scholarly journals P677 Fungal abundance is related to inflammatory status in Ulcerative Colitis

2021 ◽  
Vol 15 (Supplement_1) ◽  
pp. S598-S599
Author(s):  
C M Herrera De Guise ◽  
G Sarrabayrouse ◽  
E Varela ◽  
V Robles ◽  
N Borruel ◽  
...  
Keyword(s):  
Ulcerative Colitis ◽  
16S Rrna ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Fecal Samples ◽  
Inflammatory Status ◽  
Fungal Abundance ◽  
Gene Copies ◽  
16Srrna Gene ◽  
Over Time

Abstract Background Fungi account for approximately 0.1% of the total microorganisms in the gut. Despite the vast body of literature on the bacterial component of the gut microbiota, little has been published on the fungal microbiota. Fungal-bacterial interactions may be significant in inflammatory bowel disease (IBD), with several lines of evidence linking fungi and IBD. Our study aimed to explore and compare the fungal and bacterial loads in fecal samples from different ulcerative colitis (UC) patients’ groups. Methods Using two qPCR systems to amplify the ITS2 sequence from fungi and the 16srRNA gene from bacteria, we characterized and compared fungal and bacterial loads in 3 groups: 1) UClr: UC patients in long-term remission (≥5 years of flare-free disease, clinical, endoscopic and histological remission at inclusion); 2) UCsr: UC patients in short-term remission (3 months in clinical remission at inclusion and previously more than one relapse/year); 3) UCfl: UC patients with active disease (CAI >4 at inclusion). We obtained two frozen fecal samples from all subjects, except for the UCfl group from which we obtained 1 sample at flare onset. Results were expressed in copies/g of feces. Results We included 87 UC patients, 29 in UClr, 20 in UCsr, and 38 in UCfl groups. Median age was 39 years, women comprised 52%. Fecal samples contained a significantly lower number of ITS2 gene copies (median 9.27E+05) than 16srRNA gene copies (median 4.28E+11). 16s rRNA gene copies were similar among the different groups with a median 3.88E+11 for UClr, median 5.29E+11 for UCsr, and median 4.315E+11 for UCfl patients (FDR p=0.65). In contrast, copies of ITS2 gene were increased in UCfl (median 1.95E+06) when compared to UClr (3.68E+04, FDR p=0.0036) but not significantly different to UCsr (5.24E+05 copies, FDR p=0.20). We analyzed the variation between samples over time; we compared the number of copies of ITS2 and 16s rRNA genes in fecal samples collected at two different time points: basal versus 8-weeks. We calculated overall fold changes that reflect stability over time. We found a trend for a more significant variation in the quantity of the ITS2 gene than the 16srRNA gene, but this was not significant. Analysis of the ITS2/16S rRNA ratio assessing the frequency of fungi compared to bacteria showed that this ratio was higher in UCfl (median 6.94E-06) when compared to UClr (median 2.63E-07, FDR p=0.0005) and UCsr patients (median 5.60E-07, FDR p=0.0072), there were no differences between UClr and UCsr patients. Conclusion Fungal abundance was increased in UC flare patients compared to UC patients in long remission, while there were no differences in bacterial abundance. This high number of fungi could be involved in the inflammatory response of UC patients.

Heterogeneity between 16S ribosomal RNA gene copies borne by one Desulfitobacterium strain is caused by different 100-200 bp insertions in the 5´ region

2007 ◽  
Vol 53 (1) ◽  
pp. 116-128 ◽  
Author(s):  
Richard Villemur ◽  
Philippe Constant ◽  
Annie Gauthier ◽  
Martine Shareck ◽  
Réjean Beaudet
Keyword(s):  
In Situ Hybridization ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Ribosomal Rna ◽  
16S Ribosomal Rna ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Gene Copies

