Advancing Our Understanding of the Human Microbiome Using QIIME

Navas-Molina, José A.; Peralta‐Sánchez, Juan Manuel; González, Antonio G.; McMurdie, Paul J.; Vázquez-Baeza, Yoshiki; Xu, Zhenjiang; Ursell, Luke K.; Lauber, Christian L.; Zhou, Hongwei; Song, Se Jin; Huntley, James S; Ackermann, Gail; Berg-Lyons, Donna; Holmes, Susan; Caporaso, J. Gregory; Knight, Rob

doi:10.1016/b978-0-12-407863-5.00019-8

Cited by 508 publications

(487 citation statements)

References 98 publications

(144 reference statements)

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“…16S rRNA genes were targeted using primers 515F/806R, available on the Earth Microbiome Project website (www.earthmicrobiome.org), and a total of 4,424,307 sequences were detected. An open reference OTU picking approach was used (22) to cluster sequences, utilizing the program uclust (23). First, sequences were prefiltered to remove reads with less than 60% homology to at least one 16S rRNA gene in the Greengenes collection (24,25).…”

Section: Methodsmentioning

confidence: 99%

Variation in the Microbiota of Ixodes Ticks with Regard to Geography, Species, and Sex

Treuren

Ponnusamy

Brinkerhoff

et al. 2015

Appl Environ Microbiol

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n Ixodes scapularis is the principal vector of Lyme disease on the East Coast and in the upper Midwest regions of the UnitedStates, yet the tick is also present in the Southeast, where Lyme disease is absent or rare. A closely related species, I. affinis, also carries the pathogen in the South but does not seem to transmit it to humans. In order to better understand the geographic diversity of the tick, we analyzed the microbiota of 104 adult I. scapularis and 13 adult I. affinis ticks captured in 19 locations in South Carolina, North Carolina, Virginia, Connecticut, and New York. Initially, ticks from 4 sites were analyzed by 454 pyrosequencing. Subsequently, ticks from these sites plus 15 others were analyzed by sequencing with an Illumina MiSeq machine. By both analyses, the microbiomes of female ticks were significantly less diverse than those of male ticks. The dissimilarity between tick microbiomes increased with distance between sites, and the state in which a tick was collected could be inferred from its microbiota. The genus Rickettsia was prominent in all locations. Borrelia was also present in most locations and was present at especially high levels in one site in western Virginia. In contrast, members of the family Enterobacteriaceae were very common in North Carolina I. scapularis ticks but uncommon in I. scapularis ticks from other sites and in North Carolina I. affinis ticks. These data suggest substantial variations in the Ixodes microbiota in association with geography, species, and sex.

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Section: Methodsmentioning

confidence: 99%

Variation in the Microbiota of Ixodes Ticks with Regard to Geography, Species, and Sex

Treuren

Ponnusamy

Brinkerhoff

et al. 2015

Appl Environ Microbiol

Self Cite

163

200

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“…Processing of sequence data, including chimera check, operational taxonomic unit (OTU) definition and taxonomy assignment, was performed using QIIME version 1.9 [25], USEARCH v8.0 and UCHIME version 4.2.40 software [26]. Singletons were removed in this study.…”

Section: S Rdna-based Taxonomic Analysis and Statistical Analysismentioning

confidence: 99%

“…bDiversity was estimated using the UniFrac metric to calculate the distances between the samples and was visualized by principal coordinate analysis (PCoA) and statistically analyzed using permutational multivariate analysis of variance (PERMANOVA). The figures were generated using QIIME version 1.9 software [25].…”

Section: A-diversity and B-diversitymentioning

confidence: 99%

Analysis of endoscopic brush samples identified mucosa-associated dysbiosis in inflammatory bowel disease

