scholarly journals Stool metabolome-microbiota evaluation among children and adolescents with obesity, overweight, and normal-weight using 1H NMR and 16S rRNA gene profiling

PLoS ONE ◽  
2021 ◽  
Vol 16 (3) ◽  
pp. e0247378
Author(s):  
José Diógenes Jaimes ◽  
Andrea Slavíčková ◽  
Jakub Hurych ◽  
Ondřej Cinek ◽  
Ben Nichols ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Alpha Diversity ◽  
Study Groups ◽  
Normal Weight ◽  
Gene Profiling ◽  
Energy Harvest ◽  
Rrna Gene ◽  
H Nmr ◽  
Significant Difference

Characterization of metabolites and microbiota composition from human stool provides powerful insight into the molecular phenotypic difference between subjects with normal weight and those with overweight/obesity. The aim of this study was to identify potential metabolic and bacterial signatures from stool that distinguish the overweight/obesity state in children/adolescents. Using 1H NMR spectral analysis and 16S rRNA gene profiling, the fecal metabolic profile and bacterial composition from 52 children aged 7 to 16 was evaluated. The children were classified into three groups (16 with normal-weight, 17 with overweight, 19 with obesity). The metabolomic analysis identified four metabolites that were significantly different (p < 0.05) among the study groups based on one-way ANOVA testing: arabinose, butyrate, galactose, and trimethylamine. Significantly different (p < 0.01) genus-level taxa based on edgeR differential abundance tests were genus Escherichia and Tyzzerella subgroup 3. No significant difference in alpha-diversity was detected among the three study groups, and no significant correlations were found between the significant taxa and metabolites. The findings support the hypothesis of increased energy harvest in obesity by human gut bacteria through the growing observation of increased fecal butyrate in children with overweight/obesity, as well as an increase of certain monosaccharides in the stool. Also supported is the increase of trimethylamine as an indicator of an unhealthy state.

scholarly journals Inconsistent Patterns of Microbial Diversity and Composition Between Highly Similar Sequencing Protocols: A Case Study With Reef-Building Corals

2021 ◽  
Vol 12 ◽  
Author(s):  
Hannah E. Epstein ◽  
Alejandra Hernandez-Agreda ◽  
Samuel Starko ◽  
Julia K. Baum ◽  
Rebecca Vega Thurber
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Beta Diversity ◽  
Sequence Data ◽  
Alpha Diversity ◽  
Gene Profiling ◽  
Rrna Gene ◽  
Sequencing Platform ◽  
Alpha And Beta Diversity ◽  
Diversity Metrics

16S rRNA gene profiling (amplicon sequencing) is a popular technique for understanding host-associated and environmental microbial communities. Most protocols for sequencing amplicon libraries follow a standardized pipeline that can differ slightly depending on laboratory facility and user. Given that the same variable region of the 16S gene is targeted, it is generally accepted that sequencing output from differing protocols are comparable and this assumption underlies our ability to identify universal patterns in microbial dynamics through meta-analyses. However, discrepant results from a combined 16S rRNA gene dataset prepared by two labs whose protocols differed only in DNA polymerase and sequencing platform led us to scrutinize the outputs and challenge the idea of confidently combining them for standard microbiome analysis. Using technical replicates of reef-building coral samples from two species, Montipora aequituberculata and Porites lobata, we evaluated the consistency of alpha and beta diversity metrics between data resulting from these highly similar protocols. While we found minimal variation in alpha diversity between platform, significant differences were revealed with most beta diversity metrics, dependent on host species. These inconsistencies persisted following removal of low abundance taxa and when comparing across higher taxonomic levels, suggesting that bacterial community differences associated with sequencing protocol are likely to be context dependent and difficult to correct without extensive validation work. The results of this study encourage caution in the statistical comparison and interpretation of studies that combine rRNA gene sequence data from distinct protocols and point to a need for further work identifying mechanistic causes of these observed differences.

scholarly journals Anaplasma Infection in Ticks in Southeastern Region of Iran

2020 ◽  
Author(s):  
Reza Ranjbar ◽  
Mehdi Anjomruz ◽  
Ahmad Ali Enayati ◽  
Mehdi Khoobdel ◽  
Atiyeh Rafinejad ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Cold Chain ◽  
Rrna Gene ◽  
Infection Rates ◽  
Male And Female ◽  
Significant Difference ◽  
High Infection ◽  
Hyalomma Marginatum ◽  
Southeastern Region

