The human microbiome in Barrett’s esophagus is hard to stomach

The incidence of esophageal adenocarcinoma (EAC) has increased nearly five-fold over the last four decades in the United States. Barrett's esophagus, the replacement of the normal squamous epithelial lining with a mucus-secreting columnar epithelium, is the only known precursor to EAC. Like other parts of the gastrointestinal (GI) tract, the esophagus hosts a variety of bacteria and comparisons among published studies suggest bacterial communities in the stomach and esophagus differ. Chronic infection with Helicobacter pylori in the stomach has been inversely associated with development of EAC, but the mechanisms underlying this association remain unclear.The bacterial composition in the upper GI tract was characterized in a subset of participants (n=12) of the Seattle Barrett's Esophagus Research cohort using broad-range 16S PCR and pyrosequencing of biopsy and brush samples collected from squamous esophagus, Barrett's esophagus, stomach corpus and stomach antrum. Three of the individuals were sampled at two separate time points. Prevalence of H. pylori infection and subsequent development of aneuploidy (n=339) and EAC (n=433) was examined in a larger subset of this cohort.Within individuals, bacterial communities of the stomach and esophagus showed overlapping community membership. Despite closer proximity, the stomach antrum and corpus communities were less similar than the antrum and esophageal samples. Re-sampling of study participants revealed similar upper GI community membership in two of three cases. In this Barrett's esophagus cohort, Streptococcus and Prevotella species dominate the upper GI and the ratio of these two species is associated with waist-to-hip ratio and hiatal hernia length, two known EAC risk factors in Barrett's esophagus. H. pylori-positive individuals had a significantly decreased incidence of aneuploidy and a non-significant trend toward lower incidence of EAC

Data from: Effective online Bayesian phylogenetics via sequential Monte Carlo with guided proposals

Modern infectious disease outbreak surveillance produces continuous streams of sequence data which require phylogenetic analysis as data arrives. Current software packages for Bayesian phylogenetic inference are unable to quickly incorporate new sequences as they become available, making them less useful for dynamically unfolding evolutionary stories. This limitation can be addressed by applying a class of Bayesian statistical inference algorithms called sequential Monte Carlo (SMC) to conduct online inference, wherein new data can be continuously incorporated to update the estimate of the posterior probability distribution. In this paper we describe and evaluate several different online phylogenetic sequential Monte Carlo (OPSMC) algorithms. We show that proposing new phylogenies with a density similar to the Bayesian prior suffers from poor performance, and we develop guided proposals that better match the proposal density to the posterior. Furthermore, we show that the simplest guided proposals can exhibit pathological behavior in some situations, leading to poor results, and that the situation can be resolved by heating the proposal density. The results demonstrate that relative to the widely-used MCMC-based algorithm implemented in MrBayes, the total time required to compute a series of phylogenetic posteriors as sequences arrive can be significantly reduced by the use of OPSMC, without incurring a significant loss in accuracy

Members of the <i>Firmicutes</i> or <i>Bacteroidetes</i> phyla dominate the upper gastrointestinal tract microbiome.

<p>(A) Phylogenetic relationship of the top 45 OTUs recovered from each of the four sites sampled in individual participants. Respective phyla are noted above main branches of the phylogenetic tree. Numbers in parentheses represent total number of pyrosequencing reads recovered for a given species or genera across all samples followed by the fraction of participants in whom a relative abundance of ≥1.3% of a given species or genera were detected. (B) Species/genera-level profiles of top 45 OTUs detected by 454 sequencing in squamous esophagus, Barrett’s esophagus, stomach corpus and stomach antrum of indicated participants. Data arranged in order of increasing <i>Firmicutes</i> dominance. Individual species/genera are color-coded according to scheme presented in (A). Sequencing reads from brush samples were used when available, otherwise, data from biopsy samples are shown. Species reads were normalized to the total number of reads per corresponding site in a given individual. ^†Denotes samples collected at a second time point (P2 [t = 4 months]; P7 [t = 2 years]; P9 [t = 3 years]); <i>Hp+</i> indicates <i>H</i>. <i>pylori</i>-positive individual. Italicized participant IDs denote data from biopsy samples in cases where brush samples were not available for analysis.</p

Brush sampling of the upper gastrointestinal tract enriches for bacterial abundance and diversity.

