phenomenon · claim-type · cross-domain-transfer · mechanism · claim-relation · replication-status · limitation — grounded in the full text| phenomenon | the genetic content of the gut microbial community and its overlap between people— “The genes are largely shared among individuals of the cohort.” | |
| claim-type | method— “This result represents a proof of principle that short-read sequencing can be used to characterize complex microbiomes.” | |
| method — evidence | — “Our results also show that short-read metagenomic sequencing can be used for global characterization of the genetic potential of ecologically complex environments.” | |
| object of study — evidence | — “We have used extensive Illumina GA short-read-based sequencing of total faecal DNA from a cohort of 124 individuals of European (Nordic and Mediterranean) origin to establish a catalogue of nonredundant human intestinal microbial genes.” | |
| research question — evidence | — “The genes are largely shared among individuals of the cohort.” | |
| contribution — evidence | — “We define and describe the minimal gut metagenome and the minimal gut bacterial genome in terms of functions present in all individuals and most bacteria, respectively.” | |
| mechanism | A CATALOGUE ARGUED TO BE GENERAL BY WHAT IT ALREADY CONTAINS: 70% of the reads from earlier American and Japanese studies map onto these contigs, so coverage is demonstrated against other cohorts rather than asserted of the population— “The catalogue probably contains a large majority of prevalent intestinal microbial genes in the human population, for the following reasons: (1) over 70% of the metagenomic reads from three previous studies, including American and Japanese individuals8,16,17, can be mapped on our contigs” | mechanisms[0] |
| mechanism | SHARING MEASURED AT A STATED DEPTH: almost 40% of each individual's genes are shared with at least half the cohort, and the sentence carries its own qualifier - AT THE PRESENT DEPTH OF SEQUENCING— “At the present depth of sequencing, we found that almost 40% of the genes from each individual are shared with at least half of the individuals of the cohort.” | mechanisms[1] |
| sense | minimal gut metagenome - defined by WHAT IS PRESENT IN ALL INDIVIDUALS, so the word minimal is about the intersection across people, not about a smallest viable set— “We define and describe the minimal gut metagenome and the minimal gut bacterial genome in terms of functions present in all individuals and most bacteria, respectively.” | senses[0] |
| sense | minimal gut bacterial genome - the companion term, defined over MOST BACTERIA rather than over all individuals. TWO SENSES OF `minimal` COINED IN ONE SENTENCE, and the sentence marks which is which with `respectively`— “We define and describe the minimal gut metagenome and the minimal gut bacterial genome in terms of functions present in all individuals and most bacteria, respectively.” | senses[1] |
| control | one of the two samples was ALSO sequenced on a different platform (Roche/454) and the assemblies compared - 97.9 per cent collinear over 99.5 per cent of mapped regions — held — rules out that the assembly is an artefact of the Illumina platform or of the assembler, rather than the biology - a second technology with different error modes should not reproduce a shared artefact— “This is comparable to the contigs that were generated by 454 sequencing for one of the two samples (MH0006) as a control, of which 97.9% were collinear over 99.5% of the mapped regions.” | controls[0] |
| control | contigs from two samples mapped back to Sanger reads from those same samples — held — rules out that the short-read assembly has mis-joined or dropped sequence - Sanger reads are long and independently generated— “To assess the quality of the Illumina GA-based assembly we mapped the contigs of samples MH0006 and MH0012 to the Sanger reads from the same samples (Supplementary Table 2).” | controls[1] |
| edge | minimal gut metagenome —distinct-from→ minimal gut bacterial genome— “We define and describe the minimal gut metagenome and the minimal gut bacterial genome in terms of functions present in all individuals and most bacteria, respectively.” | concept_edges[0] |
| edge | metagenomic sequencing —contrasted-with→ rRNA sequencing— “Metagenomic sequencing represents a powerful alternative to rRNA sequencing for analysing complex microbial communities” | concept_edges[1] |
| outcome (stated by the tagger, no quotation) | control — held | controls[0] |
| outcome (stated by the tagger, no quotation) | control — held | controls[1] |
| evidence status note | limitation — the quote carries an extractor fusion: the paper's “non-redundant” is staged as “nonredundant”. Verbatim against the staged text; the damage is mid-word and no re-slice avoids it. Confidence 0.85 under an earlier note of ours.— “We have used extensive Illumina GA short-read-based sequencing of total faecal DNA from a cohort of 124 individuals of European (Nordic and Mediterranean) origin to establish a catalogue of nonredundant human intestinal microbial genes.” | limitations[1] |
| limitation | The full bacterial gene complement of each individual was NOT sampled - the paper's own first sentence of caveat— “The full bacterial gene complement of each individual was not sampled in our work.” | limitations[0] |
| limitation | The cohort is 124 European adults, Nordic and Mediterranean, and the paper states that scope in its own summary sentence— “We have used extensive Illumina GA short-read-based sequencing of total faecal DNA from a cohort of 124 individuals of European (Nordic and Mediterranean) origin to establish a catalogue of nonredundant human intestinal microbial genes.” | limitations[1] |
| limitation | The proportion of shared genes is stated to be BOUNDED BY FUTURE WORK rather than settled here, which makes the sharing figure provisional by the authors' own account— “Future studies of world-wide span, envisaged within the International Human Microbiome Consortium, will complete, as necessary, our gene catalogue and establish boundaries to the proportion of shared genes.” | limitations[2] |
| limitation | The sharing result is explicitly conditioned on the sequencing depth used— “At the present depth of sequencing, we found that almost 40% of the genes from each individual are shared with at least half of the individuals of the cohort.” | limitations[3] |
| concept | minimal gut metagenome— “We define and describe the minimal gut metagenome and the minimal gut bacterial genome in terms of functions present in all individuals and most bacteria, respectively.” | concepts[0] |
| concept | minimal gut bacterial genome— “We define and describe the minimal gut metagenome and the minimal gut bacterial genome in terms of functions present in all individuals and most bacteria, respectively.” | concepts[1] |
| concept | gene catalogue— “We have used extensive Illumina GA short-read-based sequencing of total faecal DNA… | concepts[2] |
| concept | prevalent genes | concepts[3] |
| concept | metagenomic sequencing Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[4] |
| concept | rRNA sequencing Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[5] |
| concept | proof of principle Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[6] |
| concept | contigs Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[7] |
| concept | gut microbiome Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[8] |
| concept | short-read metagenomic sequencing Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[9] |
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