Background: Anaplasmosis and Ehrlichiosis are the most important tick-borne diseases. This study was conducted in three cities of Kerman Province in Iran to investigate the circulation of the bacteria in ticks collected from sheep. Methods: Ticks were collected from animals using Srkj forceps and transferred to the Entomology lab in cold chain. After specimen’s identification, they kept at -70 ºC. Tick DNA was extracted using Bioneers DNA extraction kits followed by Nested PCR technique to amplify ribosomal 16S rRNA gene to detect Anaplasma infection in ticks. Results: 472 sheep were examined from which 349 ticks were collected and identified in laboratory using valid keys. Tick specimens belonged to two genera and four species; Hyalomma marginatum (62.47%) was the most frequent and Hylomma asiaticum (5.73%) showed the least abundance. The infestation rate to different tick species was different in three regions of Kerman Province. Observation revealed that 24 specimens (58.3%) were positive for Anaplasma. There is a significant difference between male and female infection rate. However, there is no significant difference between these variables in each of these cities. Conclusion: This study shows high infection rates to Anaplasma in hard ticks. It is essential for health and veterinary authorities and farmers to use appropriate strategies to control ticks to reduce the infestation.

Organotrophic and Mixotrofic Sulfur Oxidation in an Acidic Salt Flat in Northern Chile

2015 ◽  
Vol 1130 ◽  
pp. 63-66 ◽  
Author(s):  
Lorena Escudero ◽  
Jonathan Bijman ◽  
Guajardo M. Mariela ◽  
Juan José Pueyo Mur ◽  
Guillermo Chong ◽  
...  
Keyword(s):  
Microbial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Community Composition ◽  
Iron Concentration ◽  
Rrna Gene ◽  
Salt Flat ◽  
Significant Difference ◽  
Acidic Salt ◽  
The 16S Rrna Gene

To understand the microbial community inhabiting in an acidic salt flat the phylogenetic diversity and the geochemistry of this system was compared to acid mine drainage (AMD) systems. The microbial community structure was assessed by DNA extraction/PCR/DGGE and secuencing for the 16S rRNA gene and the geochemistry was analyzed using several approaches. Prediction of metagenome functional content was performed from the 16S rRNA gene survey using the bioinformatics software package Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt). The geochemical results revealed a much lower iron concentration in the salt flat than in AMD systems (39 and 21804 mg L-1, respectively) and a significant difference in chloride levels. Sequences inferred to be from potential sulfur metabolizing organisms constituted up to 70% of the microbial community in the acidic salt flat meanwhile predominat iron-metabolizing acidophile populations were reported in AMD systems. Interestingly, the microbial assemblage in the acidic salt flat was dominated by mixotrophic and organotrophic sulfur oxidizers as well as by photoautotrophic acidophiles. Our results suggests that the salt concentration in Salar de Gorbea (average Cl-= 40 gL-1) is in the limit for the occurrence of chemolithotrophic oxidation of sulfur compounds. In addition, the investigation allows concluding that salinity rather than extremes of pH is the major environmental determinant of microbial community composition.

scholarly journals First Experience of a Multicenter External Quality Assessment of Molecular 16S rRNA Gene Detection in Bone and Joint Infections

2014 ◽  
Vol 53 (2) ◽  
pp. 419-424 ◽  
Author(s):  
Chloé Plouzeau ◽  
Pascale Bémer ◽  
Anne Sophie Valentin ◽  
Geneviève Héry-Arnaud ◽  
Didier Tandé ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Joint Infection ◽  
Rrna Gene ◽  
Gene Detection ◽  
External Quality ◽  
Multicenter Studies ◽  
Joint Infections ◽  
Significant Difference ◽  
Bead Mill

