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Description

Probiotics are widely prescribed for prevention of antibiotics-associated dysbiosis and related adverse effects. However, probiotic impact on post-antibiotic reconstitution of the gut mucosal host-microbiome niche remains elusive. We invasively examined the effects of multi-strain probiotics or autologous fecal microbiome transplantation (aFMT) on post-antibiotic reconstitution of the murine and human mucosal microbiome niche. Contrary to homeostasis, antibiotic perturbation enhanced probiotics colonization in the human mucosa but only mildly improved colonization in mice. Compared to spontaneous post-antibiotic recovery, probiotics induced a markedly delayed and persistently incomplete indigenous stool/mucosal microbiome reconstitution and host transcriptome recovery toward homeostatic configuration, while aFMT induced a rapid and near-complete recovery within days of administration. In vitro, Lactobacillus-secreted soluble factors contributed to probiotics-induced microbiome inhibition. Collectively, potential post-antibiotic probiotic benefits may be offset by a compromised gut mucosal recovery, highlighting a need of developing aFMT or personalized probiotic approaches achieving mucosal protection without compromising microbiome recolonization in the antibiotics-perturbed host.

Summary

Project accession BioProject accession Keywords PMID #Samples
ERP110263 PRJEB28097 Colon Cecum Duodenum Ileum Jejunum Stomach Feces C57BL/6 Harlan Envigo Laboratory 30193113 140

