&lt;title&gt;Feasibility of high-resolution oligonucleotide separation on a microchip&lt;/title&gt;

Minalla, Abdel; Dubrow, Robert; Bousse, Luc

doi:10.1117/12.443044

Cited by 14 publications

(12 citation statements)

References 0 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Samples were barcoded with a unique combination of forward and reverse indexes allowing for simultaneous processing of multiple samples. PCR products were pooled, column-purified, and size selected through microfluidic DNA fractionation (Minalla & Dubrow, 2001). Consolidated libraries were quantified using quantitative real-time PCR using the Kapa iCycler qPCR kit (Bio-Rad) on a BioRad Myio before loading into the sequencer.…”

Section: Gut Microbiome Analysesmentioning

confidence: 99%

Rapid gut microbiome changes in a world‐class ultramarathon runner

2019

View full text Add to dashboard Cite

In 2007 the National Institutes of Health launched the Human Microbiome Project (HMP), an interdisciplinary research initiative seeking to characterize the contribution of human gut microbiota to health and disease (Turnbaugh et al., 2007). Subsequent findings have demonstrated compelling relationships between human gut microbiome composition and many leading causes of death worldwide including cardiovascular disease (Wang et al., 2011), diabetes (Larsen et al., 2010), and cancer (Ahn et al., 2013). Although the gut microbiome is suggested to exhibit exceptional plasticity (Gomez et al., 2019), a detailed understanding of the factors determining human microbiome assembly is lacking (Relman, 2015).

show abstract

Section: Gut Microbiome Analysesmentioning

confidence: 99%

Rapid gut microbiome changes in a world‐class ultramarathon runner

2019

View full text Add to dashboard Cite

show abstract

“…Samples were barcoded with a unique combination of forward and reverse indexes allowing for simultaneous processing of multiple samples. PCR products were pooled, column-purified, and size-selected through microfluidic DNA fractionation 20 . Consolidated libraries were quantified by quantitative real-time PCR using the Kapa Bio-Rad iCycler qPCR kit on a BioRad MyiQ before loading into the sequencer.…”

Section: Methodsmentioning

confidence: 99%

Local oral and nasal microbiome diversity in age-related macular degeneration

Rullo

Far

Quinn

et al. 2020

Sci Rep

View full text Add to dashboard Cite

Age-related macular degeneration (AMD) is a chronic degenerative disease of the retina. Recent reports have highlighted the potential role of mucosal surface microbes in the pathogenesis of AMD. in this case-control study, the composition of the nasal and oral microbiota in newly diagnosed neovascular age-related macular degeneration cases (6 male, 7 female) was compared to controls without retinal diseases (2 male, 3 female). PCR amplification of 16S rRNA genes was performed with universal primers amplifying the V4 variable region (515F-806R). Distinct microbial community characterization was achieved using principal coordinates Analysis (pcoA) of the Bray-curtis index with comparative analysis between cases and controls performed within QIIME 2. Sequencing of all cases and controls revealed clear separation with strong beta diversity between oral and nasal microbial communities (p < 0.001). Microbial composition differed between cases and controls in both oral and nasal samples. The top three oral microbes identified as different compared to controls included Burkholderiales (7.41 log2fold change, p = 3.29E-05), Actinomyceataceae (6.22 log2fold change, p = 3.73E-06) and Gemella (5.28 log2fold change, p = 0.0002). The top three nasal microbes identified as different compared to controls included Rothia (13.6 log2fold change, p = 3.63E-18), Actinobacteria (10.29 log2fold change, p = 9.81E-10) and Propionibacteriales (8.73 log2fold change, p = 6.74E-09). These relative shifts in communities of bacteria detected in newly diagnosed neovascular AMD patients may suggest additional mechanistic links in disease pathogenesis.

show abstract

“…Primers also contained Illumina tags and barcodes with unique combination of forward and reverse indexes to allow multiplexing. Pooled PCR products were column-purified and selected through microfluidic DNA fractionation based on size [37]. Real-time qPCR quantified consolidated libraries using the Kapa Bio-Rad iCycler qPCR kit on a BioRad MyiQ prior to sequencing.…”

Section: S Ribosomal Rna (Rrna) Gene Sequencing Dna Extraction Anmentioning

confidence: 99%

Initial Sequencing and Characterization of Gastrointestinal and Oral Microbiota in Urban Pakistani Adults Reveals Abnormally High Levels of Potentially Starch Metabolizing Bacteria in the General Population

Batool

Ali

Jaan

et al. 2018

Preprint

View full text Add to dashboard Cite

We describe the characterization of the gastrointestinal tract (gut) and oral microbiota (bacteria) in 32 urban Pakistani adults representing seven major geographies and six ethnicities in the country. Study participants were between ages 18 and 40, had body mass index between 18 and 25 Kg/m 2 , and were early-career students or professionals belonging to 25 major cities of the country. These individuals donated a total of 61 samples (32 gut and 29 oral) that were subjected to 16S ribosomal RNA (rRNA) gene sequencing. Microbiome composition of Pakistani individuals was compared against the uBiome database of selected individuals who self-reported to be in excellent health. Using the crude measure of percentage overlap or similarity between the gut microbiota profile of Pakistani and uBiome dataset as proxy for health, our sequencing indicated that the Pakistani gut microbiota was moderately healthy relative to the uBiome dataset and Pakistani women appeared healthier relative to men. The Pakistani gut microbiome seemed susceptible to obesity and weight gain, levels of probiotics was very high likely due to the popularity of milk-based and fermented foods in the Pakistani diet, and bacteria that metabolize starch and carbohydrates (typically seen in the gut microbiota of honey bee) were abnormally enriched in the gut of Pakistani men. Our investigations reveal serious issues with the dietary habits and lifestyle of Pakistani individuals of consuming food enriched in high carbohydrates and fats, overcooked in oil and spices, following a sedentary lifestyle, little or no daily intake of fresh fruits, over-consumption of antibiotics from a very early age, and health and hygiene standards that do not meet international standards. Our sequencing is the first step towards generating a countrywide understanding of the impact of the local diet and lifestyle on Pakistani gut microbiota and can help understand its overall association with health and wellness.

show abstract

<title>Feasibility of high-resolution oligonucleotide separation on a microchip</title>

Cited by 14 publications

References 0 publications

Rapid gut microbiome changes in a world‐class ultramarathon runner

Rapid gut microbiome changes in a world‐class ultramarathon runner

Local oral and nasal microbiome diversity in age-related macular degeneration

Initial Sequencing and Characterization of Gastrointestinal and Oral Microbiota in Urban Pakistani Adults Reveals Abnormally High Levels of Potentially Starch Metabolizing Bacteria in the General Population

Contact Info

Product

Resources

About