<p>(A) Diagram of the human upper gastrointestinal tract indicating regions sampled via biopsy or brush collection method. Anatomic sites were abbreviated with the first and second letter indicating the sampled organ and intra-organ tissue, respectively (ES—squamous esophagus; EB—Barrett’s esophagus; SC—stomach corpus; SA—stomach antrum). (B) Total bacterial versus human DNA recovered from biopsy or brush samples segregated by anatomical site as measured by qPCR and plotted as copy number of bacterial 16S rRNA gene and human 18S rRNA gene. Error bars indicate standard deviation from the mean. (C) Ratio of human 18S rRNA to bacterial 16S rRNA copy number in all biopsy (n = 26) or brush (n = 35) samples. Error bars indicate standard deviation from the mean. (D) Species diversity in biopsy and brush samples as measured by quadratic entropy analysis. The central line within each box represents the median of the data, the whiskers represent the 5^th and 95^th percentiles and data outside that range are plotted as individual points. Statistical difference between biopsy and brush samples was measured by Wilcoxon rank sum test with continuity correction (p = 0.000594).</p

<i>Streptococcus</i> to <i>Prevotella</i> species ratio corresponds to phylogenetic distance sample clustering and correlates with Barrett’s esophagus risk factors.

<p>(A) Cluster analysis of KR distances between microbial communities of individual study samples. Pyroseq. <i>Strep</i>:<i>Prev</i> ratio was calculated using relative abundance of mapped reads for all <i>Streptococcus</i> and <i>Prevotella</i> species as determined by pyrosequencing. ddPCR <i>Strep</i>:<i>Prev</i> ratio was calculated using copies/μl of a <i>Streptococcus</i> or <i>Prevotella</i>-specific 16s rRNA gene segment as determined by droplet digital PCR. Samples color-coded based on the majority of calculated Pyroseq. <i>Strep</i>:<i>Prev</i> ratios in a group being <0.5 (blue), 0.5–1.5 (green), 1.5–4.0 (magenta) or >4.0 (red). (B) Boxplots comparing <i>Streptococcus</i> to <i>Prevotella</i> ratio as determined by pyrosequencing and ddPCR. The central line within each box represents the median of the data, the whiskers represent the 5^th and 95^th percentiles and data outside that range are plotted as individual points. (C) Relationship of <i>Streptococcus</i> to <i>Prevotella</i> ratio (measured by ddPCR) and waist-hip ratio of all male participants segregated by anatomic site. Strength of association between these two variables was determined by Pearson’s correlation test with correlation coefficient squared (r²) values as indicated. (D) Relationship of <i>Streptococcus</i> to <i>Prevotella</i> ratios (measured by ddPCR) and hiatal hernia length in all participants segregated by anatomic site. Strength of association tween these two variables was determined by Pearson’s correlation test with correlation coefficient squared (r²) values as indicated.</p

Participant Demographics.

<p>^a LG = low grade HG = high grade</p><p>^b Denotes samples collected at a second time point (P2 [t = 2 years]; P7 [t = 4 months]; P9 [t = 3 years])</p><p>^c Denotes <i>H</i>. <i>pylori</i>-positive participant</p><p>Participant Demographics.</p

Upper gastrointestinal microbiome similarity with replicate sampling.

<p>(A–C) Species/genera-level profiles of microbiota detected by 454 sequencing in squamous esophagus, Barrett’s esophagus, stomach corpus and stomach antrum of individuals P7 at the time of first [t = 0] and second sample collection [t = 4 months] (A), P2 at t = 0 and t = 2 years (B) and P9 at t = 0 and t = 3 years (C). Individual species/genera are presented according to coloring scheme described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0129055#pone.0129055.g002" target="_blank">Fig 2</a> (D) Phylogenetic KR distance between (inter) samples from participants P2, P7 and P9 at both time points and within those individuals comparing the 1^st and 2^nd time points from the indicated anatomic site. The central line within each box represents the median and the whiskers represent the minimum and maximum values.</p