A Framework for Human Microbiome Research
Nature, 2012 · paper · Biomedicine
Presents resources from the Human Microbiome Project: 16S rRNA profiles and metagenomic sequence from 242 healthy adults sampled at up to 18 body sites, plus about 800 sequenced reference strains. Describes standardized methods and the resulting data as a framework for future studies.
Checked: PDF from nature.com, fetched 4 Oct 2026. Page numbers are those of that PDF.
4 findings
Substance Table 1 'Total WGS samples' column: the 18 body-site entries sum to 678, but the Total row prints "681"; the Stool row ("352 337 ... 136 ... 124") is the only row where total ≠ 16S + WGS − both, and it is short by the same 3.
- p. 2 Table 1, Stool row, 'Total WGS samples' column
136
- p. 2 Table 1, Total row, 'Total WGS samples' column
681
- p. 2 Table 1, Total WGS samples column
Total 5,298 5,177 2,971 19 4,879 26.3 2,673 681
- p. 3 Metagenomic assembly section
From a high-qualityset of681 samples
Only the authors can say what is right here.
Judge's note: Read Table 1 on the page image and crop. The WGS column sums to 678 against a printed 681. Every other row I checked satisfies total = 16S + WGS − both (buccal mucosa, tongue dorsum, anterior nares), and the Total row does too (5,177 + 681 − 560 = 5,298). Stool gives 349 against a printed 352, so the stool WGS cell would need to be 139. The text also uses 681, so the total looks right and a cell looks wrong, but only the authors can say which. No explanatory statement or correction notice is in the files.
Second check: another model agreed
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Substance Text: "mid-vagina (96%), anterior nares (82%) and throat (75%)). Preparations from saliva were also high in human DNA sequence (80%)"; Table 1 'Human reads (%)' gives 99, 96, 79 and 91 for those sites.
- p. 3 Metagenomic assembly and gene cataloguing, 1st paragraph
mid-vagina (96%), anterior nares (82%) and throat (75%)). Preparations from saliva were also high in human DNA sequence (80%)
- p. 2 Table 1, 'Human reads (%)' column: mid-vagina, anterior nares, throat, saliva rows
99
- p. 3 Metagenomic assembly and gene cataloguing, para 1
mid-vagina (96%)
- p. 2 Table 1, Mid-vagina, Human reads (%)
Mid-vagina 145 143 91 0.6 140 1.0 88 2 22.6 0 99
Only the authors can say what is right here.
Judge's note: Text read on the page 3 image, table on the page 2 image. All four site values differ from Table 1, while the overall 49% and stool 1% in the same passage match it. The table values fit its own remaining-depth column (anterior nares 14.3 of 1,129.9 G is about 1% remaining; 82% human would leave far more). The passage cites Supplementary Fig. 4, which is not among the files, so the text may use a different statistic such as a per-sample mean; nothing in the article says so. Hence a query to the authors, not a correction. Two of the text values (96, 82) equal the table values for the adjacent sites anterior nares and buccal mucosa.
Second check: another model agreed
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Reference or label Table 1 footnote † defines the WGS depth unit (G) as "1 x 10^9 reads (Supplementary Information)", but the text reports the same totals as bases: "an average depth of 13 Gb (± 4.3) ... a total of 8.8 Tb" and "the remaining 3.5 Tb from 681 samples".
- p. 2 Table 1 footnote †
1 x 109 reads (Supplementary Information).
- p. 3 Metagenomic assembly and gene cataloguing, 1st paragraph
an average depth of 13 Gb (± 4.3) was achieved per sample, collectively producing a total of 8.8 Tb
- p. 3 Metagenomic assembly and gene cataloguing, 2nd paragraph
the remaining 3.5 Tb from 681 samples
Judge's note: Footnote † read on the page 2 image; the text read on the page 3 image. Table totals 8,863.3 G and 3,538.1 G correspond to 8.8 Tb and 3.5 Tb, and 8,863.3/681 = 13.0 matches "13 Gb" per sample. With 101-bp reads, 10^9 reads cannot be the unit, so the columns are in gigabases and the footnote label is wrong.