Strains of Desulfitobacterium hafniense, such as strains PCP-1, DP7, TCE1, and TCP-A, have unusual long 16S ribosomal RNA (rRNA) genes due to an insertion of approximately 100 bp in the 5' region. In this report, we analyzed the 16S rRNA genes of different Desulfitobacterium strains to determine if such an insertion is a common feature of desulfitobacteria. We amplified this region by polymerase chain reaction (PCR) from eight Desulfitobacterium strains (D. hafniense strains PCP-1, DP7, TCP-A, TCE1, and DCB-2; D. dehalogenans; D. chlororespirans; and Desulfitobacterium sp. PCE1) and resolved each PCR product by denaturing gradient gel electrophoresis (DGGE). All strains had from two to seven DGGE- migrating bands, suggesting heterogeneity in their 16S rRNA gene copies. For each strain, the 5' region of the 16S rRNA genes was amplified and a clone library was derived. Clones corresponding to most PCR–DGGE migration bands were isolated. Sequencing of representative clones revealed that the heterogeneity was generated by insertions of 100–200 bp. An insertion was found in at least one copy of the 16S rRNA gene in all examined strains. In total, we found eight different types of insertions (INS1–INS8) that varied from 123 to 193 nt in length. Two-dimensional structural analyses of transcribed sequences predicted that all insertions would form an energetically stable loop. Reverse transcriptase – PCR experiments revealed that most of the observed insertions in the Desulfitobacterium strains were excised from the mature 16S rRNA transcripts. Insertions were not commonly found in bacterial 16S rRNA genes, and having a different insertion in several 16S rRNA gene copies borne by a single bacterial species was rarely observed. The function of these insertions is not known, but their occurrence can have an important impact in deriving 16S rRNA oligonucleotidic fluorescence in situ hybridization probes, as these insertions can be excised from 16S rRNA transcripts.Key words: Desulfitobacterium, 16S ribosomal RNA genes, heterogeneity, gene insertions, fluorescence in situ hybridization.

scholarly journals Pyrosequencing of 16S rRNA genes in fecal samples reveals high diversity of hindgut microflora in horses and potential links to chronic laminitis

2012 ◽  
Vol 8 (1) ◽  
pp. 231 ◽  
Author(s):  
Samantha M Steelman ◽  
Bhanu P Chowdhary ◽  
Scot Dowd ◽  
Jan Suchodolski ◽  
Jan E Janečka
Keyword(s):  
16S Rrna ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Fecal Samples ◽  
High Diversity

Molecular phylogeny of Barbin fishes of North - East Indiabased on mitochondrial 16SrRNA gene sequences

2016 ◽  
Author(s):  
N. Sobita ◽  
Ch. Basudha
Keyword(s):  
16S Rrna ◽  
Molecular Phylogeny ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Maximum Parsimony Tree ◽  
North East India ◽  
North East ◽  
Parsimony Tree ◽  
High Bootstrap ◽  
16Srrna Gene

The Barbin fishes (Cypriniformes: Barbinae) have achieved great diversity in the world and cosmopolitan in distribution but their phyletic classification is ambiguous. Molecular phylogeny of barbin fishes of North-East India was studied by using mitochondrial 16S rRNA sequences. Partial sequences (540-615 bp) of mit. 16S rRNA genes of four species of barbin fishes – Pethia atra, Puntius chola, P. javanicus, and P. sophore were generated and sequences of 7 species were downloaded from GenBank for present study. The aim of our present study is to resolve the taxonomic relationship and to establish the molecular phylogeny of Barbin fishes of North-East India based on mitochondrial 16S rRNA genes sequences. The Maximum Parsimony Tree shows three clusters with high bootstrap value and present data indicates that all fishes in this group had a common ancestor but now they have separated into distinct evolutionary lineages.

scholarly journals Vertical variation in Vibrio community composition in Sansha Yongle Blue Hole and its ability to degrade macromolecules

2019 ◽  
Vol 2 (1) ◽  
pp. 60-72 ◽  
Author(s):  
Bei Li ◽  
Jiwen Liu ◽  
Shun Zhou ◽  
Liang Fu ◽  
Peng Yao ◽  
...  
Keyword(s):  
Organic Carbon ◽  
16S Rrna ◽  
Community Composition ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Tween 20 ◽  
Rrna Gene ◽  
Free Living ◽  
Blue Hole ◽  
Gene Copies

