Fig 1.
Summarized WSS scores from donor-recipient pairs.
The WSS scores were obtained comparing 1) the donor’s sample to paired recipient’s pre- and post-FMT samples; and 2) the recipient’s pre-FMT sample to the same recipient’s post-FMT samples for (A) donor 18–0031 and recipient 19–0013, and (B) donor 18–0006 and recipient 19–0002. All samples used for the analysis were listed in S1 Table. The summarized WSS scores per pair were grouped into different color boxes (see the figure key) or numerical numbers (when observed WSS score was below each species’ cutoff value; NS = No Score). The NS indicates the strains were unable to reliably determine relatedness due to any sample in pairs not satisfying the criteria of WSS analysis (minimum coverage > 30% and average depth > 3.5).
Fig 2.
Summarized WSS scores with the taxonomic profile for the donor 18–0014 and recipient 19–0024 FMT pair.
(A) The WSS scores were determined by comparing 1) the donor’s sample to paired recipient’s pre- and post-FMT samples; and 2) the recipient’s pre-FMT sample to the same recipient’s post-FMT samples for donor 18–0014 and recipient 19–0024. Detailed information for this pair of samples was shown in S1 Table. The summarized WSS result was grouped into different color boxes (see the figure key) or numerical numbers (when determined WSS score was below the cutoff value; NS = No Score). (B and C) Relative abundance was determined for Bacteroides uniformis and Bacteroides vulgatus for this pair using MetaPhlAn2 analysis.
Fig 3.
StrainPhlAn analysis for B. uniformis from FMT donor 18–0014 and recipient 19–0024 pair.
StrainPhlAn analysis on FMT pair donor 18–0014 and recipient 19–0024 was done for B. uniformis across all samples in this pair. A neighbor-joining (NJ) tree was built and the tree is drawn to scale with branch lengths. Then, the distances were calculated using the Maximum Composite Likelihood method and are in the units of the number of base substitutions per site using MEGA X. The blue and purple color boxes shown next to the NJ tree match the color boxes shown in Fig 2A and the orange color boxes indicate a recombinant strain which is shown as both numerical numbers in Fig 2A. A white asterisk indicates a donor and recipient pre FMT sample.
Fig 4.
StrainPhlAn analysis for B. vulgatus on donor 18–0014 and recipient 19–0024 pair.
StrainPhlAn analysis on FMT donor 18–0014 and recipient 19–0024 pair was done for B. vulgatus across all samples in this pair. A neighbor-joining (NJ) tree was constructed and the tree is drawn to scale with branch lengths. Then, the same steps described in the legend of Fig 3 were applied to complete constructing the tree using MEGA X. The blue and purple color boxes shown next to the NJ tree match the color boxes shown in Fig 2A and the orange color boxes show a recombinant strain which is displayed as both numerical numbers in Fig 2A. A white asterisk indicates a donor and recipient pre FMT sample.
Fig 5.
Summarized WSS scores with the taxonomic profile for the FMT donor 18-0002- recipient 18–0018 pair.
(A) The WSS scores were determined by comparing 1) the donor’s sample to paired recipient’s pre- and post-FMT samples; and 2) the recipient’s pre-FMT sample to the same recipient’s post-FMT samples for donor 18–0002 and recipient 18–0018. Sample information for this pair was shown in S1 Table. The resultant WSS scores were grouped into different color boxes (see the figure key) or numerical numbers (when the score was below the cutoff value; NS = No Score). (B and C) Relative abundance was obtained for B. uniformis and B. vulgatus for this pair using MetaPhlAn2 analysis. For B. vulgatus, relative abundance for the Recipient was 0.03% and day 21 was 0.05%. For B. uniformis, relative abundance for the day 42 was 0.02% and day 342 was 0.01%.
Fig 6.
StrainPhlAn analysis for B. uniformis FMT donor 18–0002 and recipient 18–0018 pair.
StrainPhlAn analysis on donor 18–0002 and recipient 18–0018 pair was done for B. uniformis across all samples in this pair. A neighbor-joining (NJ) tree was constructed, and the tree is drawn to scale with branch lengths. The same steps which written in the legend of Fig 3 were then applied to complete the tree using MEGA X. The blue and purple boxes displayed next to the NJ tree match the color boxes shown in Fig 5A and the orange color boxes shows a recombinant strain which displayed as both numerical numbers in Fig 5A. A white asterisk indicates a donor and recipient pre FMT sample.
Fig 7.
StrainPhlAn analysis for B. vulgatus FMT donor 18–0002 and recipient 18–0018 pair.
StrainPhlAn analysis on donor 18–0002 and recipient 18–0018 pair was done for Bacteroides vulgatus across all samples in this pair. A neighbor-joining (NJ) tree was constructed and the tree is drawn to scale with branch lengths. The same steps described in the legend of Fig 3 were then applied to complete the tree using MEGA X. The blue and purple boxes shown next to the NJ tree match the color boxes shown in Fig 5A, the yellow boxes depict a new strain and orange boxes indicate a recombinant strain both shown as numerical numbers in Fig 5A. The yellow boxes showed consistent WSS scores related to donor or recipient and the orange boxes showed either similar WSS scores observed between donor and recipient or a higher score found in the recipient than donor. A white asterisk indicates a donor pre FMT sample.
Fig 8.
WSS, BSAP-3 and StrainPhlAn analyses for the FMT donor 18–0005 and recipient 18–0007 pair.
(A) The WSS scores were obtained by comparing 1) the donor’s sample to paired recipient’s pre- and post-FMT samples; and 2) the recipient’s pre-FMT sample to the same recipient’s post-FMT samples for donor 18–0005 and recipient 18–0007. The purple box indicates that strain was related to the recipient’s pre-FMT. BLAST result from the BSAP-3 gene analysis was also shown in a table, indicating “+” = BSAP-3 positive and “-” = BSAP-3 negative. (B) StrainPhlAn analysis on donor 18–0005 and recipient 18–0007 pair was done for Bacteroides vulgatus across all samples in this pair. A neighbor-joining (NJ) tree was constructed and the tree is drawn to scale with branch lengths. The distances were calculated using the Maximum Composite Likelihood method and are in the units of the number of base substitutions per site using MEGA X. The blue and purple boxes shown next to the NJ tree match the color boxes shown in Fig 8A. A white asterisk indicates a donor and recipient pre FMT sample.