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IMF-095-03-0001-en	Why should an altered community found in disease not be called a cause on that basis alone?	Dysbiosis has no universal taxonomic definition, and illness, diet, drugs, transit and inflammation all change microbiota, so the change may be consequence rather than cause.	Integrated Medical Foundations; chapter 95, TTS module 3; https://theisegoria.github.io/medical-textbook/integrated-medical-foundations-expanded-english.md; module SHA256 at export: a6a5dbdc92da42ad99ba251e1848622501066c14977506c2cbbbbdd21da8433c; editorial review pending	imf lang::en chapter::095 module::095-03 review::pending
IMF-095-03-0002-en	What does a stool sample fail to represent, despite being the usual specimen?	Stool is shed luminal material and does not directly represent mucosa, small intestine, proximal colon or biofilm, and it varies with collection, storage, oxygen, extraction and transit.	Integrated Medical Foundations; chapter 95, TTS module 3; https://theisegoria.github.io/medical-textbook/integrated-medical-foundations-expanded-english.md; module SHA256 at export: a6a5dbdc92da42ad99ba251e1848622501066c14977506c2cbbbbdd21da8433c; editorial review pending	imf lang::en chapter::095 module::095-03 review::pending
IMF-095-03-0003-en	How can a taxon appear to increase when its absolute count has not changed?	Sequencing reports relative abundance, so the decline of another taxon raises the proportion occupied by an unchanged population.	Integrated Medical Foundations; chapter 95, TTS module 3; https://theisegoria.github.io/medical-textbook/integrated-medical-foundations-expanded-english.md; module SHA256 at export: a6a5dbdc92da42ad99ba251e1848622501066c14977506c2cbbbbdd21da8433c; editorial review pending	imf lang::en chapter::095 module::095-03 review::pending
IMF-095-03-0004-en	What can shotgun metagenomics resolve that sixteen-S sequencing cannot, and what can neither show?	Shotgun sequencing resolves more genes and strains than marker-region amplification, but neither proves gene expression and shotgun also detects dead organisms.	Integrated Medical Foundations; chapter 95, TTS module 3; https://theisegoria.github.io/medical-textbook/integrated-medical-foundations-expanded-english.md; module SHA256 at export: a6a5dbdc92da42ad99ba251e1848622501066c14977506c2cbbbbdd21da8433c; editorial review pending	imf lang::en chapter::095 module::095-03 review::pending
IMF-095-03-0005-en	Why does culture remain valuable alongside sequencing?	Culture proves viability and permits phenotype testing, which sequence data cannot provide, although many organisms need specialised conditions or community interactions.	Integrated Medical Foundations; chapter 95, TTS module 3; https://theisegoria.github.io/medical-textbook/integrated-medical-foundations-expanded-english.md; module SHA256 at export: a6a5dbdc92da42ad99ba251e1848622501066c14977506c2cbbbbdd21da8433c; editorial review pending	imf lang::en chapter::095 module::095-03 review::pending
IMF-095-03-0006-en	Why does a low stool butyrate concentration not establish low butyrate production?	Stool concentration reflects production minus host and microbial uptake, so heavy colonocyte consumption can leave little butyrate in stool despite active fermentation.	Integrated Medical Foundations; chapter 95, TTS module 3; https://theisegoria.github.io/medical-textbook/integrated-medical-foundations-expanded-english.md; module SHA256 at export: a6a5dbdc92da42ad99ba251e1848622501066c14977506c2cbbbbdd21da8433c; editorial review pending	imf lang::en chapter::095 module::095-03 review::pending
IMF-095-03-0007-en	How do antibiotics change bile-acid biology in a way that favours Clostridioides difficile?	They reduce microbial deconjugation and conversion to secondary bile acids, and the altered bile-acid environment changes germination and growth of Clostridioides difficile.	Integrated Medical Foundations; chapter 95, TTS module 3; https://theisegoria.github.io/medical-textbook/integrated-medical-foundations-expanded-english.md; module SHA256 at export: a6a5dbdc92da42ad99ba251e1848622501066c14977506c2cbbbbdd21da8433c; editorial review pending	imf lang::en chapter::095 module::095-03 review::pending