Abstract With the advantages of wide distribution, fast growth, and broad metabolic spectrum to organic carbon compounds, Vibrio may play an important role in organic carbon cycling. However, the ecological roles of Vibrio in many marine environments have not been explored. Here, the world’s deepest ‘blue hole’, the Sansha Yongle Blue Hole (SYBH) in the South China Sea, which is a geographically semi-enclosed environment featuring unique chemical characters, was investigated. The abundance, diversity and carbon source utilization capability of Vibrio were studied by quantification and high-throughput sequencing of Vibrio specific 16S rRNA genes and cultivation methods. The abundance of Vibrio in water column of the SYBH ranged from 3.78 × 104 to 7.35 × 106 16S rRNA gene copies L−1. Free-living Vibrio was more abundant than particle-associated Vibrio (~ 1.20 × 106 versus~ 2.68 × 105 gene copies L−1), indicating that Vibrio prefers a free-living life style. The Vibrio assemblages showed clear vertical stratification and could be divided into three groups: aerobic-transition, middle anaerobic and bottom anaerobic zones. Dissolved oxygen (DO), temperature, pH and salinity were the main environmental factors affecting the abundance and community composition. Cultivated Vibrio demonstrated a degrading capability to various macromolecular substrates, including starch, Tween 20/40/80, DNA, gelatin, alginate, casein, chitin, lecithin, κ-carrageenan, mannan, xylan and hyaluronic acid. This suggests that Vibrio could produce a variety of highly active extracellular enzymes. Our study provides new insights into the distribution pattern and possible role in carbon cycle of Vibrio in the unique environment of a ‘blue hole’.

Determination of Bifidobacterium and Lactobacillus in breast milk of healthy women by digital PCR

2016 ◽  
Vol 7 (4) ◽  
pp. 559-569 ◽  
Author(s):  
L. Qian ◽  
H. Song ◽  
W. Cai
Keyword(s):  
Breast Milk ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Digital Pcr ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Gene Copy ◽  
Rrna Gene ◽  
Qrt Pcr ◽  
Gene Copies

Breast milk is one of the most important sources of postnatal microbes. Quantitative real-time polymerase chain reaction (qRT-PCR) is currently used for the quantitative analysis of bacterial 16S rRNA genes in breast milk. However, this method relies on the use of standard curves and is imprecise when quantitating target DNA of low abundance. In contrast, droplet digital PCR (DD-PCR) provides an absolute quantitation without the need for calibration curves. A comparison between DD-PCR and qRT-PCR was conducted for the quantitation of Bifidobacterium and Lactobacillus 16S RNA genes in human breast milk, and the impacts of selected maternal factors were studied on the composition of these two bacteria in breast milk. From this study, DD-PCR reported between 0-34,460 16S rRNA gene copies of Bifidobacterium genera and between 1,108-634,000 16S rRNA gene copies of Lactobacillus genera in 1 ml breast milk. The 16S rRNA gene copy number of Lactobacillus genera was much greater than that of Bifidobacterium genera in breast milk. DD-PCR showed a 10-fold lower limit of quantitation as compared to qRT-PCR. A higher correlation and agreement was observed between qRT-PCR and DD-PCR in Lactobacillus quantitation as compared to Bifidobacterium quantitation. Based on our DD-PCR quantitation, a low abundance of Bifidobacterium bacteria in breast milk was correlated to higher pre-pregnancy body mass index (BMI). However, no significant difference was observed for these two bacteria in breast milk between mothers who had vaginal deliveries and caesarean deliveries. This study suggests that DD-PCR is a better tool to quantitate the bacterial load of breast milk compared to the conventional qRT-PCR method. The number of breast milk Bifidobacterium bacteria is influenced by maternal pre-pregnancy BMI.

scholarly journals Phylogenetic Characterization of a Polychlorinated-Dioxin- Dechlorinating Microbial Community by Use of Microcosm Studies

