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R Nalin

Publications and source records attributed to R Nalin.

9 recordsLinked to original sources
PubMed2005

Reduced diversity of faecal microbiota in Crohn's disease revealed by a metagenomic approach.

BACKGROUND AND AIM: A role for the intestinal microbial community (microbiota) in the onset and chronicity of Crohn's disease (CD) is strongly suspected. However, investigation of such a complex ecosystem is difficult, even with culture independent molecular approaches. METHODS: We used, for the first time, a comprehensive metagenomic approach to investigate the full range of intestinal microbial diversity. We used a fosmid vector to construct two libraries of genomic DNA isolated directly from faecal samples of six healthy donors and six patients with CD. Bacterial diversity was analysed by screening the two DNA libraries, each composed of 25,000 clones, for the 16S rRNA gene by DNA hybridisation. RESULTS: Among 1190 selected clones, we identified 125 non-redundant ribotypes mainly represented by the phyla Bacteroidetes and Firmicutes. Among the Firmicutes, 43 distinct ribotypes were identified in the healthy microbiota, compared with only 13 in CD (p<0.025). Fluorescent in situ hybridisation directly targeting 16S rRNA in faecal samples analysed individually (n=12) confirmed the significant reduction in the proportion of bacteria belonging to this phylum in CD patients (p<0.02). CONCLUSION: The metagenomic approach allowed us to detect a reduced complexity of the bacterial phylum Firmicutes as a signature of the faecal microbiota in patients with CD. It also indicated the presence of new bacterial species.

Adolescent↗
PubMed2001

Novel hopanoids from Frankia spp. and related soil bacteria. Squalene cyclization and significance of geological biomarkers revisited.

Three series of hopanoids, differing by their configurations at C-17 and C-21, have been identified in several Frankia spp. and other related soil bacteria. The widespread bacterial hopanoids of the 17beta(H),21beta(H) series were accompanied by their isomers of the 17beta(H),21alpha(H) (moretane) and 17alpha(H), 21beta(H) series. The latter series has not previously been found in living organisms and is considered to be a result of the abiotic isomerization of the thermodynamically less stable 17beta(H),21beta(H) hopanoids. This simultaneous presence of three isomeric hopanoid series highlights intriguing problems in the biogenesis of the bacteriohopane skeleton and partly questions the significance of hopanic biomarkers in sediments.

Actinomycetales↗
PubMed2001

Laboratory-scale evidence for lightning-mediated gene transfer in soil.

Electrical fields and current can permeabilize bacterial membranes, allowing for the penetration of naked DNA. Given that the environment is subjected to regular thunderstorms and lightning discharges that induce enormous electrical perturbations, the possibility of natural electrotransformation of bacteria was investigated. We demonstrated with soil microcosm experiments that the transformation of added bacteria could be increased locally via lightning-mediated current injection. The incorporation of three genes coding for antibiotic resistance (plasmid pBR328) into the Escherichia coli strain DH10B recipient previously added to soil was observed only after the soil had been subjected to laboratory-scale lightning. Laboratory-scale lightning had an electrical field gradient (700 versus 600 kV m(-1)) and current density (2.5 versus 12.6 kA m(-2)) similar to those of full-scale lightning. Controls handled identically except for not being subjected to lightning produced no detectable antibiotic-resistant clones. In addition, simulated storm cloud electrical fields (in the absence of current) did not produce detectable clones (transformation detection limit, 10(-9)). Natural electrotransformation might be a mechanism involved in bacterial evolution.

Culture Media↗
PubMed2000

A recA gene phylogenetic analysis confirms the close proximity of Frankia to Acidothermus.

The closer proximity of Frankia and Acidothermus cellulolyticus relative to the morphologically close Geodermatophilus found previously was confirmed by resequencing the rrs gene of Acidothermus cellulolyticus and the housekeeping gene, recA. The diagnostic sugar 2-O-methyl-D-mannose was detected only in Frankia, while hopanoid lipids were present at high levels in both Acidothermus and Frankia.

Actinomycetales↗
PubMed1999

Rhodanobacter lindaniclasticus gen. nov., sp. nov., a lindane-degrading bacterium.

Lindane-degrading activity under aerobic conditions has been observed in two bacterial strains: UT26, phenotypically identified as Sphingomonas paucimobilis, and a new single unidentified isolate named RP5557T. The rrs (16S rDNA) sequences for both strains and the phenotypic characteristics for the unidentified isolate RP5557T were determined. RP5557T does not have high identity (less than 90% in all cases) with any sequence in the GenBank or RDP databases. A phylogenetic analysis based on rrs sequences indicated that RP5557T belongs to the gamma-Proteobacteria in a coherent phylum that includes the genera Xanthomonas and Xylella (100% bootstrap), whereas UT26 is clearly separate from the Xanthomonas cluster. Based on the phylogenetic analyses and on the phenotypic characteristics, a new genus, Rhodanobacter, containing a single species, Rhodanobacter lindaniclasticus, is proposed for strain RP5557T (= LMG 18385T), which becomes the type strain.

Bacteria, Aerobic↗
PubMed1997

The nodular microsymbionts of Gymnostoma spp. are Elaeagnus-infective Frankia strains.

The phylogenetic relationships of Frankia strains infective on Gymnostoma with other Frankia strains was analyzed. Partial sequencing of the 16S rDNA and use of specific primers showed that the Frankia strains present in Gymnostoma are phylogenetically close to Elaeagnus-infective strains. This finding was confirmed by using the sequences of the hypervariable nifDK intergenic spacer. The strains present in Gymnostoma nodules were close to one another. Clustered with Elaeagnus-infective strains, and distantly related to Casuarina and Alnus-infective strains. Morphological observations of strains and cross-inoculation trials showed that Gymnostoma-infective strains are indistinguishable from Elaeagnus-infective strains. Results of both phenotypic and genotypic approaches indicate that Gymnostoma-infective strains are Elaeagnus infective and not Casuarina infective.

Bacteria↗
PubMed1995

Molecular structure of the Frankia spp. nifD-K intergenic spacer and design of Frankia genus compatible primer.

The nifD-K intergenic spacer (IGS) of ArI3 and ACoN24d were found to have a length 265 and 199 nucleotides, respectively. They are markedly less conserved than the two neighbouring genes and have, in some instances, a repeated structure reminiscent of an insertion event. The repeated sequence and the IGSs have no detectable homology with sequences in DNA databanks. The IGS has a stem-loop structure with a low folding energy, lower than that between nifH and nifD. No convincing alignment of IGS sequences could be obtained among Frankia strains. Only between ACoN24d and ArI3, which belong to the same genomic species, was the alignment good enough to permit detection of a doubly repeated structure. No promoter could be detected in the IGSs. The putative nifK open reading frame (ORF) in Frankia strain ArI3 has a length of 1587 nucleotides, starting with a GTG codon, preceded by a ribosome binding site of a structure similar to that of nifH (GGAGGN7). The codon usage was similar to that of previously sequenced Frankia genes with a strong bias toward G- and C-ending codons except in the case of glycine where GGT is frequent. Alignment of the three Frankia nifK sequences (EUN1f; ArI3 and ACoN24d) with those of other nitrogen-fixing bacteria permitted detection of a sequence conserved among the three Frankia strains but absent in the other sequences. A primer targeted to that region in combination with FGPD807-85 amplified the nifD-KIGS sequences of all Frankia strains (except the non-nitrogen-fixing Frankia strains CN3 and AgB1-9) and yet failed to amplify DNA of all other nitrogen-fixing bacteria.(ABSTRACT TRUNCATED AT 250 WORDS)

Actinomycetales↗