Chapter 27 — Self-Check Quiz

20 questions. Answers with explanations at the end. Aim for 16+.

Questions

1. The ratio of microbial cells to human cells is now estimated at approximately:

• a) 10 to 1
• b) Roughly 1 to 1
• c) 100 to 1
• d) 1 to 10

2. Which does 16S rRNA sequencing not provide?

• a) Genus-level identification
• b) Gene content and functional potential
• c) Relative abundances
• d) A cheap survey of the community

3. Neither sequencing method tells you:

• a) What the community is doing, whether findings are causal, what the mucosal community looks like, or what it will look like next week
• b) Which organisms are present
• c) Anything at all
• d) The sample's DNA content

4. Two labs analysing the same stool sample can disagree because of:

• a) Fraud
• b) Extraction method, 16S region, reference database, pipeline, handling, and an unpublished comparison population
• c) Random chance only
• d) They never disagree

5. Consumer microbiome tests receive ❌ mainly because:

• a) The sequencing doesn't work
• b) There is no validated reference range, platforms disagree, recommendations come from associations rather than trials, and no regulatory framework applies
• c) They are too expensive
• d) They are illegal

6. Butyrate is significant because it:

• a) Is absorbed into the bloodstream and used by muscle
• b) Is the primary energy source for colonocytes — the cells lining your colon are fed by your bacteria
• c) Causes inflammation
• d) Is produced from protein

7. According to §27.4b, the single most powerful modifier of your microbiome is:

• a) Probiotic supplements
• b) Antibiotics
• c) Exercise
• d) A short-term diet change

8. Which is ranked LAST in §27.4b?

• a) Long-term dietary pattern
• b) Probiotic supplements
• c) Early-life factors
• d) Medications

9. Human milk oligosaccharides are notable because they are:

• a) Digested by the infant for energy
• b) Indigestible by the infant and exist to feed bifidobacteria — a prebiotic evolved for the purpose
• c) Added to formula only
• d) A recent discovery with no function

10. Microbial diversity as an individual target is:

• a) The primary goal of gut health
• b) A useful population-level correlate and a poor individual target — some healthy states are low-diversity and some disease states are high-diversity
• c) Meaningless
• d) Precisely measurable

11. The single most important fact about probiotic evidence is that effects are:

• a) Universal across all products
• b) Strain-specific — evidence for one strain does not transfer to another strain of the same species
• c) Dose-independent
• d) Permanent after one course

12. Two large 2018 NEJM trials found that L. rhamnosus GG in children with acute gastroenteritis:

• a) Substantially shortened illness
• b) Provided no benefit
• c) Was harmful
• d) Was never tested

13. After a course of antibiotics, the studies described in §27.7 found that microbiome recovery was fastest with:

• a) Probiotic supplementation
• b) Autologous faecal transplant — the person's own pre-antibiotic stool
• c) Spontaneous recovery
• d) No difference between groups

14. In the fermented food trial (Wastyk et al., Cell, 2021):

• a) The high-fibre arm increased diversity and the fermented arm did not
• b) The fermented food arm increased diversity and decreased inflammatory markers; the high-fibre arm did not increase diversity over ten weeks
• c) Neither arm changed anything
• d) Both arms performed identically

15. Which contains live microbes as eaten?

• a) Sourdough bread
• b) Kefir
• c) Shop pickles in vinegar
• d) Filtered beer

16. FMT works spectacularly for recurrent C. difficile because:

• a) It replaces all gut bacteria permanently
• b) That disease IS destroyed colonization resistance — restoring the community restores the resistance
• c) It contains antibiotics
• d) It works equally well for all conditions

17. DIY faecal transplant is:

• a) Safe if a family member donates
• b) Genuinely dangerous — it can transmit infections including drug-resistant organisms, hepatitis and HIV
• c) Recommended for IBS
• d) Regulated in all countries

18. The low-FODMAP diet has three phases. The common failure is:

• a) Skipping restriction
• b) Doing phase 1 — restriction — indefinitely and never reintroducing
• c) Reintroducing too fast
• d) Not restricting enough

19. Staying in the restriction phase long-term risks:

• a) Nothing
• b) Reduced fibre, reduced microbial diversity, nutritional inadequacy, social restriction and disordered eating
• c) Only boredom
• d) Excess weight gain

20. Exclusive enteral nutrition is established as:

• a) A weight-loss method
• b) An effective induction therapy for paediatric Crohn's disease, comparable to corticosteroids
• c) A treatment for IBS
• d) A probiotic delivery system

Answers

1. b) Roughly 1 to 1. ⚠️ The 10:1 figure came from an estimate that propagated for decades without being checked, and was revised in 2016. Chapter 15's eight-glasses problem in a different field. §27.1.

2. b) Gene content and functional potential. 16S reads one conserved gene as a barcode — cheap, usually genus-level, and it tells you who is present, not what they can do. §27.2.