The objective of this study was to assess the performance of seven French laboratories for 16S rRNA gene detection by real-time PCR in the diagnosis of bone and joint infection (BJI) to validate a large multicenter study. External quality control (QC) was required owing to the differences in extraction procedures and the molecular equipment used in the different laboratories. Three proficiency sets were organized, including four bacterial DNA extracts and four bead mill-pretreated osteoarticular specimens. Extraction volumes, 16S rRNA gene primers, and sequencing interpretation rules were standardized. In order to assess each laboratory's ability to achieve the best results, scores were assigned, and each QC series was classified as optimal, acceptable, or to be improved. A total of 168 QCs were sent, and 160 responses were analyzed. The expected results were obtained for 93.8%, with the same proportion for extracts (75/80) and clinical specimens (75/80). For the specimens, there was no significant difference between manual and automated extraction. This QC demonstrated the ability to achieve good and homogeneous results using the same 16S rRNA gene PCR with different equipment and validates the possibility of high-quality multicenter studies using molecular diagnosis for BJI.

scholarly journals Bacterial DNAemia is associated with serum zonulin levels in older subjects

2020 ◽  
Author(s):  
Giorgio Gargari ◽  
Valentina Taverniti ◽  
Cristian Del Bo’ ◽  
Stefano Bernardi ◽  
Cristina Andres-Lacueva ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Serum Levels ◽  
Gene Profiling ◽  
Rrna Gene ◽  
Bacterial Dna ◽  
Blood Samples ◽  
Gene Copies ◽  
Older Subjects ◽  
Pcr Targeting

AbstractThe increased presence of bacteria in blood is a plausible contributing factor in the development and progression of aging-associated diseases. In this context, we performed the quantification and the taxonomic profiling of the bacterial DNA in blood samples collected from a group of forty-three older subjects enrolled in a nursing home. Quantitative PCR targeting the 16S rRNA gene revealed that all the older volunteers contained detectable amounts of bacterial DNA in their blood. The total amount of 16S rRNA gene copies varied considerably between subjects. Correlation analyses revealed that the bacterial DNAemia (expressed as concentration of 16S rRNA gene copies in blood) significantly correlated with the serum levels of zonulin, an emerging marker of intestinal permeability. This result was confirmed by the analysis of a second set of blood samples collected after approximately four months from the same subjects. Analyses of 16S rRNA gene profiling revealed that most of the bacterial DNA detected in blood was ascribable to the phylum Proteobacteria with a predominance of Pseudomonadaceae and Enterobacteriaceae. Several control samples were also analyzed to assess the influence exerted by contaminant bacterial DNA potentially originating from reagents and materials. The date reported here suggest that para-cellular permeability of epithelial (and potentially also endothelial) cell layers may play an important role in bacterial migration into the bloodstream. Bacterial DNAemia is likely to impact on several aspects of host physiology and could underpin the development and prognosis of various diseases in older subjects.

scholarly journals 2576. The Microbiome of Recurrent Bacterial Vaginosis Compared with Asymptomatic Controls

2019 ◽  
Vol 6 (Supplement_2) ◽  
pp. S895-S895
Author(s):  
Elizabeth O Shay ◽  
Oluwatosin Goje ◽  
Roshan Padmanabhan ◽  
Charis Eng
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Bacterial Vaginosis ◽  
Alpha Diversity ◽  
Dna Probe ◽  
Gardnerella Vaginalis ◽  
Rrna Gene ◽  
Vaginal Microbiome ◽  
Β Diversity ◽  
Probe Test

