Association between microbial diversity changes and outcomes of cellular therapy
| Therapy . | Sampling sites∗ . | Technology and pipeline∗ . | Findings . | Reference . |
|---|---|---|---|---|
| Human | ||||
| Auto-HCT | US | 16S UPARSE | Increased α-diversity in perineutrophil engraftment fecal samples is associated with increased OS and PFS | 16 |
| US | 16S QIIME2 and DADA2 | Increased α-diversity in perineutrophil engraftment fecal samples is correlated with CR/VGPR vs PR | 21 | |
| US | 16S QIIME | Increased α-diversity in posttransplant samples is correlated with less severe diarrhea; increased diversity is associated with the development of neutropenic fever. | 26 | |
| US | 16S DADA2 | Increased oral microbial α-diversity is correlated with higher salivary and serum melphalan levels | 28 | |
| Allo-HCT | US | 16S Mothur | Low baseline fecal α-diversity is associated with pulmonary complications | 27 |
| France | 16S QIIME | Decreased α-diversity in pretreatment fecal samples is associated with subsequent bacteremia | 22 | |
| Italy and Poland† | 16S QIIME2 | Increased α-diversity in pretreatment fecal samples is associated with increased OS and lower grades of aGVHD | 18 | |
| US | 16S DADA2 | Increased α-diversity in periengraftment samples is associated with MAIT and Vδ2 T-cell frequency at day 30 in patients who received unmodified PBMC grafts | 29 | |
| US, Germany, and Japan | 16S vsearch, usearch, and QIIME | Increased α-diversity in periengraftment fecal samples is associated with increased OS and a lower transplantation-related mortality rate | 19 | |
| US | 16S DADA2 | Increased α-diversity in periengraftment fecal samples is associated with increased OS, decreased nonrelapse mortality, and better CD4 and CD8 T-cell recovery | 17 | |
| US | 16S DADA2 | Increased α-diversity in perineutrophil recovery fecal samples is associated with lower grades of aGVHD | 24 | |
| US | Shotgun metagenomics QIIME2 and vegan.R | Patients who developed cGVHD showed a change of β-diversity and a greater loss of α-diversity from baseline to after engraftment | 25 | |
| US | 16S Mothur | Increased α-diversity in postengraftment fecal samples is associated with increased OS and a lower transplantation-related mortality rate | 20 | |
| Auto-HCT/allo-HCT | China | 16S QIIME and UPARSE | Increased α-diversity in posttransplant samples is associated with decreased bacteremia | 23 |
| CAR T cell | China | 16S QIIME2 | α-Diversity is decreased in fecal samples from PR patients compared with fecal samples from CR patients at the CRS peak time point. β-Diversity is different between PR and CR samples at the same time point. | 30 |
| Mouse | ||||
| Syngeneic BMT | US | 16S Mothur | Authors defined intestinal microbiota score = Shannon index × fecal bacterial abundance. Higher intestinal microbiota score is associated with higher weight of periovarian fat, bone marrow, and thymic cellularity after transplantation. | 31 |
| Allo-HCT | US | 16S Mothur | Higher α-diversity in posttransplant samples is associated with better survival and lower GVHD score | 32 |
| US | 16S | Orally gavaging B fragilis increases posttransplant α-diversity in the ileum, and ameliorates GVHD | 33 | |
| US | 16S QIIME2 and DADA2 | High vitamin A diet is associated with decreased α-diversity in posttransplant fecal samples and more severe lung GVHD | 34 | |
| Australia | Metagenomics QIIME | Wild-type mice cohoused continuously with IL-17RA–deficient mice display decreased α-diversity and accelerated GVHD | 35 | |
| CAR T cell | US | 16S QIIME2 | Oral vancomycin treatment decreased the α-diversity of fecal samples from mice with human FMT. CAR T-cell therapy in combination with vancomycin slowed down tumor progression. | 36 |
| Therapy . | Sampling sites∗ . | Technology and pipeline∗ . | Findings . | Reference . |
|---|---|---|---|---|
| Human | ||||