IMF-095-03-0008-en	Why is the association between trimethylamine N-oxide and cardiovascular outcomes hard to read causally?	Diet supplies the choline and carnitine precursors and kidney clearance determines the concentration, so both confound the association and therapeutic causality is still under study.	Integrated Medical Foundations; chapter 95, TTS module 3; https://theisegoria.github.io/medical-textbook/integrated-medical-foundations-expanded-english.md; module SHA256 at export: a6a5dbdc92da42ad99ba251e1848622501066c14977506c2cbbbbdd21da8433c; editorial review pending	imf lang::en chapter::095 module::095-03 review::pending
IMF-095-03-0009-en	Why are facultative organisms that expand during inflammation best seen as markers and amplifiers?	Inflammation raises oxygen and alternative electron acceptors and releases nutrients, so these organisms exploit conditions the host created, then worsen barrier and inflammation through feedback.	Integrated Medical Foundations; chapter 95, TTS module 3; https://theisegoria.github.io/medical-textbook/integrated-medical-foundations-expanded-english.md; module SHA256 at export: a6a5dbdc92da42ad99ba251e1848622501066c14977506c2cbbbbdd21da8433c; editorial review pending	imf lang::en chapter::095 module::095-03 review::pending
IMF-095-03-0010-en	Why does testing formed stool for Clostridioides difficile promote overdiagnosis?	Detection of a toxigenic organism without compatible diarrhoea may represent colonisation rather than infection, so testing patients without the syndrome mislabels carriers.	Integrated Medical Foundations; chapter 95, TTS module 3; https://theisegoria.github.io/medical-textbook/integrated-medical-foundations-expanded-english.md; module SHA256 at export: a6a5dbdc92da42ad99ba251e1848622501066c14977506c2cbbbbdd21da8433c; editorial review pending	imf lang::en chapter::095 module::095-03 review::pending
IMF-095-03-0011-en	Why does the success of faecal microbiota transplantation in recurrent Clostridioides difficile infection not justify its use across dysbiosis-associated disease?	That indication has a clear ecological mechanism of restoring community function, while donor screening cannot eliminate unknown risks and other conditions lack comparable evidence.	Integrated Medical Foundations; chapter 95, TTS module 3; https://theisegoria.github.io/medical-textbook/integrated-medical-foundations-expanded-english.md; module SHA256 at export: a6a5dbdc92da42ad99ba251e1848622501066c14977506c2cbbbbdd21da8433c; editorial review pending	imf lang::en chapter::095 module::095-03 review::pending
IMF-095-03-0012-en	Why can evidence for one probiotic strain not be transferred to another product?	Effects are strain, dose, formulation, outcome and host specific, and many commercial organisms act only transiently without durable colonisation.	Integrated Medical Foundations; chapter 95, TTS module 3; https://theisegoria.github.io/medical-textbook/integrated-medical-foundations-expanded-english.md; module SHA256 at export: a6a5dbdc92da42ad99ba251e1848622501066c14977506c2cbbbbdd21da8433c; editorial review pending	imf lang::en chapter::095 module::095-03 review::pending
IMF-095-03-0013-en	Why does a randomised dietary or antibiotic intervention still leave attribution to the microbiota uncertain?	These interventions have direct host effects as well as microbial ones, so an improved outcome need not have travelled through the proposed microbial mediator.	Integrated Medical Foundations; chapter 95, TTS module 3; https://theisegoria.github.io/medical-textbook/integrated-medical-foundations-expanded-english.md; module SHA256 at export: a6a5dbdc92da42ad99ba251e1848622501066c14977506c2cbbbbdd21da8433c; editorial review pending	imf lang::en chapter::095 module::095-03 review::pending
IMF-095-03-0014-en	Why are Koch's postulates difficult to apply to polymicrobial ecological disease?	No single organism may be necessary or sufficient, so causal reasoning shifts to temporality, dose, manipulation, mechanism and reversibility, and a community function can be causal across differing taxonomic configurations.	Integrated Medical Foundations; chapter 95, TTS module 3; https://theisegoria.github.io/medical-textbook/integrated-medical-foundations-expanded-english.md; module SHA256 at export: a6a5dbdc92da42ad99ba251e1848622501066c14977506c2cbbbbdd21da8433c; editorial review pending	imf lang::en chapter::095 module::095-03 review::pending