Abstract Background Bacterial vaginosis (BV) affects nearly 1 in 3 women in the United States and is poorly understood. The study of the vaginal microbiome, using 16S rRNA-gene amplicon sequencing, has increased our knowledge of BV. We aimed to characterize the vaginal microbiome of women with recurrent BV firstly in comparison to controls, and secondly in comparison to a sub-population of our asymptomatic controls, positive for Gardnerella vaginalis via a vaginal pathogens DNA direct probe test (DNA probe). Methods Women aged 18–40 years, with recurrent BV, and asymptomatic controls were prospectively enrolled. Vaginal samples were collected from each participant. DNA was extracted, amplified using primers targeting the V3-V4 variable region of the 16S rRNA-gene, and then sequenced and processed through a hybrid Qiime MICCA bioinformatics pipeline. We also tested for G. vaginalis using the DNA probe. Results Seventeen recurrent BV patients and 46 controls were enrolled. Β diversity (P = 0.045), but not alpha diversity (P = 0.076) differed between groups. The genera Gardnerella and Prevotella were relatively more abundant, while Lactobacillus was relatively less abundant in recurrent BV vs. control groups. Of the patients for whom results of the DNA probe for Gardnerella vaginalis were available, 11 (69%) recurrent BV patients and 14 (35%) controls were positive. Control patients, negative by the DNA probe test, showed decreased alpha diversity (P = 0.0001) and significantly different β diversity (P = 0.001) compared with recurrent BV patients. Neither alpha (P = 0.31) nor β (P = 0.096) diversity differed between recurrent BV patients and controls that were G. vaginalis positive. Conclusion The microbiome of recurrent BV patients is distinct from that of asymptomatic controls; recurrent BV patients exhibit different β diversity, less Lactobacillus and more Gardnerella and Prevotella. Asymptomatic Gardnerella vaginalis-colonized controls demonstrate similar microbiome profiles to those of recurrent BV patients. These findings suggest that individual factors may influence whether or not a patient with a BV microbiomic profile experiences symptoms. Further investigation into these mechanisms could yield insights into the treatment of recurrent BV. Disclosures All authors: No reported disclosures.

scholarly journals Correction: Temporal dynamics of in-situ fiber-adherent bacterial community under ruminal acidotic conditions determined by 16S rRNA gene profiling

PLoS ONE ◽  
2018 ◽  
Vol 13 (9) ◽  
pp. e0204600
Author(s):  
Renee M. Petri ◽  
Poulad Pourazad ◽  
Ratchaneewan Khiaosa-ard ◽  
Fenja Klevenhusen ◽  
Barbara U. Metzler-Zebeli ◽  
...  
Keyword(s):  
Bacterial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Temporal Dynamics ◽  
Gene Profiling ◽  
Rrna Gene

scholarly journals Benchmark taxonomic classification of chicken gut bacteria based on 16S rRNA gene profiling in correlation with various feeding strategies

2020 ◽  
Vol 32 (1) ◽  
pp. 1034-1041
Author(s):  
Zubia Rashid ◽  
Syed Muddassar Hussain Gilani ◽  
Asma Ashraf ◽  
Sitwat Zehra ◽  
Abid Azhar ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gut Bacteria ◽  
Taxonomic Classification ◽  
Gene Profiling ◽  
Feeding Strategies ◽  
Rrna Gene

scholarly journals Standardization of Plant Microbiome Studies: Which Proportion of the Microbiota is Really Harvested?

2020 ◽  
Vol 8 (3) ◽  
pp. 342 ◽  
Author(s):  
Abdoul Razack Sare ◽  
Gilles Stouvenakers ◽  
Mathilde Eck ◽  
Amber Lampens ◽  
Sofie Goormachtig ◽  
...  
Keyword(s):  
16S Rrna ◽  
Scientific Community ◽  
Human Microbiome ◽  
Alpha Diversity ◽  
Rrna Gene ◽  
Alpha And Beta Diversity ◽  
Significant Difference ◽  
Plant Microbiota ◽  
Root Microbiome ◽  
Plant Microbiome

Studies in plant-microbiome currently use diverse protocols, making their comparison difficult and biased. Research in human microbiome have faced similar challenges, but the scientific community proposed various recommendations which could also be applied to phytobiome studies. Here, we addressed the isolation of plant microbiota through apple carposphere and lettuce root microbiome. We demonstrated that the fraction of the culturable epiphytic microbiota harvested by a single wash might only represent one-third of the residing microbiota harvested after four successive washes. In addition, we observed important variability between the efficiency of washing protocols (up to 1.6-fold difference for apple and 1.9 for lettuce). QIIME2 analysis of 16S rRNA gene, showed a significant difference of the alpha and beta diversity between protocols in both cases. The abundance of 76 taxa was significantly different between protocols used for apple. In both cases, differences between protocols disappeared when sequences of the four washes were pooled. Hence, pooling the four successive washes increased the alpha diversity for apple in comparison to a single wash. These results underline the interest of repeated washing to leverage abundance of microbial cells harvested from plant epiphytic microbiota whatever the washing protocols, thus minimizing bias.

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