Nephele: a cloud platform for simplified, standardized and reproducible microbiome data analysis

Weber, Nick; Liou, David; Dommer, Jennifer; MacMenamin, Philip; Quiñones, Mariam; Misner, Ian; Oler, Andrew J.; Wan, Joe; Lewis, Kim; McCarthy, Meghan C; Ezeji, Samuel; Noble, Karlynn; Hurt, Darrell E.

doi:10.1093/bioinformatics/btx617

Cited by 117 publications

(80 citation statements)

References 13 publications

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“…However, there is still no clear consensus of the impact of STH on microbiota diversity and composition. This could be in part because of differences in the STH species, prevalence, and intensity of infection in these different locations, as well as differences in the laboratory and analytical methodologies employed (28)(29)(30)(31). In the present study, we used samples collected in Kenya as part of a larger study to examine differences in the stool microbiota of individuals with and without STH infections and before and after deworming treatment.…”

Section: Discussionmentioning

confidence: 99%

The Impact of Anthelmintic Treatment on Human Gut Microbiota Based on Cross-Sectional and Pre- and Postdeworming Comparisons in Western Kenya

Easton

Quiñones

Vujkovic-Cvijin

et al. 2019

mBio

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Murine studies suggest that the presence of some species of intestinal helminths is associated with changes in host microbiota composition and diversity. However, studies in humans have produced varied conclusions, and the impact appears to vary widely depending on the helminth species present. To demonstrate how molecular approaches to the human gut microbiome can provide insights into the complex interplay among disparate organisms, DNA was extracted from cryopreserved stools collected from residents of 5 rural Kenyan villages prior to and 3 weeks and 3 months following albendazole (ALB) therapy. Samples were analyzed by quantitative PCR (qPCR) for the presence of 8 species of intestinal parasites and by MiSeq 16S rRNA gene sequencing. Based on pretreatment results, the presence of neither Ascaris lumbricoides nor Necator americanus infection significantly altered the overall diversity of the microbiota in comparison with age-matched controls. Following ALB therapy and clearance of soil-transmitted helminths (STH), there were significant increases in the proportion of the microbiota made up by Clostridiales (P = 0.0002; average fold change, 0.57) and reductions in the proportion made up by Enterobacteriales (P = 0.0004; average fold change, −0.58). There was a significant posttreatment decrease in Chao1 richness, even among individuals who were uninfected pretreatment, suggesting that antimicrobial effects must be considered in any posttreatment setting. Nevertheless, the helminth-associated changes in Clostridiales and Enterobacteriales suggest that clearance of STH, and of N. americanus in particular, alters the gut microbiota. IMPORTANCE The gut microbiome is an important factor in human health. It is affected by what we eat, what medicines we take, and what infections we acquire. In turn, it affects the way we absorb nutrients and whether we have excessive intestinal inflammation. Intestinal worms may have an important impact on the composition of the gut microbiome. Without a complete understanding of the impact of mass deworming programs on the microbiome, it is impossible to accurately calculate the cost-effectiveness of such public health interventions and to guard against any possible deleterious side effects. Our research examines this question in a “real-world” setting, using a longitudinal cohort, in which individuals with and without worm infections are treated with deworming medication and followed up at both three weeks and three months posttreatment. We quantify the impact of roundworms and hookworms on gut microbial composition, suggesting that the impact is small, but that treatment of hookworm infection results in significant changes. This work points to the need for follow-up studies to further examine the impact of hookworm on the gut microbiota and determine the health consequences of the observed changes.

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Section: Discussionmentioning

confidence: 99%

The Impact of Anthelmintic Treatment on Human Gut Microbiota Based on Cross-Sectional and Pre- and Postdeworming Comparisons in Western Kenya

Easton

Quiñones

Vujkovic-Cvijin

et al. 2019

mBio

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“…of Cyber Infrastructure and Computational Biology (OCICB) in Bethesda, Maryland, USA (25). The LefSe Galaxy web application tool developed by the Huttenhower group was performed using default parameters as previously published (26).…”

Section: Methodsmentioning

confidence: 99%

Indole-3-carbinol prevents colitis and associated microbial dysbiosis in an IL-22–dependent manner

Busbee¹,

Menzel²,

Alrafas³

et al. 2020

JCI Insight

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“…We analyzed the 16S-V4 phylogenetic data with the PICRUSt software package [71] to predict functional traits based on the Kyoto Encyclopedia of Genes and Genomes Orthology (KO) classification [72] on the Nephele cloud platform [73]. Visualization of the taxonomic and functional profiles for each sample used heatmaps generated with the HemI toolkit [74].…”

Section: Discussionmentioning

confidence: 99%

Identification of a dynamic middle ear microbiome in healthy adults

Lee

Kashefi

Reguera

2020

Preprint

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Background The entrenched dogma of a sterile middle ear in health is incongruent with its periodic exposure to exhaled air when the tympanic (Eustachian) tube opens while swallowing, yawning or inhaling deeply. Tubal patency is brief but frequent to provide adequate aeration, equalize pressure across the eardrum and drain mucus down the sides of the oropharynx. It also provides a mechanism for aerial dispersal of microorganisms from the aerodigestive tract. Method We designed a pilot study and received institutional approval to collect otic secretions that naturally drain on the sides of the oropharynx, behind the palatopharyngeal arch. This protocol bypassed the need to surgically access the middle ear through or around the eardrum, allowed us to collect samples from individuals with no underlying otic conditions, and prevented sample cross-contamination. As controls, we also collected samples from the center of the oropharynx and buccal mucosae seeded by saliva, which may serve as sources of microbial dispersal into the middle ear. Results We sequenced 16S rRNA-V4 amplicons from otic, oropharyngeal and buccal samples collected from a cohort of 19 healthy young adults. The survey identified in the otic samples a diverse bacterial community with many oropharyngeal and buccal keystone taxa and most of the functional traits of the neighboring oral microbiomes. Neutral community models predicted a large contribution of oral dispersal to the composition of the otic microbiome as well as several taxa responsive to positive selection. This was further supported by the enrichment in the otic communities of obligate anaerobes of Bacteroidetes and Fusobacteria over facultative anaerobic Proteobacteria and Firmicutes. Furthermore, the prevalence of the anaerobic members decreased with the more frequent otic aeration predicted from the equalization training of scuba divers recruited to the study. Conclusions These results challenge the long held view of a sterile middle ear and suggest instead that frequent seeding with oral microbes supports the establishment of a rich and robust otic community dynamically adapted to the episodic ventilation of the tympanic space.

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Nephele: a cloud platform for simplified, standardized and reproducible microbiome data analysis

Cited by 117 publications

References 13 publications

The Impact of Anthelmintic Treatment on Human Gut Microbiota Based on Cross-Sectional and Pre- and Postdeworming Comparisons in Western Kenya

The Impact of Anthelmintic Treatment on Human Gut Microbiota Based on Cross-Sectional and Pre- and Postdeworming Comparisons in Western Kenya

Indole-3-carbinol prevents colitis and associated microbial dysbiosis in an IL-22–dependent manner

Identification of a dynamic middle ear microbiome in healthy adults

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