2005 ◽  
Vol 71 (8) ◽  
pp. 4325-4334 ◽  
Author(s):  
Naoko Yoshida ◽  
Nobutaka Takahashi ◽  
Akira Hiraishi
Keyword(s):  
16S Rrna ◽  
Oxidative Degradation ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Aerobic Bacteria ◽  
Rrna Gene ◽  
Phylogenetic Characterization ◽  
Gene Copies ◽  
Primer Sets ◽  
Microcosm Studies

ABSTRACT Microcosms capable of reductive dechlorination of polychlorinated dibenzo-p-dioxins/dibenzofurans (PCDD/Fs) were constructed in glass bottles by seeding them with a polluted river sediment and incubating them anaerobically with an organic medium. All of the PCDD/F congeners detected were equally reduced without the accumulation of significant amounts of less-chlorinated congeners as the intermediate or end products. Alternatively, large amounts of catechol and salicylic acid were produced in the upper aqueous phase. Thus, the dechlorination of PCDD/Fs and the oxidative degradation of the dechlorinated products seemed to take place simultaneously in the microcosm. Denaturing gel gradient electrophoresis and clone library analyses of PCR-amplified 16S rRNA genes from the microcosm showed that members of the phyla Firmicutes, Proteobacteria, and Bacteroidetes predominated. A significant number of Chloroflexi clones were also detected. Quantitative real-time PCR with specific primer sets showed that the 16S rRNA genes of a putative dechlorinator, “Dehalococcoides,” and its relatives accounted for 0.1% of the total rRNA gene copies of the microcosm. Most of the clones thus obtained formed a cluster distinct from the typical “Dehalococcoides” group. Quinone profiling indicated that ubiquinones accounted for 18 to 25% of the total quinone content, suggesting the coexistence and activity of ubiquinone-containing aerobic bacteria. These results suggest that the apparent complete dechlorination of PCDD/Fs found in the microcosm was due to a combination of the dechlorinating activity of the “Dehalococcoides”-like organisms and the oxidative degradation of the dechlorinated products by aerobic bacteria with aromatic hydrocarbon dioxygenases.

Correlations between maximum reductive dechlorination rates and specific biomass parameters in Dehalococcoides mccartyi consortia enriched on chloroethenes PCE, TCE, and cis-1,2-DCE

2021 ◽  
Author(s):  
B Matturro ◽  
M Majone ◽  
F Aulenta ◽  
S Rossetti
Keyword(s):  
16S Rrna ◽  
Reductive Dechlorination ◽  
Correlation Factor ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Activity Levels ◽  
Dehalococcoides Mccartyi ◽  
Gene Copies ◽  
Specific Biomass

Abstract One of the challenges to implementing the modeling of the biological reductive dechlorination (RD) process is the evaluation of biological parameters that represent the abundance/activity levels of the microorganisms involved in the biodegradation of chloroethenes. Here we report a combined analysis of kinetic and specific biomass parameters conducted on three dechlorinating consortia enriched on PCE, TCE, and cis-1,2-DCE. In these consortia, Dehalococcoides mccartyi (Dhc) represented ≥ 70% of the bacterial population identified via 16S rRNA gene amplicon sequencing. Quantitative biomolecular methods were used to generate specific biomass parameters targeting either the Dhc population (16S rRNA genes or cells) or specific genes encoding RD process-involved reductive dehalogenases. The correlation factor between the abundance of active Dhc cells or tceA gene copies and maximum RD rates allowed to predict an increment of 7E+09 of active Dhc cells or 5E+09 tceA gene copies L−1 under controlled conditions. Diversely, the utilization of gene transcripts as biomass parameters for RD modeling did not provide reliable correlations with kinetic performances. This study provides valuable insights for further modeling of the RD process through the utilization of specific biomass parameters.

scholarly journals Comparison of Gull Feces-Specific Assays Targeting the 16S rRNA Genes of Catellicoccus marimammalium and Streptococcus spp.

