Ultrastructural analysis of inclusions generated upon infection of Vero cells with isolate 10-1398/6 at 48h post infection.

<p>Two typical inclusions were observed, less (A) or more (B) mature.</p

Circular representation of the 10-1398/6 genome compared to <i>C. psittaci</i> 6BC and <i>C</i><i>. pecorum</i> E58 genomes.

<p>Outermost to innermost tracks represent: (i) % GC; (ii) all genes in 10-1398/6 (black); (iii) core genes shared by all three genomes, based on a BSR similarity >0.5 (grey); (iv) unique genes to 10-1398/6 based on a BSR similarity of <0.4 (red); (v) variable genes shared by 10-1398/6 and 6BC but absent from E58 (blue); (vi) variable genes shared by 10-1398/6 and E58 but absent from 6BC (green). Track iv (red) illustrates the presence of clusters of unique genes spanning the entire 10-1398/6 genome. The chlamydial plasticity zone is highlighted in grey.</p

Dendrogram based on the analysis of the nearly complete 16S rRNA gene sequences (about 1350 nt) from the Ibis isolates (10-1398/6 and 10-1398/11) and from the type strains of nine <i>Chlamydiaceae</i>.

<p>The dendrogram was constructed by UPGMA method from a similarity matrix calculated by pairwise alignment. Branch quality was calculated by cophenetic correlation. Horizontal distances correspond to genetic distances expressed in percentage of sequence similarity.</p

Phylogenetic tree of 31 conserved genes including corresponding sequences of <i>C</i><i>. caviae</i><i>, C. felis</i>, <i>C. psittaci, </i><i>C</i><i>. abortus</i><i>, </i><i>C</i><i>. pecorum</i><i>, C. pneumoniae, C. muridarum, C. trachomatis</i> and 10-1398/6 <i>C</i>. <i>ibidis</i> isolate.

<p>The 31 conserved housekeeping genes were concatenated, and Amphora alignments used to generate a maximum likelihood phylogeny using the PhyML implementation of the WAG model of amino acid substitution. 100 bootstrap replicates were generated.</p

Comparison of genome structure of <i>C</i><i>. ibidis</i> 10-1398/6 and all other members of the family <i>Chlamydiaceae</i>, specifically: A) <i>C</i><i>. abortus</i> S263, B) <i>C. felis</i> FEC56, C) <i>C</i><i>. pecorum</i> E58, D) <i>C. pneumoniae</i> AR39, E) <i>C. psittaci</i> 6BC, F) <i>C. trachomatis</i> D/UW-3/CX, G) <i>C</i><i>. caviae</i> GPIC and H) <i>C. muridarum</i> Nigg.

<p>Each dot represents a peptide sequence, with color coding corresponding to the degree of similarity based on BSR.</p

Comparison of the plasticity zones of <i>C. psittaci</i> and 10-1398/6 Ibis isolate, along with other representatives of the former genus <i>Chlamydophila</i>.

<p>Comparison of the plasticity zones of <i>C. psittaci</i> and 10-1398/6 Ibis isolate, along with other representatives of the former genus <i>Chlamydophila</i>.</p

The “Most Wanted” Taxa from the Human Microbiome for Whole Genome Sequencing

<div><p>The goal of the Human Microbiome Project (HMP) is to generate a comprehensive catalog of human-associated microorganisms including reference genomes representing the most common species. Toward this goal, the HMP has characterized the microbial communities at 18 body habitats in a cohort of over 200 healthy volunteers using 16S rRNA gene (16S) sequencing and has generated nearly 1,000 reference genomes from human-associated microorganisms. To determine how well current reference genome collections capture the diversity observed among the healthy microbiome and to guide isolation and future sequencing of microbiome members, we compared the HMP’s 16S data sets to several reference 16S collections to create a ‘most wanted’ list of taxa for sequencing. Our analysis revealed that the diversity of commonly occurring taxa within the HMP cohort microbiome is relatively modest, few novel taxa are represented by these OTUs and many common taxa among HMP volunteers recur across different populations of healthy humans. Taken together, these results suggest that it should be possible to perform whole-genome sequencing on a large fraction of the human microbiome, including the ‘most wanted’, and that these sequences should serve to support microbiome studies across multiple cohorts. Also, in stark contrast to other taxa, the ‘most wanted’ organisms are poorly represented among culture collections suggesting that novel culture- and single-cell-based methods will be required to isolate these organisms for sequencing.</p> </div

Body habitat distribution of non-chimeric and most wanted HMP OTUs.

<p>The distributions of 1,468 non-chimeric HMP OTUs (left panel) and 119 most wanted OTUs (right panel) are shown as phyla (outer circle) and genera (inner circle) at each of the 5 sampled body habitats. Distribution profiles were based on the habitat in which the HMP OTU was found most frequently. Bar graphs illustrate the relative proportion of HMP OTUs from each 16S variable region, shown as phyla. Color codes for all phyla and ‘most wanted’ genera with more than one representative are shown in left and right figure legends, respectively.</p

Rank Abundance curves for V1–V3 (black symbols) and V3–V5 (gray symbols) OTUs.

<p>(A) The number of sequences in each OTU. (B) Cumulative rank abundance. For both V1–V3 and V3–V5, on the order of 10–15 OTUs captured half of all individual sequences.</p

Nearly all sequenced taxa have been cultured but not all cultured taxa have been sequenced.

<p>For each taxa, the percent identity from the best match to a human sequenced database (GOLD-Human or HMP-strains) versus the best match to a sequence database of cultured organisms (named or unnamed). The colors in all panels indicate assignment to priority groups for whole genome sequencing: red = highest priority, blue = medium priority, gray = low priority. (A) OTUs that are present in at least 20% of all samples in at least one body habitat; (B) all HMP OTUs.</p