Second check: another model agreed
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Reference or label Reference 15 DOI printed as "http://dx.doi.org/10.1371/journal.pone.002904 (14 June 2012)" has a six-digit article number, whereas the other PLoS ONE DOIs in the list (refs 6 and 12: pone.0039315, pone.0036427) have seven digits.
- p. 5 Reference 15
journal.pone.002904 (14 June 2012)
- p. 5 Reference 6
http:dx.plos.org/10.1371/
Only the authors can say what is right here.
Judge's note: Rests on outside knowledge: that PLoS ONE DOI suffixes have seven digits and what the true DOI of the Goll et al. paper is. The crop of the reference list shows "journal.pone.002904" contiguous on one line, so no digit is lost to a line break. Refs 6 and 12 in the same list show seven digits, so the DOI appears truncated; the correct digits must come from the authors or publisher. The ref 6 URL part of this cluster is handled under C013.
Second check: another model agreed
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12 minor (typos and the like; most checked by the judge only)
Typo Table 1, Left and Right antecubital fossa rows print "0 NA NA NA 0 NA": remaining read depth is 0 while total read depth is NA, and 'Samples 16S and WGS' is NA while other rows with no overlap (keratinized gingiva, saliva, mid-vagina) print 0.
- p. 2 Table 1, Left and Right antecubital fossa rows, last two columns
0 NA NA NA 0 NA
Judge's note: Confirmed on the page 2 image and crop. The NA/0 coding is inconsistent within these rows and against other rows. It has no numerical effect on the column totals, and either coding could be defended, so this is an observation only.
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Typo Table 1 Total row prints the V13 read depth as "19" (no decimal), whereas all row entries and the V35 total ("26.3") have one decimal; the rows sum to 19.3.
- p. 2 Table 1, Total row, V13 read depth (M)
19
Judge's note: Confirmed on the page 2 image and crop. The row values sum to 19.3, so the printed 19 is a correct integer rounding but is formatted inconsistently with the rest of the column. Cosmetic.
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Typo Figure 1a curve label reads "L antecubita fossa" (missing final 'l'); the neighbouring label reads "R antecubital fossa".
- p. 4 Figure 1, panel a curve label
L antecubita fossa
- p. 4 Figure 1a, curve label
L antecubita
Judge's note: Visible in the figure crop: the label is "L antecubita / fossa" and the adjacent one is "R antecubital / fossa". It is a typo in the figure itself, not an extraction artefact.
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Typo Reference 6 URL printed as "http:dx.plos.org/10.1371/journal.pone.0039315" (missing '//'); affiliation 11 reads "Guleph, Ontario" (same affiliation begins "University of Guelph"); affiliation 29 reads "6701 Democracy Boulavard".
- p. 5 Reference 6
http:dx.plos.org/10.1371/
- p. 6 Affiliation 11
Guleph, Ontario
- p. 6 Affiliation 29
6701 Democracy Boulavard
Judge's note: All three are visible on the images: the ref 6 URL on page 5 lacks the slashes that refs 12, 13 and 15 have; "Guleph" appears directly after "University of Guelph" in the page 6 crop; "Boulavard" is in the page 6 crop. These are cosmetic typos. The "Ochman. H." item mentioned by one reviewer is handled under C014.
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Typo Reference 7 prints "Ochman. H. & Hugenholtz, P." with a full stop instead of a comma after the surname.
- p. 5 Reference 7
Ochman. H. & Hugenholtz, P.
- p. 5 Reference 7
Ochman. H. & Hugenholtz
Judge's note: Visible on the page 5 image and in the text layer; the other authors in the same entry use commas. Cosmetic.
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Typo Acknowledgements: "U54HG003067 to E. S. Lander.;" (stray full stop) and "RC1DE020298and R01DE021574" (missing space); Author Contributions: "J. Ravel., T.M.S." (stray full stop).