Alpha diversity

Samples

Sample accession Project accession Sampling location Genotype Vendor Origin
ERS2715761 ERP110263 Colon C57BL/6 Harlan Envigo Laboratory
ERS2715768 ERP110263 Colon C57BL/6 Harlan Envigo Laboratory
ERS2715779 ERP110263 Colon C57BL/6 Harlan Envigo Laboratory
ERS2715790 ERP110263 Colon C57BL/6 Harlan Envigo Laboratory
ERS2715801 ERP110263 Colon C57BL/6 Harlan Envigo Laboratory
ERS2715812 ERP110263 Colon C57BL/6 Harlan Envigo Laboratory
ERS2715823 ERP110263 Colon C57BL/6 Harlan Envigo Laboratory
ERS2715825 ERP110263 Colon C57BL/6 Harlan Envigo Laboratory
ERS2715826 ERP110263 Colon C57BL/6 Harlan Envigo Laboratory
ERS2715827 ERP110263 Colon C57BL/6 Harlan Envigo Laboratory
ERS2715828 ERP110263 Colon C57BL/6 Harlan Envigo Laboratory
ERS2715835 ERP110263 Colon C57BL/6 Harlan Envigo Laboratory
ERS2715846 ERP110263 Colon C57BL/6 Harlan Envigo Laboratory
ERS2715857 ERP110263 Colon C57BL/6 Harlan Envigo Laboratory
ERS2715868 ERP110263 Colon C57BL/6 Harlan Envigo Laboratory
ERS2715879 ERP110263 Colon C57BL/6 Harlan Envigo Laboratory
ERS2715890 ERP110263 Colon C57BL/6 Harlan Envigo Laboratory
ERS2715892 ERP110263 Colon C57BL/6 Harlan Envigo Laboratory
ERS2715893 ERP110263 Colon C57BL/6 Harlan Envigo Laboratory
ERS2715894 ERP110263 Colon C57BL/6 Harlan Envigo Laboratory
ERS2715895 ERP110263 Cecum C57BL/6 Harlan Envigo Laboratory
ERS2715902 ERP110263 Cecum C57BL/6 Harlan Envigo Laboratory
ERS2715913 ERP110263 Cecum C57BL/6 Harlan Envigo Laboratory
ERS2715924 ERP110263 Cecum C57BL/6 Harlan Envigo Laboratory
ERS2715935 ERP110263 Cecum C57BL/6 Harlan Envigo Laboratory
ERS2715946 ERP110263 Cecum C57BL/6 Harlan Envigo Laboratory
ERS2715957 ERP110263 Cecum C57BL/6 Harlan Envigo Laboratory
ERS2715959 ERP110263 Cecum C57BL/6 Harlan Envigo Laboratory
ERS2715960 ERP110263 Cecum C57BL/6 Harlan Envigo Laboratory
ERS2715961 ERP110263 Cecum C57BL/6 Harlan Envigo Laboratory
ERS2715962 ERP110263 Cecum C57BL/6 Harlan Envigo Laboratory
ERS2715969 ERP110263 Cecum C57BL/6 Harlan Envigo Laboratory
ERS2715980 ERP110263 Cecum C57BL/6 Harlan Envigo Laboratory
ERS2715991 ERP110263 Cecum C57BL/6 Harlan Envigo Laboratory
ERS2716002 ERP110263 Cecum C57BL/6 Harlan Envigo Laboratory
ERS2716013 ERP110263 Cecum C57BL/6 Harlan Envigo Laboratory
ERS2716024 ERP110263 Cecum C57BL/6 Harlan Envigo Laboratory
ERS2716026 ERP110263 Cecum C57BL/6 Harlan Envigo Laboratory
ERS2716027 ERP110263 Cecum C57BL/6 Harlan Envigo Laboratory
ERS2716028 ERP110263 Cecum C57BL/6 Harlan Envigo Laboratory
ERS2716079 ERP110263 Duodenum C57BL/6 Harlan Envigo Laboratory
ERS2716086 ERP110263 Duodenum C57BL/6 Harlan Envigo Laboratory
ERS2716097 ERP110263 Duodenum C57BL/6 Harlan Envigo Laboratory
ERS2716108 ERP110263 Duodenum C57BL/6 Harlan Envigo Laboratory
ERS2716119 ERP110263 Duodenum C57BL/6 Harlan Envigo Laboratory
ERS2716130 ERP110263 Duodenum C57BL/6 Harlan Envigo Laboratory
ERS2716141 ERP110263 Duodenum C57BL/6 Harlan Envigo Laboratory
ERS2716143 ERP110263 Duodenum C57BL/6 Harlan Envigo Laboratory
ERS2716144 ERP110263 Duodenum C57BL/6 Harlan Envigo Laboratory
ERS2716145 ERP110263 Duodenum C57BL/6 Harlan Envigo Laboratory
ERS2716146 ERP110263 Duodenum C57BL/6 Harlan Envigo Laboratory
ERS2716164 ERP110263 Duodenum C57BL/6 Harlan Envigo Laboratory
ERS2716175 ERP110263 Duodenum C57BL/6 Harlan Envigo Laboratory
ERS2716186 ERP110263 Duodenum C57BL/6 Harlan Envigo Laboratory
ERS2716197 ERP110263 Duodenum C57BL/6 Harlan Envigo Laboratory
ERS2716208 ERP110263 Duodenum C57BL/6 Harlan Envigo Laboratory
ERS2716213 ERP110263 Ileum C57BL/6 Harlan Envigo Laboratory
ERS2716220 ERP110263 Ileum C57BL/6 Harlan Envigo Laboratory
ERS2716231 ERP110263 Ileum C57BL/6 Harlan Envigo Laboratory
ERS2716242 ERP110263 Ileum C57BL/6 Harlan Envigo Laboratory
ERS2716253 ERP110263 Ileum C57BL/6 Harlan Envigo Laboratory
ERS2716264 ERP110263 Ileum C57BL/6 Harlan Envigo Laboratory
ERS2716275 ERP110263 Ileum C57BL/6 Harlan Envigo Laboratory
ERS2716277 ERP110263 Ileum C57BL/6 Harlan Envigo Laboratory
ERS2716278 ERP110263 Ileum C57BL/6 Harlan Envigo Laboratory
ERS2716279 ERP110263 Ileum C57BL/6 Harlan Envigo Laboratory
ERS2716280 ERP110263 Ileum C57BL/6 Harlan Envigo Laboratory
ERS2716287 ERP110263 Ileum C57BL/6 Harlan Envigo Laboratory
ERS2716298 ERP110263 Ileum C57BL/6 Harlan Envigo Laboratory
ERS2716309 ERP110263 Ileum C57BL/6 Harlan Envigo Laboratory