et al. 2017

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Background The mucosa-associated gut microbiota directly modulates epithelial and mucosal function. In this study, we investigated the mucosa-associated microbial community in patients with inflammatory bowel disease (IBD), using endoscopic brush samples. Methods A total of 174 mucus samples from 43 patients with ulcerative colitis (UC), 26 with Crohn's disease (CD) and 14 non-IBD controls were obtained by gentle brushing of mucosal surfaces using endoscopic cytology brushes. The gut microbiome was analyzed using 16S rRNA gene sequencing. Results There were no significant differences in microbial structure among different anatomical sites (the ileum, cecum and sigmoid colon) within individuals. There was, however, a significant difference in microbial structure between CD, UC and non-IBD controls. The difference between CD and non-IBD controls was more marked than that between UC patients and non-IBD controls. a-Diversity was significantly lower in UC and CD patients than non-IBD controls. When comparing CD patients with non-IBD controls, the phylum Proteobacteria was significantly increased and the phyla Firmicutes and Bacteroidetes were significantly reduced. These included a significant increase in the genera Escherichia, Ruminococcus (R. gnavus), Cetobacterium, Actinobacillus and Enterococcus, and a significant decrease in the genera Faecalibacterium, Coprococcus, Prevotella and Roseburia. Comparisons between CD and UC patients revealed a greater abundance of the genera Escherichia, Ruminococcus (R. gnavus), Clostridium, Cetobacterium, Peptostreptococcus in CD patients, and the genera Faecalibacterium, Blautia, Bifidobacterium, Roseburia and Citrobacter in UC patients. Conclusions Mucosa-associated dysbiosis was identified in IBD patients. CD and UC may be distinguishable from the mucosa-associated microbial community structure.

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“…Quality control of the FASTQ files was performed, with quality assessment and filtering using the FASTX toolkit. The rest of the steps were performed using the QIIME suite (version 1.8) (23)(24)(25).…”

Section: Animalsmentioning

confidence: 99%

Response of Germfree Mice to Colonization by Oxalobacter formigenes and Altered Schaedler Flora

Ellis

Dowell

et al. 2016

Appl Environ Microbiol

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Colonization with Oxalobacter formigenes may reduce the risk of calcium oxalate kidney stone disease. To improve our limited understanding of host-O. formigenes and microbe-O. formigenes interactions, germfree mice and mice with altered Schaedler flora (ASF) were colonized with O. formigenes. Germfree mice were stably colonized with O. formigenes, which suggests that O. formigenes does not require other organisms to sustain its survival. Examination of intestinal material indicated no viable O. formigenes in the small intestine and ϳ4 ؋ 10 6 CFU O. formigenes per 100 mg contents in the cecum and proximal colon, with ϳ0.02% of total cecal O. formigenes cells being tightly associated with the mucosa. O. formigenes did not alter the overall microbial composition of ASF, and ASF did not affect the capacity of O. formigenes to degrade dietary oxalate in the cecum. Twentyfour-hour collections of urine and feces in metabolic cages in semirigid isolators demonstrated that the introduction of ASF into germfree mice significantly reduced urinary oxalate excretion. These experiments also showed that O. formigenes-monocolonized mice excreted significantly more urinary calcium than did germfree mice, which may be due to degradation of calcium oxalate crystals by O. formigenes and subsequent intestinal absorption of free calcium. In conclusion, the successful establishment of mouse models with defined flora and O. formigenes should improve our understanding of O. formigenes-host and O. formigenes-microbe interactions. These data support the use of O. formigenes as a probiotic that has limited impact on the composition of the resident microbiota but provides an efficient oxalate-degrading function. Oxalobacter formigenes is part of the bacterial flora in the large intestine of many humans and other mammalian species and is unique in that it is the only bacterium yet identified in the intestines of mammals that requires oxalate as both an energy source and a carbon source. Recent evidence suggests that a lack of colonization with this oxalate-degrading specialist is a risk factor for idiopathic recurrent calcium oxalate stone disease (1, 2). A review of worldwide data indicated that 38% to 77% of a normal population and only 17% of stone formers were colonized with O. formigenes (1). The ability to recolonize individuals lacking O. formigenes was previously addressed in a study in which two healthy adults not colonized with O. formigenes became colonized following the ingestion of cultured O. formigenes (3) and remained colonized for 9 months. However, studies in which O. formigenes was provided in either a lyophilized form in enteric coated capsules or as a frozen paste to patients suffering from primary hyperoxaluria resulted in only a minority of the patients remaining colonized posttreatment (4, 5). Therefore, although it seems quite possible that O. formigenes colonization of noncolonized stone formers may be an effective way to minimize the risk of recurrent calcium oxalate stone disease, a better understanding o...

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Advancing Our Understanding of the Human Microbiome Using QIIME

Cited by 508 publications

References 98 publications

Variation in the Microbiota of Ixodes Ticks with Regard to Geography, Species, and Sex

Variation in the Microbiota of Ixodes Ticks with Regard to Geography, Species, and Sex

Analysis of endoscopic brush samples identified mucosa-associated dysbiosis in inflammatory bowel disease

Response of Germfree Mice to Colonization by Oxalobacter formigenes and Altered Schaedler Flora

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