2012 ◽  
Vol 78 (6) ◽  
pp. 1909-1916 ◽  
Author(s):  
Hodon Ryu ◽  
John F. Griffith ◽  
Izhar U. H. Khan ◽  
Stephen Hill ◽  
Thomas A. Edge ◽  
...  
Keyword(s):  
16S Rrna ◽  
Water Samples ◽  
Environmental Water ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Taqman Assay ◽  
Rrna Gene ◽  
Recreational Waters ◽  
Fecal Samples ◽  
Content Type

ABSTRACTTwo novel gull-specific quantitative PCR (qPCR) assays were developed using 16S rRNA gene sequences from gull fecal clone libraries: a SYBR green assay targetingStreptococcusspp. (gull3) and a hydrolysis TaqMan assay targetingCatellicoccus marimammalium(gull4). The objectives of this study were to compare the host specificity of a previousC. marimammaliumqPCR assay (gull2) with that of the new markers and to examine the presence of the three gull markers in environmental water samples from different geographic locations. Most of the gull fecal samples tested (n= 255) generated positive signals with the gull2 and gull4 assays (i.e., >86%), whereas only 28% were positive with gull3. Low prevalence and abundance of tested gull markers (0.6 to 15%) were observed in fecal samples from six nonavian species (n= 180 fecal samples), whereas the assays cross-reacted to some extent (13 to 31%) with other (nongull) avian fecal samples. The gull3 assay was positive against fecal samples from 11 of 15 avian species, including gull. Of the presumed gull-impacted water samples (n= 349), 86%, 59%, and 91% were positive with the gull2, the gull3, and the gull4 assays, respectively. Approximately 5% of 239 non-gull-impacted water samples were positive with the gull2 and the gull4 assays, whereas 21% were positive witg the gull3 assay. While the relatively high occurrence of gull2 and gull4 markers in waters impacted by gull feces suggests that these assays could be used in environmental monitoring studies, the data also suggest that multiple avian-specific assays will be needed to accurately assess the contribution of different avian sources in recreational waters.

scholarly journals Colonization and Development of the Fecal Microflora of South China Tiger Cubs (Panthera tigris amoyensis) by Sequencing of the 16S rRNA Gene

2021 ◽  
pp. 1-12
Author(s):  
Yanfa Sun ◽  
Jie Yao ◽  
Min Zhang ◽  
Tengteng Chen ◽  
Weihua Xu ◽  
...  
Keyword(s):  
16S Rrna ◽  
South China ◽  
Fecal Microbiota ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Panthera Tigris ◽  
Gut Health ◽  
Fecal Samples ◽  
Fecal Microflora

Postnatal colonization and development of the gut microbiota is linked to health and growth. A comprehensive understanding of the postnatal compositional changes and development of the microbial community is helpful to understand the gut health and improve the survival rate of South China tiger cubs (<i>Panthera tigris amoyensis</i>). Fecal samples from three tiger cubs were collected on the day of birth in 2018 (June 17–21 [G0], July 18 [G1], July 31 [G2], and August 7 [G3]). The 16S rRNA genes of the fecal microflora were sequenced. Results showed that 38 phyla, 58 classes, 134 orders, 272 families, and 636 genera of bacteria from 3,059 operational taxonomic units were identified from 12 fecal samples. The diversity and abundance of species of group G0 were significantly higher (<i>p</i> &#x3c; 0.05 or 0.01) than those of groups G2 and G3. The predominant phylum was Proteobacteria in groups G0 and G1 (38.85% and 48%, respectively) and Firmicutes in groups G2 and G3 (71.42% and 75.29%, respectively). At the phylum level, the abundance of Deinococcus-Thermus was significantly decreased in groups G1, G2, and G3 as compared to group G0 (<i>p</i> &#x3c; 0.05), while that of Firmicutes was significantly increased in groups G2 and G3 (<i>p</i> &#x3c; 0.05). At the genus level, the abundance of <i>Faecalibacterium</i>, <i>Ralstonia</i>, and unidentified <i>Rickettsiales</i> was significantly decreased in groups G1, G2, and G3 as compared with group G0 (<i>p</i> &#x3c; 0.05), while that of <i>Pseudomonas</i> was significantly decreased in groups G2 and G3 (<i>p</i> &#x3c; 0.05). The composition and structure of fecal microbiota of South China tiger cubs changed after birth.

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