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1 1] FAS Center for Systems Biology, Harvard University, Cambridge, Massachusetts 02138, USA [2] Society of Fellows, Harvard University, Cambridge, Massachusetts 02138, USA [3] Molecular Genetics & Microbiology and Institute for Genome Sciences & Policy, Duke University, Durham, North Carolina 27708, USA.
2 FAS Center for Systems Biology, Harvard University, Cambridge, Massachusetts 02138, USA.
3 Division of Endocrinology, Children's Hospital Boston, Harvard Medical School, Boston, Massachusetts 02115, USA.
4 Department of Bioengineering & Therapeutic Sciences and the California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, California 94158, USA.
1 1] FAS Center for Systems Biology, Harvard University, Cambridge, Massachusetts 02138, USA [2] Society of Fellows, Harvard University, Cambridge, Massachusetts 02138, USA [3] Molecular Genetics & Microbiology and Institute for Genome Sciences & Policy, Duke University, Durham, North Carolina 27708, USA.
2 FAS Center for Systems Biology, Harvard University, Cambridge, Massachusetts 02138, USA.
3 Division of Endocrinology, Children's Hospital Boston, Harvard Medical School, Boston, Massachusetts 02115, USA.
4 Department of Bioengineering & Therapeutic Sciences and the California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, California 94158, USA.
Long-term dietary intake influences the structure and activity of the trillions of microorganisms residing in the human gut, but it remains unclear how rapidly and reproducibly the human gut microbiome responds to short-term macronutrient change. Here we show that the short-term consumption of diets composed entirely of animal or plant products alters microbial community structure and overwhelms inter-individual differences in microbial gene expression. The animal-based diet increased the abundance of bile-tolerant microorganisms (Alistipes, Bilophila and Bacteroides) and decreased the levels of Firmicutes that metabolize dietary plant polysaccharides (Roseburia, Eubacterium rectale and Ruminococcus bromii). Microbial activity mirrored differences between herbivorous and carnivorous mammals, reflecting trade-offs between carbohydrate and protein fermentation. Foodborne microbes from both diets transiently colonized the gut, including bacteria, fungi and even viruses. Finally, increases in the abundance and activity of Bilophila wadsworthia on the animal-based diet support a link between dietary fat, bile acids and the outgrowth of microorganisms capable of triggering inflammatory bowel disease. In concert, these results demonstrate that the gut microbiome can rapidly respond to altered diet, potentially facilitating the diversity of human dietary lifestyles.
Ten subjects were tracked across each diet arm. (A) Fiber
intake on the plant-based diet rose from a median baseline value of
9.3±2.1 to 25.6±1.1 g/1,000kcal (p=0.007; two-sided Wilcoxon
signed-rank test), but was negligible on the animal-based diet (p=0.005).
(B) Daily fat intake doubled on the animal-based diet from a
baseline of 32.5±2.2% to 69.5±0.4% kcal
(p=0.005), but dropped on the plant-based diet to 22.1±1.7%
(p=0.02). (C) Protein intake rose on the animal-based diet to
30.1±0.5% kcal from a baseline level of
16.2±1.3% (p=0.005) and decreased on the plant-based diet to
10.0±0.3% (p=0.005). (D) Within-sample species
diversity (α-diversity, Shannon’s Diversity Index), did not
significantly change during either diet. (E) The similarity of each
individual’s gut microbiota to their baseline communities
(β-diversity, Jensen-Shannon distance) decreased on the animal-based
diet (dates with q<0.05 identified with asterisks; Bonferroni-corrected,
two-sided Mann-Whitney U test). Community differences were apparent one day
after a tracing dye showed the animal-based diet reached the gut (blue arrows
depict appearance of food dyes added to first and last diet day meals; Extended Data Fig.
3a).
Fig. 2. Bacterial cluster responses to diet…
Fig. 2. Bacterial cluster responses to diet arms
Cluster log2 fold-changes on each diet arm…
Fig. 2. Bacterial cluster responses to diet arms
Cluster log2 fold-changes on each diet arm were computed relative to
baseline samples across all subjects and are drawn as circles. Clusters with
significant fold-changes on the animal-based diet are colored in red, and
clusters with significant fold-changes on both the plant- and animal-based diets
are colored in both red and green. Uncolored clusters exhibited no significant
fold-change on either the animal or plant-based diet (q
Fig. 3. Diet alters microbial activity and…
Fig. 3. Diet alters microbial activity and gene expression
Fecal concentrations of SCFAs from (…
Fig. 3. Diet alters microbial activity and gene expression
Fecal concentrations of SCFAs from (A) carbohydrate and
(B) amino acid fermentation (*p<0.05, two-sided
Mann-Whitney U test; n=9–11 fecal samples/diet arm; Supplementary Table 11).
