Lesson 9 Plant Diet

Environmental Biotechnology

🌍 1. The Big Picture: Why This Study?

Crohn’s Disease (CD) = chronic gut inflammation 🔥 + microbial imbalance (dysbiosis) ⚖️. Medication helps, but many patients relapse — so scientists asked: 👉 Could a plant-based diet (PBD) calm inflammation and rebalance gut microbes?

The team also tested a clever new tool: 🧬 trnL gene sequencing, which detects plant DNA in poop! 💩 This lets them objectively check what plants people actually ate (instead of relying only on diaries).

🥦 2. Study Design: Who, What, How

14 Crohn’s patients (aged ~50)
12-week PBD program 🌱 (mostly plant foods; fish allowed twice a week)
Samples collected at week 0, week 4, and week 12
Monitored by:
- trnL sequencing → which plants they ate
- 16S rRNA sequencing → which bacteria were in the gut
- Calprotectin test → how inflamed the gut was

💡 All participants used their own baseline as control.

🔬 3. How the Science Was Done

DNA extraction & sequencing via Oxford Nanopore MinION
Target genes:
- 🧫 16S rRNA → bacteria
- 🌿 trnL (chloroplast) → plants
- 🐄 cytochrome b → meat traces (cow/pig)
Bioinformatics in R (using 'ampvis2', 'MaAsLin2', 'ggplot2') to track changes in microbial diversity and link them to inflammation markers.

🍎 4. Key Findings

🌱 Plant Diversity Went Up

trnL detected 55 plant genera, while diaries listed only 41 → trnL = more accurate 🎯
Median plant genera rose from 24 → 35 by week 4 (p = 0.032).
Herbs like oregano & basil appeared in DNA but not diaries — showing hidden intake.
Meat DNA dropped sharply, proving participants stuck to the plan. ✅

🦠 Gut Microbiota Got Healthier

Microbial diversity increased (p ≈ 0.089 = strong trend).
The “good guys” flourished:
- Faecalibacterium, Bacteroides, Blautia, Subdoligranulum, Akkermansia muciniphila 🦠⬆️
- All linked to short-chain fatty acid (SCFA) production → fuels gut cells + lowers inflammation.
Some unexpected decreases:
- Eubacterium rectale & Dialister invisus ⬇️ (both also SCFA producers) → needs more study.

💬 Patients’ gut communities became more similar — the PBD “harmonized” them.

🧩 Starting Diet Matters

Those who ate few plants before the trial showed bigger improvements in microbiota diversity than plant-heavy eaters. 👉 The bigger the change, the bigger the benefit.

💊 Inflammation Dropped

Calprotectin (inflammation marker) fell from 472 → 207 mg/kg 📉
Some bacterial groups correlated with inflammation levels:
- Ruminococcus faecis & Lachnospiraceae sp. → higher calprotectin (worse)
- Oscillospiraceae UCG-005 → lower calprotectin (better)

🧠 5. Discussion – What It All Means

PBDs may restore microbial diversity and lower gut inflammation in CD.
trnL sequencing is a powerful tool for diet tracking in clinical research — far more reliable than self-reports.
The small sample size limited statistical power, but trends were strong. → Future trials should include ~40 patients for 80% power.

🌈 6. Conclusion

A plant-based diet:

✅ boosts beneficial gut microbes
✅ reduces inflammation
✅ is safe and feasible for Crohn’s patients
🔬 and trnL sequencing offers a modern way to monitor real-world diet adherence

💡 Take-home message:Eat the rainbow — your microbiome will thank you! 🌽🥕🥦🥭

Quiz

Score: 0/31 (0%)

Q0. What was the main goal of Østergaard et al. (2024)?

To test new drug therapy for Crohn’s disease

To study how a plant-based diet affects gut microbiota and inflammation in Crohn’s disease patients

To compare different probiotic supplements

To evaluate surgical outcomes in Crohn’s disease

Q1. Which gene was used to monitor plant residue diversity in fecal samples?

16S rRNA

trnL

cytochrome b

ITS

Q2. How many patients completed the 12-week intervention?

Q3. What sequencing platform was used for DNA analysis?

Illumina MiSeq

PacBio Sequel

Oxford Nanopore MinION

Ion Torrent

Q4. Which bacterial gene was targeted to analyze the microbiota composition?

18S rRNA

23S rRNA

16S rRNA

ITS region

Q5. What was used as a marker of intestinal inflammation?

C-reactive protein

Fecal calprotectin

Lactoferrin

TNF-α levels

Q6. What was the average fecal calprotectin at baseline?

207 mg/kg

350 mg/kg

472 mg/kg

600 mg/kg

Q7. What was the average fecal calprotectin after 12 weeks?

102 mg/kg

207 mg/kg

330 mg/kg

550 mg/kg

Q8. What was the observed fold increase in plant genera detected after 4 weeks?

1.2-fold

1.4-fold

2-fold

3-fold

Q9. Which bacterial genera increased in abundance after the diet?

Faecalibacterium and Bacteroides

Clostridium and Salmonella

Escherichia and Campylobacter

Staphylococcus and Enterococcus

Q10. Which sequencing marker was used to detect meat consumption?

trnL

16S rRNA

cytochrome b

COI gene

Q11. Which class contained most of the bacterial genera showing large changes?

Gammaproteobacteria

Clostridia

Actinobacteria

Bacteroidia

Q12. Which statistical test was used to compare groups?

t-test and ANOVA

Wilcoxon and Kruskal-Wallis

Chi-square and Fisher’s exact

Mann–Whitney U only

Q13. Which R packages were used for microbiome visualization and statistics?

phyloseq and vegan

ampvis2 and ggplot2

QIIME2 and Pandas

MEGAN and Excel

Q14. What happened to patients who initially ate few plant types?

They showed greater microbial diversity increase

They showed no change

They lost microbial diversity

They dropped out

Q15. The trnL sequencing detected more plant genera than self-reported diaries.

True

False

Q16. Fecal calprotectin is produced by intestinal bacteria.

True

False

Q17. A 1.4-fold increase means the new value is 1.4 times the old one.

True

False

Q18. All patients were on biological treatment during the intervention.

True

False

Q19. The study design included a separate control group of healthy individuals.

True

False

Q20. Plant genera richness continued increasing throughout all 12 weeks.

True

False

Q21. Porcine and bovine DNA signals were used to check for meat consumption violations.

True

False

Q22. Akkermansia muciniphila decreased after the plant-based diet.

True

False

Q23. The trnL method can quantify exact amounts of each plant eaten.

True

False

Q24. Reduced microbial diversity is a hallmark of Crohn’s disease.

True

False

Q25. The alpha diversity increase was statistically significant (p < 0.05).

True

False

Q26. Fecal samples were collected at weeks 0, 4, and 12.

True

False

Q27. The study was approved by The North Denmark Region Committee on Health Research Ethics.

True

False

Q28. trnL sequencing could detect coffee and cocoa consumption accurately.

True

False

Q29. The authors estimated that future studies should recruit about 40 participants for adequate power.

True

False

Q30. The study concluded that a plant-based diet can positively influence the gut microbiome and reduce inflammation in Crohn’s patients.

True

False