Application of a suite of 16S rRNA-specific oligonucleotide probes designed to investigate bacteria of the phylum cytophaga-flavobacter-bacteroides in the natural environment

Manz, Werner; Amann, Rudolf; Ludwig, Wolfgang; Vancanneyt, Marc; Schleifer, Karl‐Heinz

doi:10.1099/13500872-142-5-1097

Cited by 1,093 publications

(552 citation statements)

References 44 publications

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“…The probes used were: EREC 482 [19] for Eubacterium rectaleClostridium coccoides group, Lab158 [20] for lactobacilli and enterococci and Bif164 [21] for Bifidobacterium spp. (Gram-positive bacteria); and Bac303 [22] for BacteroidesPrevotella spp., MIB 661 [23] for Bacteroides mouse intestinal bacteria (MIB), SRB 687 [24] for sulphatereducing bacteria and probe D [25] for Enterobacteriaceae spp. (Gram-negative bacteria) within the murine intestinal microflora.…”

Section: Methodsmentioning

confidence: 99%

Selective increases of bifidobacteria in gut microflora improve high-fat-diet-induced diabetes in mice through a mechanism associated with endotoxaemia

et al. 2007

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Aims/hypothesis Recent evidence suggests that a particular gut microbial community may favour occurrence of the metabolic diseases. Recently, we reported that high-fat (HF) feeding was associated with higher endotoxaemia and lower Bifidobacterium species (spp.) caecal content in mice. We therefore tested whether restoration of the quantity of caecal Bifidobacterium spp. could modulate metabolic endotoxaemia, the inflammatory tone and the development of diabetes. Methods Since bifidobacteria have been reported to reduce intestinal endotoxin levels and improve mucosal barrier function, we specifically increased the gut bifidobacterial content of HF-diet-fed mice through the use of a prebiotic (oligofructose [OFS]). Results Compared with normal chow-fed control mice, HF feeding significantly reduced intestinal Gram-negative and Gram-positive bacteria including levels of bifidobacteria, a dominant member of the intestinal microbiota, which is seen as physiologically positive. As expected, HF-OFS-fed mice had totally restored quantities of bifidobacteria. HFfeeding significantly increased endotoxaemia, which was normalised to control levels in HF-OFS-treated mice. Multiple-correlation analyses showed that endotoxaemia significantly and negatively correlated with Bifidobacterium spp., but no relationship was seen between endotoxaemia and any other bacterial group. Finally, in HF-OFS-treated-mice, Bifidobacterium spp. significantly and positively correlated with improved glucose tolerance, glucose-induced insulin secretion and normalised inflammatory tone (decreased endotoxaemia, plasma and adipose tissue proinflammatory cytokines). Conclusions/interpretation Together, these findings suggest that the gut microbiota contribute towards the pathophysiological regulation of endotoxaemia and set the tone of inflammation for occurrence of diabetes and/or obesity. Thus, it would be useful to develop specific strategies for modifying gut microbiota in favour of bifidobacteria to prevent the deleterious effect of HF-diet-induced metabolic diseases.

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Section: Methodsmentioning

confidence: 99%

Selective increases of bifidobacteria in gut microflora improve high-fat-diet-induced diabetes in mice through a mechanism associated with endotoxaemia

et al. 2007

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“…Samples (20 ml) were fixed with paraformaldehyde solution (2% [wt/vol] final concentration) at room temperature for 2 h. After fixation, samples were filtered onto 0.2-m-pore-size Isopore membrane filters (47 mm; Millipore), rinsed with phosphate-buffered saline buffer and sterile Milli-Q water, dried at room temperature, and stored at Ϫ20°C. Wholecell in situ hybridizations of sections from the polycarbonate filters were performed with the five newly designed oligonucleotide probes, as well as with probes BET2-870 (Polynucleobacter cluster and a few related sequences outside the cluster, 16S rRNA targeted) (7), BET42a (Betaproteobacteria, 23S rRNA targeted) (34), GAM42a (Gammaproteobacteria, 23S rRNA targeted) (34), ALF968 (Alphaproteobacteria, 16S rRNA targeted) (37), CF319a (many Bacteroidetes, 16S rRNA targeted) (33), and EUB338 (most bacteria, 16S rRNA targeted) (3). All probes were obtained as Cy3-monolabeled probes (ThermoHybaid, Ulm, Germany).…”

Section: Methodsmentioning

confidence: 99%

Low Intraspecific Diversity in a Polynucleobacter Subcluster Population Numerically Dominating Bacterioplankton of a Freshwater Pond

