We are sorry, but NCBI web applications do not support your browser and may not function properly. More information

Results: 5

1.
Figure 5

Figure 5. Schematic depiction of oral community membership among ten healthy individuals. From: Bacterial diversity in the oral cavity of ten healthy individuals.

Inner circle, bacterial genera found in all 10 individuals (100%); second circle, present in 6 to 9 out of 10 individuals (51–99%); third circle, present in 3 to 5 individuals (21–50%); outer circle, present in 1 to 2 individuals (1–20%). Genera are grouped per phylum.

Elisabeth M. Bik, et al. ISME J. ;4(8):962-974.
2.
Figure 4

Figure 4. Checkerboard (C−) scores for each possible combination of two genera. From: Bacterial diversity in the oral cavity of ten healthy individuals.

The C-scores are shown in gray scale. White depicts a C-score of 0 for genera always found together. Darker colors show higher C-scores for genera that co-occur less frequently than expected. The highest C-score in this dataset, 16, was found for the Abiotrophia-Treponema genus pair, two fairly abundant genera never found together. Genera are ordered according to their overall abundance in the 10 individual mouth pools. The numbers after the genus names indicate the number of individuals (out of 10) in which that genus was found. The 16 taxa that were found in all 10 individuals, as expected, all show a C-score of 0 (white). Data from the subgingival pool were not included in this analysis.

Elisabeth M. Bik, et al. ISME J. ;4(8):962-974.
3.
Figure 1

Figure 1. Relative abundance of phylum members of the oral communities from 10 healthy individuals. From: Bacterial diversity in the oral cavity of ten healthy individuals.

A total of 11 368 bacterial rRNA gene sequences derived from pools of specimens from different oral habitats, from each of 10 healthy individuals (numbered 1 to 10), as well as from a pool of all subgingival samples (S), was analyzed and assigned to phyla (color-coded, according to the scheme at the right). “Total” refers to the combined set of sequences from all pools. The number of clones in each rRNA gene library is given below the name of the pool.

Elisabeth M. Bik, et al. ISME J. ;4(8):962-974.
4.
Figure 2

Figure 2. Phylogenetic relationships and relative abundance of the genera found in pools of oral specimens. From: Bacterial diversity in the oral cavity of ten healthy individuals.

A. Phylogenetic tree for the 247 OTUs found in this study, grouped by genus. A 95% sequence similarity threshold was used for unclassified groups. The tree was constructed by neighbor-joining analysis with an Olsen correction. Bootstrap values >=50 (expressed as percentages of 1000 replicates) are shown at branch points. The scale bar represents evolutionary distance (10 substitutions per 100 nucleotides). B. Relative abundance of genera in each of the 11 oral specimens pools displayed with gray scale values (white, 0% present; black, 100% of clone library; exact scale shown at the bottom). 1–10, each of the individual subject pools; S, subgingival, T, total. Genera are shown in the same order as in A.

Elisabeth M. Bik, et al. ISME J. ;4(8):962-974.
5.
Figure 3

Figure 3. Variation in patterns of diversity. From: Bacterial diversity in the oral cavity of ten healthy individuals.

Unifrac Principal Components Analysis (PCA) was performed using weighted, normalized abundance data (Lozupone 2006). A. Analysis of oral specimen pools from each of 10 healthy subjects (white circles, females, n=5; grey circles, males, n=5), and 1 pool of the subgingival specimens from all of these 10 subjects (black circle). B. Analysis of the oral specimen pool data from this study (white circles, n=11), data from additional oral specimen pools extracted with a different DNA extraction method (grey circles, n=3, unpublished data), and previously-published data from human colon samples (grey squares, n=18, Eckburg et al. 2005) and human stool samples (grey triangles, n=3, Eckburg et al. 2005; black triangles, n=15, Dethlefsen et al. 2008). All sequences were compared using the same alignment and 1253-nucleotide filter.

Elisabeth M. Bik, et al. ISME J. ;4(8):962-974.

Supplemental Content

Recent activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...
Write to the Help Desk