ERS2716320 ERP110263 Ileum C57BL/6 Harlan Envigo Laboratory
ERS2716331 ERP110263 Ileum C57BL/6 Harlan Envigo Laboratory
ERS2716342 ERP110263 Ileum C57BL/6 Harlan Envigo Laboratory
ERS2716344 ERP110263 Ileum C57BL/6 Harlan Envigo Laboratory
ERS2716345 ERP110263 Ileum C57BL/6 Harlan Envigo Laboratory
ERS2716346 ERP110263 Ileum C57BL/6 Harlan Envigo Laboratory
ERS2716354 ERP110263 Jejunum C57BL/6 Harlan Envigo Laboratory
ERS2716365 ERP110263 Jejunum C57BL/6 Harlan Envigo Laboratory
ERS2716376 ERP110263 Jejunum C57BL/6 Harlan Envigo Laboratory
ERS2716387 ERP110263 Jejunum C57BL/6 Harlan Envigo Laboratory
ERS2716398 ERP110263 Jejunum C57BL/6 Harlan Envigo Laboratory
ERS2716409 ERP110263 Jejunum C57BL/6 Harlan Envigo Laboratory
ERS2716411 ERP110263 Jejunum C57BL/6 Harlan Envigo Laboratory
ERS2716412 ERP110263 Jejunum C57BL/6 Harlan Envigo Laboratory
ERS2716413 ERP110263 Jejunum C57BL/6 Harlan Envigo Laboratory
ERS2716421 ERP110263 Jejunum C57BL/6 Harlan Envigo Laboratory
ERS2716432 ERP110263 Jejunum C57BL/6 Harlan Envigo Laboratory
ERS2716443 ERP110263 Jejunum C57BL/6 Harlan Envigo Laboratory
ERS2716476 ERP110263 Jejunum C57BL/6 Harlan Envigo Laboratory
ERS2716478 ERP110263 Jejunum C57BL/6 Harlan Envigo Laboratory
ERS2716479 ERP110263 Jejunum C57BL/6 Harlan Envigo Laboratory
ERS2716480 ERP110263 Jejunum C57BL/6 Harlan Envigo Laboratory
ERS2716481 ERP110263 Jejunum C57BL/6 Harlan Envigo Laboratory
ERS2716488 ERP110263 Jejunum C57BL/6 Harlan Envigo Laboratory
ERS2716499 ERP110263 Jejunum C57BL/6 Harlan Envigo Laboratory
ERS2716510 ERP110263 Jejunum C57BL/6 Harlan Envigo Laboratory
ERS2716521 ERP110263 Jejunum C57BL/6 Harlan Envigo Laboratory
ERS2716532 ERP110263 Jejunum C57BL/6 Harlan Envigo Laboratory
ERS2716543 ERP110263 Jejunum C57BL/6 Harlan Envigo Laboratory
ERS2716545 ERP110263 Jejunum C57BL/6 Harlan Envigo Laboratory
ERS2716547 ERP110263 Jejunum C57BL/6 Harlan Envigo Laboratory
ERS2716548 ERP110263 Jejunum C57BL/6 Harlan Envigo Laboratory
ERS2716555 ERP110263 Jejunum C57BL/6 Harlan Envigo Laboratory
ERS2716566 ERP110263 Jejunum C57BL/6 Harlan Envigo Laboratory
ERS2716577 ERP110263 Jejunum C57BL/6 Harlan Envigo Laboratory
ERS2716588 ERP110263 Jejunum C57BL/6 Harlan Envigo Laboratory
ERS2716610 ERP110263 Jejunum C57BL/6 Harlan Envigo Laboratory
ERS2716612 ERP110263 Jejunum C57BL/6 Harlan Envigo Laboratory
ERS2716613 ERP110263 Jejunum C57BL/6 Harlan Envigo Laboratory
ERS2716614 ERP110263 Jejunum C57BL/6 Harlan Envigo Laboratory
ERS2716615 ERP110263 Stomach C57BL/6 Harlan Envigo Laboratory
ERS2716622 ERP110263 Stomach C57BL/6 Harlan Envigo Laboratory
ERS2716633 ERP110263 Stomach C57BL/6 Harlan Envigo Laboratory
ERS2716644 ERP110263 Stomach C57BL/6 Harlan Envigo Laboratory
ERS2716655 ERP110263 Stomach C57BL/6 Harlan Envigo Laboratory
ERS2716666 ERP110263 Stomach C57BL/6 Harlan Envigo Laboratory
ERS2716677 ERP110263 Stomach C57BL/6 Harlan Envigo Laboratory
ERS2716679 ERP110263 Stomach C57BL/6 Harlan Envigo Laboratory
ERS2716680 ERP110263 Stomach C57BL/6 Harlan Envigo Laboratory
ERS2716681 ERP110263 Stomach C57BL/6 Harlan Envigo Laboratory
ERS2716682 ERP110263 Stomach C57BL/6 Harlan Envigo Laboratory
ERS2716689 ERP110263 Stomach C57BL/6 Harlan Envigo Laboratory
ERS2716700 ERP110263 Stomach C57BL/6 Harlan Envigo Laboratory
ERS2716711 ERP110263 Stomach C57BL/6 Harlan Envigo Laboratory
ERS2716722 ERP110263 Stomach C57BL/6 Harlan Envigo Laboratory
ERS2716733 ERP110263 Stomach C57BL/6 Harlan Envigo Laboratory
ERS2716744 ERP110263 Stomach C57BL/6 Harlan Envigo Laboratory
ERS2716746 ERP110263 Stomach C57BL/6 Harlan Envigo Laboratory
ERS2716747 ERP110263 Stomach C57BL/6 Harlan Envigo Laboratory
ERS2716748 ERP110263 Stomach C57BL/6 Harlan Envigo Laboratory
ERS2716837 ERP110263 Feces C57BL/6 Harlan Envigo Laboratory
ERS2716838 ERP110263 Feces C57BL/6 Harlan Envigo Laboratory
ERS2716839 ERP110263 Feces C57BL/6 Harlan Envigo Laboratory
ERS2716840 ERP110263 Feces C57BL/6 Harlan Envigo Laboratory
ERS2716841 ERP110263 Feces C57BL/6 Harlan Envigo Laboratory
ERS2716842 ERP110263 Feces C57BL/6 Harlan Envigo Laboratory
ERS2716843 ERP110263 Feces C57BL/6 Harlan Envigo Laboratory
ERS2716844 ERP110263 Feces C57BL/6 Harlan Envigo Laboratory
ERS2716845 ERP110263 Feces C57BL/6 Harlan Envigo Laboratory
ERS2716846 ERP110263 Feces C57BL/6 Harlan Envigo Laboratory