are taxonomically closely related or whether they belong to different species.In a recent study, the 16s rRNA-encoding gene sequence of SFB obtained from mice was determined (19). This study was greatly facilitated by the use of a monoculture of these organisms in formerly germfree mice (12). A comparative 16s rRNA * Corresponding author. Mailing address: Central Animal Laboratory, University of Nijmegen, P.O. Box 9101, NL-6500 HB Nijmegen, 'The Netherlands. analysis revealed that th...

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Section: Discussionsupporting

confidence: 83%

Section: Animalsmentioning

confidence: 99%

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Comparison of 16S rRNA Sequences of Segmented Filamentous Bacteria Isolated from Mice, Rats, and Chickens and Proposal of "Candidatus Arthromitus"

Snel

Heinen²,

Blok³

et al. 1995

International Journal of Systematic Bacteriology

Self Cite

153

122

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“…A phylogenetic analysis of this murine symbiont proved it, too, to be a member of the low-GϩC gram-positive bacteria but not a specific relative of Epulopiscium spp. (35) (Fig. 3).…”

Section: Discussionmentioning

confidence: 97%

Phylogenetic analysis of Metabacterium polyspora: clues to the evolutionary origin of daughter cell production in Epulopiscium species, the largest bacteria

1996

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It is rare that there are molecular clues to the evolutionary origin of developmental traits. We have encountered an evolutionary juxtaposition that may explain the origin of the unique replicative morphology of Epulopiscium spp., the largest known bacteria, which reproduce by the internal production of multiple live offspring. We report here a 16S rRNA-based phylogenetic analysis of Metabacterium polyspora, a multipleendospore-forming, uncultivated inhabitant of guinea pig cecum. Cells of M. polyspora were harvested from cecum contents by sedimentation in a Ficoll gradient and lysed. The bacterial 16S rRNA genes of this lysate were amplified by PCR. Sequence analysis of the cloned PCR products revealed two dominant, closely related 16S rRNA types. In situ hybridization of cecum contents with fluorescently labeled oligonucleotides, diagnostic of these two sequences, showed that they represent distinct strains of M. polyspora. Phylogenetic analyses of the sequences showed that M. polyspora is closely related to Epulopiscium spp. On the basis of this result and other correlations, we propose that the process of sporulation was modified in a predecessor of Epulopiscium spp. to produce live offspring instead of quiescent endospores.

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“…Only a few representatives of these organisms have been cultivated, but on the basis of their morphological and growth characteristics those that have been cultivated are generally considered to belong to the genera Eubacterium, Fusobacterium and Clostridium . Segmented filamentous bacteria (SFB), belonging to the Clostridium group on the basis of 16S rRNA gene analysis (Snel et al, 1994), are a clear example of a population of organisms that cannot be cultured using current methods. However, these bacteria have been shown to account for a significant percentage of the mouse gut microflora, especially in young mice (Talham et al, 1999).…”

Section: Introductionmentioning

confidence: 99%

Analysis of 16S libraries of mouse gastrointestinal microflora reveals a large new group of mouse intestinal bacteria b bThe GenBank accession numbers for the clone sequences reported in this paper can be found in Table 1 T1 ; the accession number for isolate MIB-CB3 is AJ418059.

et al. 2002

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Total genomic DNA from samples of intact mouse small intestine, large intestine, caecum and faeces was used as template for PCR amplification of 16S rRNA gene sequences with conserved bacterial primers. Phylogenetic analysis of the amplification products revealed 40 unique 16S rDNA sequences. Of these sequences, 25 % (10/40) corresponded to described intestinal organisms of the mouse, including Lactobacillus spp., Helicobacter spp., segmented filamentous bacteria and members of the altered Schaedler flora (ASF360, ASF361, ASF502 and ASF519) ; 75 % (30/40) represented novel sequences. A large number (11/40) of the novel sequences revealed a new operational taxonomic unit (OTU) belonging to the Cytophaga-Flavobacter-Bacteroides phylum, which the authors named ' mouse intestinal bacteria '. 16S rRNA probes were developed for this new OTU. Upon analysis of the novel sequences, eight were found to cluster within the Eubacterium rectale-Clostridium coccoides group and three clustered within the Bacteroides group. One of the novel sequences was distantly related to Verrucomicrobium spinosum and one was distantly related to Bacillus mycoides. Oligonucleotide probes specific for the 16S rRNA of these novel clones were generated. Using a combination of four previously described and four newly designed probes, approximately 80 % of bacteria recovered from the murine large intestine and 71 % of bacteria recovered from the murine caecum could be identified by fluorescence in situ hybridization (FISH).

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Phylogenetic Characterization of Clostridium Related Segmented Filamentous Bacteria in Mice Based on 16S Ribosomal RNA Analysis

Cited by 34 publications

References 32 publications

Comparison of 16S rRNA Sequences of Segmented Filamentous Bacteria Isolated from Mice, Rats, and Chickens and Proposal of "Candidatus Arthromitus"

Comparison of 16S rRNA Sequences of Segmented Filamentous Bacteria Isolated from Mice, Rats, and Chickens and Proposal of "Candidatus Arthromitus"

Phylogenetic analysis of Metabacterium polyspora: clues to the evolutionary origin of daughter cell production in Epulopiscium species, the largest bacteria

Analysis of 16S libraries of mouse gastrointestinal microflora reveals a large new group of mouse intestinal bacteria b bThe GenBank accession numbers for the clone sequences reported in this paper can be found in Table 1 T1 ; the accession number for isolate MIB-CB3 is AJ418059.

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