Gut Microbiota from Twins Discordant for Obesity Modulate Metabolism in Mice
2013 · paper · Biomedicine
Transplants gut microbiota from human twin pairs discordant for obesity into germ-free mice, including cultured collections, and examines effects on body composition and metabolism. It also uses cohousing of mice to see which bacterial taxa invade others' gut communities and how diet affects this.
Checked: PDF from scienceintheclassroom.org, fetched 4 Oct 2026. Page numbers are those of that PDF.
9 findings
Substance Fig. 1D legend: "n = 3 to 12 animals per donor microbiota; 51 to 52 mice per BMI bin; total of 103 mice" — with four donors per BMI bin (Fig. 1A), a maximum of 12 animals per donor gives at most 48 per bin, below the stated 51 to 52.
- p. 4 Fig. 1 legend, panel D
n = 3 to 12 animals per donor microbiota; 51 to 52 mice per BMI bin; total of 103 mice
- p. 3 Reproducibility of Microbiota Transplants, first paragraph
n = 3 to 4 mice per donor microbiota sample per experiment; n = 1 to 5 independent experiments per microbiota
Only the authors can say what is right here.
Judge's note: Read the Fig. 1 legend and Fig. 1A on the page 4 image: four twin pairs, so four lean and four obese donors. 4 x 12 = 48 < 51 and 8 x 12 = 96 < 103. The page 3 text gives 3 to 4 mice per donor per experiment and 1 to 5 experiments per microbiota (up to 20 per donor), so the 103 total is feasible, but the per-donor upper bound of 12 cannot be reconciled with the per-bin counts. No statement in the article explains it. Which figure is wrong is for the authors to say.
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Reference or label Colour keys in Fig. 3A and Fig. 4C are labelled "Absolute Spearman's correlation coefficient rho" but the scale runs from −0.5 to 0.5.
- p. 7 Fig. 3A colour key
Absolute Spearman’s correlation coefficient rho
- p. 8 Fig. 4C colour key
Absolute Spearman’s correlation coefficient rho
Judge's note: Both keys viewed (Fig. 3A in the crop and on page 7; Fig. 4C on page 8): ticks at −0.5, 0 and 0.5, and the text on page 9 reads the maps as positive and negative correlations. A signed scale is not an absolute value, so the label does not match what is plotted; the plotted data are not in question.
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Reference or label The LoSF-HiFV diet's fat content is given on an energy basis as "(LoSF-HiFV, ~33% kcal of fat per 100 g)" (p.10 text) but on a weight basis as "(33% fat by weight)" in the Fig. 6 panel title and "LoSF-HiFV diet (33% fat by weight)" on p.11.
- p. 10 Diet-Specific Effects, first paragraph
LoSF-HiFV, ~33% kcal of fat per 100 g
- p. 11 Diet-Specific Effects, second paragraph of page
LoSF-HiFV diet (33% fat by weight)
- p. 10 Fig. 6 panel title
(33% fat by weight)
- p. 10 Diet-Specific Effects, first paragraph
(LoSF-HiFV, ~33% kcal of fat per 100 g)
Only the authors can say what is right here.
Judge's note: Read on the p.10 and p.11 page images: the p.10 text has '~33% kcal of fat per 100 g', the Fig. 6 title has '(33% fat by weight)', and p.11 has 'LoSF-HiFV diet (33% fat by weight)'. The same number carries two different unit bases (share of energy versus share of weight). The other diets are also given by weight (4% for LF-HPP chow, 44% for HiSF-LoFV). Table S13, which would say which basis is right, is not among the files, so only the authors can settle it.
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Wording Text says fecal samples were collected "1, 2, 3, 5, 6, 7, 8, 10, and 15 days after gavage", but Fig. 2E has a 12 dpc column and the invader criterion uses samples "7 and 10 days after initiation of cohousing" (12 and 15 dpc, as cohousing began at 5 dpc).