The animal-based diet was associated with significant increases in gene
expression (normalized to reads per kilobase per million mapped, or RPKM;
n=13–21 datasets/diet arm) among (C) glutamine
amidotransferases (K08681, vitamin B6 metabolism), (D)
methyltransferases (K00599, polycyclic aromatic hydrocarbon degradation), and
(E) beta-lactamases (K01467). (F) Hierarchical
clustering of gut microbial gene expression profiles collected on the
animal-based (red) and plant-based (green) diets. Expression profile similarity
was significantly associated with diet (p<0.003; two-sided
Fisher’s exact test excluding replicate samples), despite
inter-individual variation that preceded the diet (Extended Data Figs.
6a,b). Enrichment on animal-based diet (red) and plant-based diet (green)
for expression of genes involved in (G) amino acid metabolism and
(H) central metabolism. Numbers indicate the mean fold-change
between the two diets for each KEGG orthologous group assigned to a given
enzymatic reaction (Supplementary Table 17). Enrichment patterns on the animal- and
plant-based diets agree perfectly with patterns observed in carnivorous and
herbivorous mammals, respectively2 (p<0.001,
Binomial test). Note: Pyr Cx is represented by two groups, which showed
divergent fold-changes. Asterisks in panels C-E and
G,H indicate p<0.05, Student’s
t test. Values in panels A-E are mean±sem.
Abbreviations: glutamate dehydrogenase (GDH), glutamate decarboxylase (Glu Dx),
succinate-semialdehyde dehydrogenase (SSADH), phosphoenolpyruvate carboxylase
(PEPCx), pyruvate carboxylase (Pyr Cx), phosphotransferase system (PTS), PEP
carboxykinase (PEPCk), oxaloacetate decarboxylase (ODx), pyruvate,
orthophosphate dikinase (PPDk).
Fig. 4. Foodborne microbes are detectable in…
Fig. 4. Foodborne microbes are detectable in the distal gut
(A) Common bacteria and fungi…
Fig. 4. Foodborne microbes are detectable in the distal gut
(A) Common bacteria and fungi associated with the
animal-based diet menu items, as measured by 16S rRNA and ITS gene sequencing,
respectively. Taxa are identified on the genus (g) and species (s) level. A full
list of foodborne fungi and bacteria on the animal-based diet can be found in
Supplementary Table
21. Foods on the plant-based diet were dominated by matches to the
Streptophyta, which derive from chloroplasts within plant matter (Extended Data Fig. 7a).
(B-E). Fecal RNA transcripts were significantly enriched
(q<0.1, Kruskal-Wallis test; n=6–10 samples/diet arm) for
several food-associated microbes on the animal-based diet relative to baseline
(BL) periods, including (B) Lactococcus lactis,
(C) Staphylococcus carnosus, (D)
Pediococcus acidilactici, and (E) a
Penicillium sp. A complete table of taxa with significant
expression differences can be found in Supplementary Table 22. (F) Fungal
concentrations in feces before and 1–2 days after the animal-based diet
were also measured using culture media selective for fungal growth (plate count
agar with milk, salt, and chloramphenicol). Post-diet fecal samples exhibit
significantly higher fungal concentrations than baseline samples
(p<0.02; two-sided Mann-Whitney U test; n=7–10 samples/diet
arm). (G) Increased RNA transcripts from the plant-derived Rubus chlorotic mottle virus transcripts increase on the plant-based diet (q<0.1, Kruskal-Wallis
test; n=6–10 samples/diet arm). Barplots (B-G) all display
mean±sem.
Fig. 5. Changes in the fecal concentration…
Fig. 5. Changes in the fecal concentration of bile acids and biomarkers for Bilophila on…
Fig. 5. Changes in the fecal concentration of bile acids and biomarkers for Bilophila on the animal-based diet
(A) Deoxycholic acid, a secondary bile acid known to
promote DNA damage and hepatic carcinomas, accumulates significantly on the animal-based diet
(p<0.01, two-sided Wilcoxon signed-rank test; see Supplementary Table 23
for the diet response of other secondary bile acids). (B) RNA-Seq
data also supports increased microbial metabolism of bile acids on the
animal-based diet, as we observe significantly increased expression of microbial
bile salt hydrolases (K01442) during that diet arm (q<0.05,
Kruskal-Wallis test; normalized to reads per kilobase per million mapped, or
RPKM; n=8–21 samples/diet arm). (C) Total fecal bile acid
concentrations also increase significantly on the animal-based diet, relative to
the preceding baseline period (p<0.05, two-sided Wilcoxon signed-rank
test), but do not change on the plant-based diet (Extended Data Fig. 9).
Bile acids have been shown to cause IBD in mice by stimulating the growth of the
bacterium Bilophila, which is known to reduce sulfite to hydrogen sulfide via
the sulfite reductase enzyme (dsrA; Extended Data Fig. 10). (D) Quantitative PCR
showed a significant increase in microbial DNA coding for dsrA on the
animal-based diet (p<0.05; two-sided Wilcoxon signed-rank test), and
(E) RNA-Seq identified a significant increase in sulfite
reductase expression (q<0.05, Kruskal-Wallis test; n=8–21
samples/diet arm). Barplots (B,E) display mean±sem.
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