An Obesity-Associated Gut Microbiome with Increased Capacity for Energy Harvest
2006 · paper · Biomedicine
Uses metagenomic and biochemical analyses of gut microbes in obese and lean mice. The obese microbiome has greater capacity to harvest energy from diet, and colonizing germ-free mice with an obese microbiota produces a larger increase in body fat than a lean one.
Checked: PDF from cbcb.umd.edu, fetched 4 Oct 2026. Page numbers are those of that PDF.
2 findings
Reference or label Reference 9 prints the DOI as "Nature doi:10.1038/nature4441023a (this issue)", which mixes the two Nature DOI forms and does not appear to be the companion paper's DOI.
- p. 4 Reference 9
Nature doi:10.1038/nature4441023a (this issue)
- p. 4 Reference 9
doi:10.1038/nature4441023a (this issue)
Only the authors can say what is right here.
Judge's note: Rests on outside knowledge: that the companion paper by Ley et al. is Nature 444, 1022-1023 with DOI 10.1038/4441022a. The page 4 image shows the reference exactly as quoted. Internal evidence supports that the string is malformed: this article's own DOI on page 1 is 10.1038/nature05414 (prefix 'nature' plus five digits), whereas the printed string joins 'nature' to a volume-page-letter form. The correct DOI cannot be confirmed from the files.
Second check: another model agreed
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Reference or label "deposited in GenBank under the accession numbers EF95962-100118": the first accession has five digits and the second six, so the range as printed is not a valid pair of accessions (probably EF095962-EF100118).
- p. 5 Author Information
accession numbers EF95962-100118
- p. 5 Author Information
EF95962-100118
Only the authors can say what is right here.
Judge's note: Rests on outside knowledge: that GenBank nucleotide accessions with a two-letter prefix carry six digits. The crop of page 5 shows 'EF95962-100118' exactly as extracted. The start has five digits and the end six; read literally, the start is not a valid accession and a reader cannot retrieve the sequences from it. A dropped zero (EF095962) is the likely cause, but only the authors or GenBank can confirm the range.
Second check: another model agreed
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4 minor (typos and the like; most checked by the judge only)
Wording Legend says Fig. 1c,d show categories "consistently enriched or depleted in the caecal microbiomes of both obese mice", but in Fig. 1c "[V] Defense mechanisms" is enriched for ob1 versus lean1 (both platforms) and depleted for ob2 versus lean2; [D] and [U] are black in all three columns.
- p. 2 Figure 1c, row [V]
[V] Defense mechanisms
- p. 2 Figure 1 legend
consistently enriched or
- p. 3 Comparative metagenomic analysis, paragraph 2
functional profiles (Fig. 1c)
Judge's note: In the Fig. 1c crop, row [V] is red, red, green; rows [D] and [U] are black throughout; [O] is green in one column only. So the panel contains rows that are not consistently enriched or depleted, contrary to the legend's description. The legend partly covers this: asterisks mark the groups that were consistent between both sibling pairs under the stricter threshold, and [V], [D], [U] and [O] carry none, and 'a subset of COG categories' can be read loosely. The text's 'similar differences' (Fig. 1c) refers to the two sequencing methods, which do agree for [V]. Hence a minor wording point, not an error in the data.
Second check: another model agreed
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Wording "47 ± 8.3 versus 27 ± 3.6 percentage increase or 1.3 ± 0.2 versus 0.86 ± 0.1 g fat" with initial body fat "2.7 ± 0.2 g for both groups": 0.86 g on 2.7 g is about 32%, against 27% printed (1.3 g on 2.7 g is about 48%, against 47%).
- p. 4 Microbiota transplantation, last sentence before Discussion
47 ± 8.3 versus 27 ± 3.6 percentage
- p. 4 Microbiota transplantation
1.3 ± 0.2 versus 0.86 ± 0.1 g fat
- p. 4 Microbiota transplantation
2.7 ± 0.2 g for both groups
Judge's note: Page 4 image shows the three values as quoted. The ratio of group means gives 48% and 32%; the first agrees with the printed 47%, the second does not agree with 27%. This need not be an error: the printed percentages are presumably means of per-animal percentage increases, which differ from the ratio of means when initial fat varies between animals (s.e.m. 0.2 g on about 10 animals is a wide spread), and all inputs are rounded. Fig. 3c's lean bar is at about 26-27%, matching the printed percentage. The derived figures check out: the difference of 0.44 g at 9.3 kcal/g is about 4 kcal, which is about 2% of roughly 203 kcal consumed. Kept as a minor consistency point.
Second check: another model agreed
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Typo "the Bacteroidetes and the Firmicutes, consisted of more than 90% of all phylogenetic types": 'consisted of' is used where 'constituted' (made up) is meant.
- p. 1 Introduction, paragraph 3
consisted of more than 90% of all phylogenetic types
Judge's note: Page 1 image shows the wording as quoted. The two divisions make up more than 90% of the phylotypes; 'consisted of' reverses the relation. The meaning is recoverable, so this is a wording slip only.
Second check: none (judge only)
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Typo "1.4% Euryarcheota; 0.07% Crenarcheota" is misspelled; the same page later prints "Euryarchaeota and Crenarchaeota".
- p. 2 Taxonomic analysis of microbiomes, paragraph 1
1.4% Euryarcheota; 0.07% Crenarcheota
- p. 2 Taxonomic analysis of microbiomes, paragraph 2
(Euryarchaeota and Crenarchaeota)
- p. 2 Taxonomic analysis of microbiomes, paragraph 2 (right column)
Euryarchaeota and Crenarchaeota
- p. 2 following paragraph
Archaea (Euryarchaeota and Crenarchaeota)
Judge's note: Page 2 image shows both spellings: 'Euryarcheota'/'Crenarcheota' in the left column and 'Euryarchaeota and Crenarchaeota' in the right column. Not an extraction artefact. The paper's own second spelling is the standard one.
Second check: none (judge only)