- p. 5 Cohousing section, methods sentence
1, 2, 3, 5, 6, 7, 8, 10, and 15 days after gavage
- p. 6 Fig. 2E column headers (dpc)
10 12 15
- p. 5 Definition of successful invader
when sampled 7 and 10 days after initiation of cohousing
- p. 6 Fig. 2 legend, panel B
Changes from the first day after cohousing to 10 days after cohousing
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Judge's note: On the page 6 image the Fig. 2E dpc header reads 1 2 3 5 6 7 8 10 12 15 for the Lnch and Obch blocks and 6 7 8 10 12 15 for GFch; the text layer also carries '12'. The page 5 list has no day 12, yet the criterion on the same page needs a sample 7 days after cohousing (5 + 7 = 12 dpc). The text list appears incomplete. Secondary point from the same cluster: the Fig. 2B legend baseline "the first day after cohousing" does not match the stated QMR days (1 and 5 days after gavage, and after 10 days of cohousing); this is loose wording, probably meaning the first day of cohousing.
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Wording Fig. 5 legend: "Average fold-change (fc) in relative abundance of taxa before and after colonization was defined as in the legend to Fig. 2E" — the comparison is before and after cohousing.
- p. 9 Fig. 5 legend
relative abundance of taxa before and after colonization
- p. 6 Fig. 2 legend, panel E
points before and after cohousing is shown
- p. 9 Fig. 5 legend
fold-change (fc) in relative abundance of taxa before and after colonization was
- p. 9 Fig. 5 legend
before and after colonization was
Judge's note: On page 9 the same legend defines b and a as before (3 and 4 dpc) and after (8, 10 and 14 dpc) cohousing, and the panel key reads 'b (before), a (after) cohousing'. The Fig. 2E legend on page 6 defines fold change for time points "before and after cohousing". 'Colonization' is the wrong word.
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Wording Text says Fig. 3A summarises correlations in "Ob-Ob, Ln-Ln, Lnch, Obch and GFch mice", while the Fig. 3 legend says samples were from "Obch, Lnch, GFch, Ln39ch, and ObchLn39 cage mates and from Ob-Ob and Ln-Ln controls".
- p. 9 Paragraph beginning 'Significant correlations between cecal metabolite levels'
Ob-Ob, Ln-Ln, Lnch, Obch and GFch
- p. 7 Fig. 3 legend, panel A
Obch, Lnch, GFch, Ln39ch, and ObchLn39 cage mates and from Ob-Ob and Ln-Ln controls
- p. 9 left column, second paragraph
microbiota of Ob-Ob, Ln-Ln, Lnch, Obch and GFch mice consuming the LF-HPP diet are summarized in Fig. 3A
Only the authors can say what is right here.
Judge's note: Both passages read on the page 9 and page 7 images. The legend adds two groups from the 39-member consortium experiment, which the text introduces only later (page 10). The text gives the significance criterion as Benjamini-Hochberg corrected P values and the legend as "correlations with P ≤ 0.0001"; these can coexist. Only the authors can say which set of groups was analysed.
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Wording Fig. 4 legend attributes a diet effect to the comparison "see (A) versus (D), and (B) versus (E)", but panels A and B are mice given culture collections from DZ pair 1 and panels D and E are mice given "intact uncultured microbiota from DZ twin pair 2".
- p. 8 Fig. 4 legend, final sentence
see (A) versus (D), and (B) versus (E)
- p. 8 Fig. 4 legend, panels A/B and D/E
intact uncultured microbiota from DZ twin pair 2
Only the authors can say what is right here.
Judge's note: Legend read on the page 8 image. The paired panels differ in donor twin pair and in cultured versus uncultured inoculum as well as in diet, so the panels pointed to do not isolate diet. The text on page 11 says pair 2 uncultured microbiota recipients were also fed the LoSF-HiFV diet, so the two-way ANOVA may rest on data not shown in Fig. 4; the authors would need to say which data the comparison uses.
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Wording Test is named "one-way unpaired Student’s t test" on p.10, whereas the paper elsewhere uses "one-tailed unpaired Student’s t test" and the Fig. 4 legend names "a one-way ANOVA after Fisher’s least significant difference test" for the same panels.
- p. 10 Diet-Specific Effects, end of first paragraph
one-way unpaired Student’s t test
Only the authors can say what is right here.
Judge's note: The crop of p.10 shows 'one-way unpaired Student’s t test; P ≤ 0.001'. A text search finds 'one-tailed unpaired Student’s t test' in every other instance (for example the Fig. 1 and Fig. 3 legends). 'One-way' is ANOVA terminology and the Fig. 4 legend on p.8 names a one-way ANOVA. Whether the intended wording is 'one-tailed' t test or one-way ANOVA is for the authors to say.
