Studies of inflammatory bowel disease (IBD) have been inconclusive in relating microbiota with distribution of inflammation. We report microbiota, host transcriptomics, epigenomics and genetics from ...matched inflamed and non-inflamed colonic mucosa 50 Crohn's disease (CD); 80 ulcerative colitis (UC); 31 controls. Changes in community-wide and within-patient microbiota are linked with inflammation, but we find no evidence for a distinct microbial diagnostic signature, probably due to heterogeneous host-microbe interactions, and show only marginal microbiota associations with habitual diet. Epithelial DNA methylation improves disease classification and is associated with both inflammation and microbiota composition. Microbiota sub-groups are driven by dominant Enterbacteriaceae and Bacteroides species, representative strains of which are pro-inflammatory in vitro, are also associated with immune-related epigenetic markers. In conclusion, inflamed and non-inflamed colonic segments in both CD and UC differ in microbiota composition and epigenetic profiles.
Recent advances have made it possible to analyze high-throughput marker-gene sequencing data without resorting to the customary construction of molecular operational taxonomic units (OTUs): clusters ...of sequencing reads that differ by less than a fixed dissimilarity threshold. New methods control errors sufficiently such that amplicon sequence variants (ASVs) can be resolved exactly, down to the level of single-nucleotide differences over the sequenced gene region. The benefits of finer resolution are immediately apparent, and arguments for ASV methods have focused on their improved resolution. Less obvious, but we believe more important, are the broad benefits that derive from the status of ASVs as consistent labels with intrinsic biological meaning identified independently from a reference database. Here we discuss how these features grant ASVs the combined advantages of closed-reference OTUs-including computational costs that scale linearly with study size, simple merging between independently processed data sets, and forward prediction-and of de novo OTUs-including accurate measurement of diversity and applicability to communities lacking deep coverage in reference databases. We argue that the improvements in reusability, reproducibility and comprehensiveness are sufficiently great that ASVs should replace OTUs as the standard unit of marker-gene analysis and reporting.
Enhancement of precipitation processes aloft over complex terrain is documented using reflectivity data from an S‐band scanning radar (NPOL) that was deployed on the west coast of Washington State ...during the Olympic Mountains Experiment (OLYMPEX). From November 2015 through mid‐January 2016, NPOL obtained high‐resolution data within sectors over the ocean and over the windward slopes of the Olympic Mountains. Contoured Frequency by Altitude Diagrams of radar reflectivity highlight a higher frequency of occurrence of larger reflectivities for all heights between 2 and 8 km over land compared to ocean, with the largest difference in the 4‐ to 6‐km range indicating a robust signature of enhancement aloft over the windward slopes. This enhancement pattern is found to some degree under all environmental conditions considered but is especially pronounced during periods of high vapor transport, high melting level height, southwest low‐level winds, and neutral stability. These conditions are generally associated with warm sectors of midlatitude cyclones and atmospheric rivers. Past studies have postulated that a secondary enhancement in reflectivity aloft was an intrinsic part of atmospheric river type systems. However, these results show that further significant enhancement of this signature occurs as deep moist‐neutral, high water vapor content flow is lifted when it encounters a mountain range. Reflectivity data from the dual‐precipitation radar aboard the Global Precipitation Measurement satellite also documents this reflectivity increase aloft over the Olympic Mountains compared to the adjacent ocean, showing the potential for Global Precipitation Measurement to provide reliable estimates of precipitation structure over remote mountainous regions.
Plain Language Summary
When frontal cyclones pass over a mountain range, modification of flow often results in precipitation enhancement on the windward slopes. Most studies of this phenomenon rely on the precipitation patterns deduced from surface networks of rain gauges or through numerical modeling. Little attention has been given to orographic modification of the precipitation processes occurring in the middle and upper layers of clouds. This paper uses high‐resolution vertical cross sections of radar reflectivity data taken during the Olympic Mountains Experiment. Measurements made over the ocean are compared to those over the windward slopes of the Olympic Mountains and a clear signature of enhancement aloft over the windward slopes is found at all heights from 2 to 8 km strongest between 4 and 6 km. This enhancement of reflectivity aloft is especially pronounced under environmental conditions of large water vapor transport, high melting level, strong onshore‐directed low‐level winds and neutral stability. Those environmental conditions are commonly found in warm sectors of midlatitude cyclones and in atmospheric river‐type events. This same signature of higher reflectivity aloft over windward slopes is found from satellite‐derived radar reflectivity measurements implying that satellites have the potential to provide reliable estimates of precipitation structure over remote mountainous regions.
Key Points
Enhancement of precipitation processes is found in radar reflectivity data above the melting level over complex terrain
Enhancement aloft is especially pronounced during periods of high vapor transport, onshore flow, and neutral low‐level static stability
Satellite‐borne radar detects this enhancement so that reliable estimates of precipitation over remote mountain regions are possible
We present the open-source software package DADA2 for modeling and correcting Illumina-sequenced amplicon errors (https://github.com/benjjneb/dada2). DADA2 infers sample sequences exactly and ...resolves differences of as little as 1 nucleotide. In several mock communities, DADA2 identified more real variants and output fewer spurious sequences than other methods. We applied DADA2 to vaginal samples from a cohort of pregnant women, revealing a diversity of previously undetected Lactobacillus crispatus variants.
