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As you can see in the table, two common conditions for which probiotics clearly trump FMT are irritable bowel syndrome (IBS) and SIBO

Removal or destruction of the stomach: Vitamin B 12 deficiency can develop in people who have had surgery to remove part or all of the stomach
Acerra NE, Souvlis T, Moseley GL (2007) Stroke, complex regional pain syndrome and phantom limb pain: can commonalities direct future management

Such cargos include proteins, siRNA, nanoparticles, oligonucleotides, and other peptides [242]
Sun J, Zhou C, Ma Q, Chen W, Atyah M, Yin Y, et al