Journal: Microbiome

Article Title: Whole microbial community viability is not quantitatively reflected by propidium monoazide sequencing approach

doi: 10.1186/s40168-020-00961-3

Figure Lengend Snippet: PMA-seq identified viable microbes in simple synthetic communities. a Expected community structures of our ten live/dead Escherichia coli and Streptococcus sanguinis mixtures before and after PMA treatment: group (1) 100% live E. coli; 100% E. coli after PMA treatment; (2) 100% dead E. coli ; 0% E. coli after PMA treatment; (3) 100% live S. sanguinis ; 100% S. sanguinis after PMA treatment; (4) 100% dead S. sanguinis ; 0% S. sanguinis after PMA treatment; (5) 50% live E. coli and 50% live S. sanguinis ; same proportion after PMA treatment; (6) 50% dead E. coli and 50% dead S. sanguinis; no nucleotides after PMA-treatment; (7) 50% live E. coli , 25% live S. sanguinis and 25% dead S. sanguinis ; 67% E. coli and 33% S. sanguinis after PMA treatment; (8) 25% live E. coli and 25% dead E. coli ; 50% live S. sanguinis ; 67% S. sanguinis and 33% E. coli after PMA treatment; (9) 50% live E. coli , 50% dead S. sanguinis ; 100% E. coli after PMA treatment; 10) 50% dead E. coli and 50% live S. sanguinis ; 100% S. sanguinis after PMA treatment. b DNA quantity (ng) (top) and 16S rRNA gene copy numbers (bottom) of the 10 synthetic cultures with and without PMA treatment. Error bars represented the standard deviations. c Relative abundances of synthetic community members by PMA-seq before and after PMA treatment. Each experiment was carried out in quadruplex

Article Snippet: We constructed ten synthetic microbial communities (part 1) comprising viable or heat-killed E. coli strain ATCC 47076 and S. sanguinis strain ATCC 10556.

Techniques:

Journal: Microbiome

Article Title: Whole microbial community viability is not quantitatively reflected by propidium monoazide sequencing approach

doi: 10.1186/s40168-020-00961-3

Figure Lengend Snippet: PMA-treatment resulted in different degrees of compositional changes in different complex communities. Our second evaluation of PMA-seq used four environmental microbial community types (high and low biomass, high and low expected viability) spiked with varying levels of cultured / heat-killed E. coli . a Relative abundances of 15 taxa detected with the highest mean abundance across all samples. Each sample type contains four biological replicates. b Bray-Curtis distances within and between community samples with PMA treatment and samples without PMA treatment. Columns labeled with the sample type alone (e.g., screen) show dissimilarities within the indicated PMA-free samples. Those annotated “type(PMA)” (e.g., screen(PMA)) show calculations within the PMA-treated samples, and “type(between)” (e.g., screen(between) represents distances between paired samples with and without PMA treatment. c After constructing an ordination based on each sample pairwise Bray-Curtis dissimilarity, variation across the first explanatory axes is largely separated by human-associated uses, while the second axes appear to be explained by sample biomass. Here, lines connect identical samples with and without PMA treatment

Article Snippet: We constructed ten synthetic microbial communities (part 1) comprising viable or heat-killed E. coli strain ATCC 47076 and S. sanguinis strain ATCC 10556.

Techniques: Cell Culture, Labeling