Hahn

Pöckl

2005

Appl Environ Microbiol

170

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Cultivation-dependent and -independent methods were combined to investigate the microdiversity of a Polynucleobacter subcluster population (Betaproteobacteria) numerically dominating the bacterioplankton of a small, humic freshwater pond. Complete coverage of the population by cultivation allowed the analysis of microdiversity beyond the phylogenetic resolution of ribosomal markers. Fluorescent in situ hybridization with two probes specific for the narrow subcluster C (PnecC bacteria) of the Polynucleobacter cluster revealed that this population contributed up to 60% to the total number of bacterioplankton cells. Microdiversity was investigated for a date at which the highest relative numbers of PnecC were observed. A clone library of fragments of the ribosomal operon (16S rRNA genes, complete 16S-23S internal transcribed spacer 1 [ITS1], partial 23S rRNA genes) amplified with universal bacterial primers was constructed. The library was stepwise screened for fragments from PnecC bacteria and for different ITS genotypes of PnecC bacteria. The isolated PnecC strains were characterized by sequencing of the 16S rRNA genes and the ITS1. Both the clone library and the established culture collection contained only the same three ITS genotypes, and one of them contributed 46% to the entire number of clones. Genomic fingerprinting of the isolates with several methods always resulted in the detection of only one fingerprint per ITS genotype. We conclude that a Polynucleobacter population with an extremely low intraspecific diversity and an uneven structure numerically dominated the bacterioplankton community in the investigated habitat. This low intraspecific diversity is in strong contrast to the high intraspecific diversities found in marine bacterial populations.Microdiversity of prokaryotes, i.e., the genetic diversity within species-like (Ͼ97% similarity of 16S rRNA genes) phylogenetic groups, receives increasing attention in microbial ecology (1,5,18,19,24,28); however, the ecological significance of this diversity is still unknown. The coexistence of different bacterial genotypes belonging to the same species-like phylogenetic group is well documented for marine (1,18,19,35,45) and freshwater habitats (8,9,10,11,27,30,43). Recently, Acinas et al. (1) demonstrated by the construction and analysis of 16S rRNA clone libraries that a coastal bacterioplankton community contained a very high diversity of ribotypes, the vast majority of which fell into phylogenetically microdiverse sequence clusters (Ͻ1% divergent 16S rRNA sequences). Similarly, extensive microdiversities were also observed in populations of sulfate-reducing bacteria inhabiting a salt marsh (29) and in a Vibrio splendidus population from coastal bacterioplankton (42). The V. splendidus population consisted of at least a thousand distinct genotypes, which demonstrated a high variability in genome size and allelic composition (42).The major aim of the study presented here was the investigation of the intraspecific structure (microdiversity) of a bacterial p...

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“…Several horseradish peroxidase probes were used to characterize the composition of the bacterial community in the original water samples, using the same procedure as described in Alonso-Sáez and Gasol (2007). The horseradish peroxidase-labeled probes used were as follows: EUB-338, EUB-II and EUB-III (target most Eubacteria; Amann et al, 1990;Daims et al, 1999); GAM42a (targets most Gammaproteobacteria; Manz et al, 1992); ALF968 (targets most Alphaproteobacteria; Neef, 1997); CF319 (targets many groups belonging to the Bacteroidetes group; Manz et al, 1996); ROS537 (targets members of the Roseobacter-SulfitobacterSilicibacter group; Eilers et al, 2001); NOR5-730 (targets members of the NOR5 cluster; Eilers et al, 2001); Alt1413 (targets Alteromonas and Colwellia; Eilers et al, 2000b); and SAR11-441 R (targets the SAR11 cluster; Morris et al, 2002); EUB antisense probe NON338 (Wallner, 1993) was used as a negative control. All probes were purchased from biomers.net (Ulm, Germany).…”

Section: Phytoplankton Cultures and Preparation Of Radiolabeled Exudatesmentioning

confidence: 99%

Bacterioplankton niche partitioning in the use of phytoplankton-derived dissolved organic carbon: quantity is more important than quality

2016

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Some prokaryotes are known to be specialized in the use of phytoplankton-derived dissolved organic carbon (DOCp) originated by exudation or cell lysis; however, direct quantification measurements are extremely rare. Several studies have described bacterial selectivity based on DOCp quality, but very few have focused on the quantity of DOCp, and the relative importance of each of these variables (for example, quantity versus quality) on prokaryote responses. We applied an adapted version of the MAR-FISH (microautoradiography coupled with catalyzed reporter deposition fluorescence in situ hybridization) protocol using radiolabelled exudates from axenic algal cultures to calculate a specialization index (d') for large bacterioplankton phylogenetic groups using DOCp from different phytoplankton species and at different concentrations to elucidate to what extent the bacterial response to DOCp is driven by resource quantity (different DOCp concentrations) or by quality (DOCp from different phytoplankton species). All bacterial phylogenetic groups studied had lower d' at higher DOCp concentration, indicating more generalist behavior at higher resource availabilities. Indeed, at increasing resource concentrations, most bacterial groups incorporated DOCp indiscriminately, regardless of its origin (or quality). At low resource concentrations, only some specialists were able to actively incorporate the various types of organic matter effectively. The variability of bacterial responses to different treatments was systematically higher at varying concentrations than at varying DOCp types, suggesting that, at least for this range of concentrations (10-100 μM), DOCp quantity affects bacterial responses more than quality does. Therefore, resource quantity may be more relevant than resource quality in the bacterial responses to DOCp and affect how bacterioplankton use phytoplankton-derived carbon.

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Application of a suite of 16S rRNA-specific oligonucleotide probes designed to investigate bacteria of the phylum cytophaga-flavobacter-bacteroides in the natural environment

Cited by 1,093 publications

References 44 publications

Selective increases of bifidobacteria in gut microflora improve high-fat-diet-induced diabetes in mice through a mechanism associated with endotoxaemia

Selective increases of bifidobacteria in gut microflora improve high-fat-diet-induced diabetes in mice through a mechanism associated with endotoxaemia

Low Intraspecific Diversity in a Polynucleobacter Subcluster Population Numerically Dominating Bacterioplankton of a Freshwater Pond

Bacterioplankton niche partitioning in the use of phytoplankton-derived dissolved organic carbon: quantity is more important than quality

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