| Auto-HCT | US | 16S UPARSE | Increased α-diversity in perineutrophil engraftment fecal samples is associated with increased OS and PFS | 16 |
| US | 16S QIIME2 and DADA2 | Increased α-diversity in perineutrophil engraftment fecal samples is correlated with CR/VGPR vs PR | 21 | |
| US | 16S QIIME | Increased α-diversity in posttransplant samples is correlated with less severe diarrhea; increased diversity is associated with the development of neutropenic fever. | 26 | |
| US | 16S DADA2 | Increased oral microbial α-diversity is correlated with higher salivary and serum melphalan levels | 28 | |
| Allo-HCT | US | 16S Mothur | Low baseline fecal α-diversity is associated with pulmonary complications | 27 |
| France | 16S QIIME | Decreased α-diversity in pretreatment fecal samples is associated with subsequent bacteremia | 22 | |
| Italy and Poland† | 16S QIIME2 | Increased α-diversity in pretreatment fecal samples is associated with increased OS and lower grades of aGVHD | 18 | |
| US | 16S DADA2 | Increased α-diversity in periengraftment samples is associated with MAIT and Vδ2 T-cell frequency at day 30 in patients who received unmodified PBMC grafts | 29 | |
| US, Germany, and Japan | 16S vsearch, usearch, and QIIME | Increased α-diversity in periengraftment fecal samples is associated with increased OS and a lower transplantation-related mortality rate | 19 | |
| US | 16S DADA2 | Increased α-diversity in periengraftment fecal samples is associated with increased OS, decreased nonrelapse mortality, and better CD4 and CD8 T-cell recovery | 17 | |
| US | 16S DADA2 | Increased α-diversity in perineutrophil recovery fecal samples is associated with lower grades of aGVHD | 24 | |
| US | Shotgun metagenomics QIIME2 and vegan.R | Patients who developed cGVHD showed a change of β-diversity and a greater loss of α-diversity from baseline to after engraftment | 25 | |
| US | 16S Mothur | Increased α-diversity in postengraftment fecal samples is associated with increased OS and a lower transplantation-related mortality rate | 20 | |
| Auto-HCT/allo-HCT | China | 16S QIIME and UPARSE | Increased α-diversity in posttransplant samples is associated with decreased bacteremia | 23 |
| CAR T cell | China | 16S QIIME2 | α-Diversity is decreased in fecal samples from PR patients compared with fecal samples from CR patients at the CRS peak time point. β-Diversity is different between PR and CR samples at the same time point. | 30 |
| Mouse | ||||
| Syngeneic BMT | US | 16S Mothur | Authors defined intestinal microbiota score = Shannon index × fecal bacterial abundance. Higher intestinal microbiota score is associated with higher weight of periovarian fat, bone marrow, and thymic cellularity after transplantation. | 31 |
| Allo-HCT | US | 16S Mothur | Higher α-diversity in posttransplant samples is associated with better survival and lower GVHD score | 32 |
| US | 16S | Orally gavaging B fragilis increases posttransplant α-diversity in the ileum, and ameliorates GVHD | 33 | |
| US | 16S QIIME2 and DADA2 | High vitamin A diet is associated with decreased α-diversity in posttransplant fecal samples and more severe lung GVHD | 34 | |
| Australia | Metagenomics QIIME | Wild-type mice cohoused continuously with IL-17RA–deficient mice display decreased α-diversity and accelerated GVHD | 35 | |
| CAR T cell | US | 16S QIIME2 | Oral vancomycin treatment decreased the α-diversity of fecal samples from mice with human FMT. CAR T-cell therapy in combination with vancomycin slowed down tumor progression. | 36 |
BMT, bone marrow transplantation; cGVHD, chronic GVHD; CRS, cytokine release syndrome; IL-17RA, interleukin 17 receptor A; PBMC, peripheral blood mononuclear cell; PR, partial response; US, United States; VGPR, very good partial response.
Conclusions may vary based on the sampling site and methodology.
All human studies were performed in adult cohorts except this one in a pediatric cohort.