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Wording Text says "60 acylcarnitine species (C2 to C22)" were measured, but Fig. 6, where "each row a different acylcarnitine", has 66 labelled rows (blocks of 10, 24 and 32).
- p. 11 Diet-Specific Effects, acylcarnitine paragraph
60 acylcarnitine species (C2 to C22)
- p. 10 Fig. 6 heat map row labels and legend
each row a different acylcarnitine
- p. 11 left column, first full paragraph
60 acylcarnitine species (C2 to C22) in liver, skeletal muscle, and serum
Only the authors can say what is right here.
Judge's note: I counted the Fig. 6 row labels from the text layer and checked them against the p.10 image. The top block (C2 to C7-DC) has 10 rows, the middle block (C6 to C14-OH/C12-DC) has 24, and the bottom block (C16:3 to C22) has 32, for 66 in total against the 60 stated on p.11. No statement in the article explains the difference (for example '60' being approximate or some rows being excluded). Table S15 is not among the files.
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16 minor (typos and the like; most checked by the judge only)
Wording "As in mice fed a LF-HPP diet, the invasive species B. uniformis and B. vulgatus were significantly and positively correlated with increased cecal propionate levels": for the LF-HPP diet, the article's text (p.9) and Fig. 3A report B. uniformis, P. merdae and A. putredinis, not B. vulgatus.
- p. 10 right column, last paragraph (continues on PDF page 11)
As in mice fed a LF-HPP diet, the invasive species B. uniformis and B. vulgatus were significantly and positively
- p. 9 left column, last paragraph
Three members of the Bacteroidetes, B. uniformis, Parabacteroides merdae, and A. putredinis
- p. 7 Fig. 3A row labels
Bacteroides uniformis*
Judge's note: Fig. 3A on p.7 has rows for Bacteroides uniformis*, Parabacteroides merdae* and Alistipes putredinis*, and no B. vulgatus row. The p.9 text names the same three species as correlating with acetate, propionate and butyrate. Fig. 4C on p.8 (LoSF-HiFV) does show B. uniformis* and B. vulgatus*. So the 'as in LF-HPP' comparison is supported in the article only for B. uniformis. Fig. 3A shows only correlations with P ≤ 0.0001, so a weaker B. vulgatus correlation may exist that is not shown; this is a minor wording point.
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Wording The Fig. 6 legend says significance was tested "between Ob-Ob and Ln-Ln, Lnch, or Obch animals", but the heat map has only Ob-Ob, Ln-Ln and Obch column groups; no Lnch animals are shown.
- p. 10 Fig. 6 legend
different between Ob-Ob and Ln-Ln, Lnch, or Obch animals
- p. 10 Fig. 6 column headers
Ob-Ob Ln-Ln Obch
- p. 10 Fig. 6 legend
cantly different between Ob-Ob and Ln-Ln, Lnch, or Obch animals
- p. 10 Fig. 6 legend
and Ln-Ln, Lnch, or Obch animals
Judge's note: The p.10 image and crop show the column headers 'Ob-Ob', 'Ln-Ln' and 'Obch' only, while the legend lists Lnch among the comparison groups. The legend may be describing the full analysis in table S15, which is not among the files, so this is a minor mismatch between legend and figure rather than a clear error.
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Wording Acylcarnitines are said to be measured "in liver, skeletal muscle, and serum (table S15, A to C)", but results are reported for "the plasma of Ob-Ob, Ln-Ln, and cohoused animals (table S15, B and C)" and rescue is claimed in "the skeletal muscle and liver (and cecum) of Obch mice".
- p. 11 Acylcarnitine paragraph
skeletal muscle, and serum (table S15, A to C)
- p. 11 Next paragraph
in the plasma of Ob-Ob, Ln-Ln, and cohoused animals (table S15, B and C)
- p. 11 left column, second paragraph
bolic phenotype in the skeletal muscle and liver (and cecum) of Obch mice
- p. 11 left column, first full paragraph
in liver, skeletal muscle, and serum (table S15, A to C)
Only the authors can say what is right here.
Judge's note: Both sentences were read on the p.11 crops. The blood matrix is called 'serum' when introduced and 'plasma' when reported. The single plasma result points to two sub-tables (B and C), where A to C were mapped to three matrices. 'Cecum' appears in the rescue sentence although the article does not describe measuring acylcarnitines in cecum. Table S15 and fig. S16 are not among the files, so the pointer cannot be checked; only the wording inconsistencies in the article are confirmed.