- p. 5 Acknowledgements
U54HG003067 to E. S. Lander.;
- p. 5 Acknowledgements
RC1DE020298and R01DE021574
- p. 5 Author Contributions, Body site experts
J. Ravel.,
- p. 5 Author contributions, Body site experts
J. Ravel., T.M.S.
Judge's note: All three are visible on the page 5 image and match the text layer, including the fused "RC1DE020298and". Cosmetic punctuation and spacing errors.
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Typo Author Contributions use "S.K.H." both for Sarah K. Highlander (H position, e.g. "K.H., S.K.H., C.H.") and, in the K position ("J.A.K., S.K.H., H.H.K., K.P.L."; "S.T.K., S.K.H., R.K., H.H.K."), evidently for Susan Kinder-Haake, who is "S.K.-H." in the Acknowledgements.
- p. 5 Author Contributions, Body site experts
J.A.K., S.K.H., H.H.K., K.P.L.
- p. 5 Acknowledgements
S.K.-H. was supported by
- p. 5 Author Contributions, 16S data analysis
S.T.K., S.K.H., R.K., H.H.K.
Judge's note: Read page 5 image and text. The contribution lists are alphabetical by surname. In 'Body site experts' and '16S data analysis', S.K.H. sits among the K surnames, where Kinder-Haake belongs; elsewhere S.K.H. sits among the H surnames (Highlander). The Acknowledgements print 'S.K.-H. was supported by'. The hyphenated form never appears in the contributions, so the initials are ambiguous between two authors. Cosmetic, but it affects attribution.
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Typo Emma Allen-Vercoe is abbreviated "E.A.-V." in the Acknowledgements ("R21HG005811 to E.A.-V.") but "E.A.V." in the Author Contributions ("K.M.A., E.A.V., G.A."; "Strain management: E.A.V.").
- p. 5 Acknowledgements
R21HG005811 to E.A.-V.
- p. 5 Author Contributions, Body site experts / Strain management
K.M.A., E.A.V., G.A.
Judge's note: Page 5 image and text show both forms. The author list on page 6 gives 'Emma Allen-Vercoe'. No other author has these initials, so this is a cosmetic inconsistency only.
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Typo Affiliation 11 misspells the city: "University of Guelph ... 50 Stone Road East, Guleph, Ontario N1G 2W1, Canada".
- p. 6 Affiliation 11
50 Stone Road East, Guleph, Ontario
Judge's note: Page 6 image shows 'Guleph' a few words after the correctly spelled 'University of Guelph' in the same affiliation. The internal inconsistency establishes the typo without outside knowledge.
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Typo Affiliation 29 misspells the street: "6701 Democracy Boulavard, MSC 4878"; affiliations 16 and 17 print "Democracy Boulevard".
- p. 6 Affiliation 29
6701 Democracy Boulavard, MSC 4878
Judge's note: Page 6 image shows 'Boulavard' in affiliation 29 and 'Boulevard' in affiliations 16 and 17 for the same street.
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Typo Affiliations 33 and 47 are word-for-word identical: "Harvard School of Dental Medicine, Department of Oral Medicine, Infection and Immunity, 188 Longwood Avenue, Boston, Massachusetts 02115, USA".
- p. 6 Affiliation 33
33Harvard School of Dental Medicine, Department of Oral Medicine, Infection and Immunity, 188 Longwood Avenue
- p. 6 Affiliation 47
47Harvard School of Dental Medicine, Department of Oral Medicine, Infection and Immunity, 188 Longwood Avenue
Judge's note: Page 6 image shows both entries with identical text, used for Dewhirst (32,33) and Izard (32,47). It is a redundant duplicate affiliation number; no reader is misled.
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Typo Affiliation 69 has transposed wording: "Annenberg Building Floor5th, Room 5-208" (for "5th Floor").
- p. 6 Affiliation 69
Annenberg Building Floor5th, Room 5-208
Judge's note: Page 6 image shows 'Building Floor 5th, Room 5-208'. The transposed word order is in the published text. Whether the space between 'Floor' and '5th' is missing cannot be told at the page-image resolution and may be an extraction artefact; I did not open the crop.
Second check: none (judge only)