3. a) All four. ⚠️ The image to keep: sequencing gives you a photograph of who was in the room, taken at the door, on one day. Not what they were doing, why, whether it mattered, or who was in the other rooms. §27.2.

4. b) Methodological choices at every step. ⚠️ None of it is fraud — every step is a defensible choice, which is why serious studies standardize the whole pipeline. What you cannot do is take a number from one pipeline and read it as a fact about a person. The measurement is relative; the report presents it as absolute. §27.3b.

5. b) No reference range, platform disagreement, associations not trials, no regulatory framework. ⚠️ And the specific harm isn't the £179: Theo was told to reduce oats, apples and onions — the three foods most likely to have helped. §27.3.

6. b) The primary energy source for colonocytes. ⚠️ Your gut lining is fed by your bacteria. Which is why fermentable fibre — the substrate — keeps reappearing in every chapter since Chapter 11. §27.4.

7. b) Antibiotics. ⚠️ Large, fast, and can persist for months to years. Which makes "don't take antibiotics you don't need" simultaneously a resistance message and the most effective microbiome advice available. §27.4b.

8. b) Probiotic supplements. ⚠️ Small, transient, strain-specific and frequently resisted. Read rows 1 and 9 together: the most powerful thing that will ever happen to your microbiome is a course of antibiotics, and the thing sold to you as microbiome care is at the bottom. ⚠️ And row 5 — PPIs, metformin and many other drugs — means a substantial fraction of people who buy a test are measuring their prescription. §27.4b.

9. b) Indigestible by the infant; they feed bifidobacteria. ⚠️ Breast milk contains a large quantity of complex carbohydrate the baby cannot digest at all. It is not there for the infant — it is there for the infant's bacteria. About as direct as biology gets that this relationship isn't incidental. §27.4c.

10. b) A population correlate and a poor individual target. ⚠️ The breastfed infant gut is low-diversity by design; SIBO is diversity in the wrong place; and two communities with identical diversity can do completely different things. "Increase your diversity" has no defined endpoint — Chapter 20 §20.13's structural problem. §27.5.

11. b) Strain-specific. ⚠️ A trial showing benefit for L. reuteri DSM 17938 says nothing about a supermarket drink containing a different Lactobacillus. This is almost never on the packaging, and it is the single most important fact in §27.6.

12. b) No benefit. ⚠️ A clean example of larger trials deflating an accepted finding — Chapter 2 §2.8's pattern, and the correct response is to update. §27.6.

13. b) Autologous faecal transplant. ⚠️ Spontaneous recovery was intermediate and the PROBIOTIC group was SLOWEST. "Take a probiotic after antibiotics to restore your gut" is the most common gut-health advice given, and the best mechanistic evidence suggests it may do the opposite. (⚠️ Small mechanistic studies, held at moderate confidence — Chapter 19 §19.5's structure again.) §27.7.

14. b) Fermented increased diversity and decreased inflammatory markers; fibre did not increase diversity in ten weeks. ⚠️ Three qualifications: this does NOT mean fibre doesn't matter — Chapter 11's evidence is about hard outcomes over decades, and ten weeks is plausibly too short for the fibre arm's community to adapt. "Fermented" is not one category. And watch the sodium in kimchi and sauerkraut. §27.9.

15. b) Kefir. ⚠️ Bread is baked, beer is filtered and pasteurized, and shop pickles in vinegar were never fermented at all — "pickled" and "fermented" are not synonyms. Kefir typically contains a more diverse population than yoghurt. §27.9.

16. b) That disease IS destroyed colonization resistance. ⚠️ The pattern generalizes: FMT works where the problem IS the missing community. Where the microbiome is one contributor among many, replacing it does much less — which should calibrate expectations for every microbiome therapy, including ones not yet invented. §27.10.

17. b) Genuinely dangerous. ⚠️ In 2019 the FDA reported serious infections including a death from transmission of a drug-resistant organism from inadequately screened donor material. Donor screening exists for this reason, and there is no safe way to do this at home. §27.10.

18. b) Doing restriction indefinitely. ⚠️ It happens constantly, because phase 1 works — so there is no symptomatic reason to progress — and because phases 2 and 3 need guidance many people never get. Low-FODMAP is a diagnostic process, not a diet: its purpose is to find your triggers so you can eat everything else. §27.11.

19. b) All of those. ⚠️ Chapter 26 §26.11b's pattern exactly — a motivated, symptomatic person handed a restriction by someone who meant well, and the restriction becomes the harm. §27.11.

20. b) Induction therapy for paediatric Crohn's disease. ⚠️ Comparable to corticosteroids for inducing remission, without the steroid side effects — and most people find this surprising. Note also: diet does not cause IBD and diet does not cure it. §27.12.

Scoring

Three items worth checking regardless of score.

Question 11. ⚠️ If strain specificity didn't land, every probiotic on a shelf will look like evidence.

Question 18. ⚠️ The most clinically useful item here, and the one most often got wrong in practice.

Question 7 and 8 together. ⚠️ The ranking inverts the marketing, and it is the single most useful reordering in the chapter.