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Wording Text: "overexpression of carnitine acyltransferase (Crat), also resolve the insulin-resistance phenotype in mice (47, 48)"; reference 48 is titled "Muscle-specific deletion of carnitine acetyltransferase compromises glucose tolerance and metabolic flexibility".
- p. 11 Acylcarnitine paragraph
overexpression of carnitine acyltransferase (Crat), also resolve the insulin-resistance phenotype in mice (47, 48)
- p. 12 Reference 48
Muscle-specific deletion of carnitine acetyltransferase compromises glucose tolerance
- p. 12 reference 48
Muscle-specific deletion of carnitine acetyltransferase compromises glucose tolerance and metabolic flexibility
Only the authors can say what is right here.
Judge's note: Rests on outside knowledge: that Crat denotes carnitine acetyltransferase, and what experiments refs 47 and 48 actually contain. On the page, the text names the enzyme 'carnitine acyltransferase (Crat)', while the title of ref 48 on p.12 says 'carnitine acetyltransferase' and describes a deletion, not an overexpression. Whether the body of ref 47 or ref 48 reports an overexpression rescue cannot be checked from the files. The naming mismatch between the text and its own reference list is visible, and the fit of the citation is a question for the authors.
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Wording "An increase in serum glucose concentration was observed ... (means ± SEM: 338.5 ± 11.07 mg/dl in Ob-Ob animals versus 304.6 ± 17.78 mg/dl in Ln-Ln animals; P = 0.06, unpaired Student's t test" is then summarised as "associated with mild glucose intolerance" although the printed P is above 0.05.
- p. 11 Glucose tolerance test paragraph
338.5 T 11.07 mg/dl in Ob-Ob animals versus 304.6 T 17.78 mg/dl in Ln-Lnanimals;P=0.06
Only the authors can say what is right here.
Judge's note: Viewed the crop of page 11 and read the surrounding text in extract/main.txt. The comparison is printed with P = 0.06, described as an observed increase, and the paragraph then says "We concluded that the elevation in skeletal muscle long-chain acylcarnitines ... is associated with mild glucose intolerance". The same paragraph reports no significant differences in insulin concentrations or insulin signalling. The wording is hedged ("mild", "may be an early manifestation"), so this is a wording point: the authors could state that the difference was a trend that did not reach significance. The difference in means is 33.9 mg/dl and the sum of squared SEMs is about 438.7 (the square root, about 20.9, I took by hand).
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Typo Author contributions list "J.J.F., F.R., J.C., J.C.C.", giving Federico E. Rey as "F.R." without the middle initial, unlike the other authors (e.g. J.J.F., A.E.D., A.L.K.).
- p. 12 Acknowledgments, author contributions
J.J.F., F.R., J.C., J.C.C.
- p. 3 Author list
Federico E. Rey
Judge's note: Viewed both crops. The byline on page 3 prints "Federico E. Rey"; the contributions on page 12 print "F.R.", whereas other authors with middle initials have them (V.K.R., J.J.F., A.E.D., A.L.K., J.C.C.). "J.C." matches Jiye Cheng, who has no middle initial, and "J.C.C." matches Jose C. Clemente, so those are not defects. Cosmetic; the evident fix is "F.E.R.".
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Typo Fig. 3 legend: "*P ≤ 0.05; **P ≤ 0.01; ****P ≤ 0.001" — four asterisks for P ≤ 0.001 with no three-asterisk level, whereas Fig. 1 uses "***P ≤ 0.001" and Fig. 2 uses "***P ≤ 0.005".
- p. 7 Fig. 3 legend, panels C to E
*P ≤ 0.05; **P ≤ 0.01; ****P ≤ 0.001
- p. 4 Fig. 1 legend, panel D
***P ≤ 0.001
- p. 7 Fig. 3 legend
****P ≤0.001
- p. 7 Fig. 3 legend
****P ≤0.001 (defined by
Judge's note: Fig. 3E does carry a '****' mark over the Lnch bar, so the legend matches its own panel. The inconsistency is only in the symbol convention between figures and the skipped three-asterisk level. Either form could be the authors' intent.
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Typo "greater capacity to breakdown and ferment polysaccharides" — the noun 'breakdown' is used as a verb; it should be 'break down'.