Despite the critical role of the human microbiota in health, our understanding of microbiota compositional dynamics during and after pregnancy is incomplete. We conducted a case-control study of 49 ...pregnant women, 15 of whom delivered preterm. From 40 of thesewomen, we analyzed bacterial taxonomic composition of 3,767 specimens collected prospectively and weekly during gestation and monthly after delivery from the vagina, distal gut, saliva, and tooth/gum. Linear mixed-effects modeling, medoid-based clustering, and Markov chain modeling were used to analyze community temporal trends, community structure, and vaginal community state transitions. Microbiota community taxonomic composition and diversity remained remarkably stable at all four body sites during pregnancy (P> 0.05 for trends over time). Prevalence of aLactobacillus-poor vaginal community state type (CST 4) was inversely correlated with gestational age at delivery (P= 0.0039). Risk for preterm birth was more pronounced for subjects with CST 4 accompanied by elevatedGardnerellaorUreaplasmaabundances. This finding was validated with a set of 246 vaginal specimens from nine women (four of whom delivered preterm). Most women experienced a postdelivery disturbance in the vaginal community characterized by a decrease in Lactobacillus species and an increase in diverse anaerobes such asPeptoniphilus, Prevotella, andAnaerococcusspecies. This disturbance was unrelated to gestational age at delivery and persisted for up to 1 y. These findings have important implications for predicting premature labor, a major global health problem, and for understanding the potential impact of a persistent, altered postpartum microbiota on maternal health, including outcomes of pregnancies following short interpregnancy intervals.
High-throughput sequencing of PCR-amplified taxonomic markers (like the 16S rRNA gene) has enabled a new level of analysis of complex bacterial communities known as microbiomes. Many tools exist to ...quantify and compare abundance levels or microbial composition of communities in different conditions. The sequencing reads have to be denoised and assigned to the closest taxa from a reference database. Common approaches use a notion of 97% similarity and normalize the data by subsampling to equalize library sizes. In this paper, we show that statistical models allow more accurate abundance estimates. By providing a complete workflow in R, we enable the user to do sophisticated downstream statistical analyses, including both parameteric and nonparametric methods. We provide examples of using the
R packages dada2, phyloseq, DESeq2, ggplot2 and vegan to filter, visualize and test microbiome data. We also provide examples of supervised analyses using random forests, partial least squares and linear models as well as nonparametric testing using community networks and the ggnetwork package.
Hydrogen (H(2)) release from photosynthetic microbial mats has contributed to the chemical evolution of Earth and could potentially be a source of renewable H(2) in the future. However, the taxonomy ...of H(2)-producing microorganisms (hydrogenogens) in these mats has not been previously determined. With combined biogeochemical and molecular studies of microbial mats collected from Elkhorn Slough, Monterey Bay, California, we characterized the mechanisms of H(2) production and identified a dominant hydrogenogen. Net production of H(2) was observed within the upper photosynthetic layer (0-2 mm) of the mats under dark and anoxic conditions. Pyrosequencing of rRNA gene libraries generated from this layer demonstrated the presence of 64 phyla, with Bacteriodetes, Cyanobacteria and Proteobacteria dominating the sequences. Sequencing of rRNA transcripts obtained from this layer demonstrated that Cyanobacteria dominated rRNA transcript pyrotag libraries. An OTU affiliated to Microcoleus spp. was the most abundant OTU in both rRNA gene and transcript libraries. Depriving mats of sunlight resulted in an order of magnitude decrease in subsequent nighttime H(2) production, suggesting that newly fixed carbon is critical to H(2) production. Suppression of nitrogen (N(2))-fixation in the mats did not suppress H(2) production, which indicates that co-metabolic production of H(2) during N(2)-fixation is not an important contributor to H(2) production. Concomitant production of organic acids is consistent with fermentation of recently produced photosynthate as the dominant mode of H(2) production. Analysis of rRNA % transcript:% gene ratios and H(2)-evolving bidirectional NiFe hydrogenase % transcript:% gene ratios indicated that Microcoelus spp. are dominant hydrogenogens in the Elkhorn Slough mats.
High-throughput sequencing of PCR-amplified taxonomic markers (like the 16S rRNA gene) has enabled a new level of analysis of complex bacterial communities known as microbiomes. Many tools exist to ...quantify and compare abundance levels or OTU composition of communities in different conditions. The sequencing reads have to be denoised and assigned to the closest taxa from a reference database. Common approaches use a notion of 97% similarity and normalize the data by subsampling to equalize library sizes. In this paper, we show that statistical models allow more accurate abundance estimates. By providing a complete workflow in R, we enable the user to do sophisticated downstream statistical analyses, whether parametric or nonparametric. We provide examples of using the R packages dada2, phyloseq, DESeq2, ggplot2 and vegan to filter, visualize and test microbiome data. We also provide examples of supervised analyses using random forests and nonparametric testing using community networks and the ggnetwork package.
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