- p. 5 Results, Functional differences, end of paragraph
capacity to breakdown and ferment poly-
Judge's note: Read on the page 5 image, left column. Cosmetic.
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Typo Fig. 3A metabolite axis label "Dissacharide similar to maltose" misspells 'Disaccharide'.
- p. 7 Fig. 3A, metabolite axis labels
Dissacharide similar to maltose
Judge's note: The rotated label is clearly legible in the crop and reads 'Dissacharide'. The Fig. 2D label and legend spell it 'disaccharide'.
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Typo Fig. 4 legend: "An asterisk in the colored box indicates that that a taxon or metabolite is significantly enriched" — duplicated 'that'.
- p. 8 Fig. 4 legend, panel C
indicates that that a taxon or metabolite
Judge's note: On the page 8 image the left legend column ends "indicates that" and the right column begins "that a taxon"; both words are printed.
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Typo The butyryl/isobutyryl acylcarnitine is written "C4:C4i" in the p.11 text ("C2, C4:C4i, and C4-OH") but "C4:Ci4" in the Fig. 6 row label (which also has "C4-DC:Ci4-DC").
- p. 11 Acylcarnitine paragraph
C2, C4:C4i, and C4-OH
- p. 10 Fig. 6 row label
C4:Ci4
- p. 11 left column, first full paragraph
(C2, C4:C4i, and C4-OH)
- p. 10 Diet-Specific Effects
P ≤0.001) (Fig. 4, A and B, and table S14)
Judge's note: The p.11 crop shows 'C4:C4i'. The Fig. 6 crop shows 'C4:Ci4' and 'C4-DC:Ci4-DC'. This is a cosmetic notation inconsistency for the same species. The third reviewer note in this cluster (P ≤0.001 versus **) is a different issue, judged in C024.
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Typo "Fgf15, secrted by the gut epithelium and delivered to hepatocytes" — 'secrted' should be 'secreted'.
- p. 9 Bile acid / FXR paragraph, third column
secrted by the gut epithelium
- p. 9
secrted by the gut epithelium and delivered to
Judge's note: Seen on the page 9 image, third column; not an extraction artefact.
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Typo Misspelling: "We subsequently colonized GF mice with a con-sorium of 39 sequenced taxa" should read "consortium".
- p. 10 Taxa-Specific Effects, first sentence
con-sorium of 39 sequenced taxa
- p. 10 Taxa-Specific Effects, first sentence
sorium of 39 sequenced taxa
Judge's note: The crop shows the line break 'con-' / 'sorium' with no 't'. The word is spelled 'consortium' later in the same paragraph. This is on the page, not an extraction artefact.
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Typo Missing letter: "a significant increase in both adipose and ean body mass" should read "lean body mass".
- p. 10 Diet-Specific Effects, end of left column
ean body mass (one-way unpaired
- p. 10 Diet-Specific Effects, left column last lines
ean bodymass
Judge's note: The crop of the bottom of the left column on p.10 shows the line beginning 'ean body mass (one-way unpaired Student’s t test;' after 'both adipose and'. The 'l' is absent on the page, so this is not an extraction artefact.
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Typo The same group is written "(ObchLn39)" and then "Obch-Ln39" (superscripts) within one paragraph on p.10; the Fig. 3 legend uses ObchLn39.
- p. 10 Taxa-Specific Effects, left column
Ob chLn39
Judge's note: The crop of p.10 shows the superscript 'chLn39' at first mention and 'ch-Ln39' twice later in the paragraph. The Fig. 3 legend on p.7 has 'ObchLn39' without a hyphen. This is a cosmetic notation inconsistency and the meaning is clear.
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Typo Text names the Crat enzyme "carnitine acyltransferase (Crat)" while the paper's own reference 48, cited for it, reads "carnitine acetyltransferase".
- p. 11 left column, first full paragraph
carnitine acyltransferase (Crat)
- p. 12 reference 48
carnitine acetyltransferase
Judge's note: Viewed both crops. Page 11 left column prints "overexpression of carnitine acyltransferase (Crat)"; reference 48 on page 12 prints "Muscle-specific deletion of carnitine acetyltransferase". The two names differ within the paper. "Acyltransferase" is a broader class name that could be a legitimate if loose usage, so this is a minor consistency point rather than a clear error.
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