phenomenon · claim-type · cross-domain-transfer · mechanism · claim-relation · replication-status · limitation — grounded in the full text| phenomenon | wide variation in the microbiota of healthy people, stable within a person and large between people— “The uniqueness of each individual’s microbial community thus seems to be stable over time (relative to the population as a whole), which may be another feature of the human microbiome specifically associated with health.” | |
| claim-type | existence— “No taxa were observed to be universally present among all body habitats and individuals at the sequencing depth employed here” | |
| method — evidence | — “Within-subject variation over time was consistently lower than between-subject variation, both in organismal composition and in metabolic function” | |
| object of study — evidence | — “Adult subjects lacking evidence of disease were recruited based on a lengthy list of exclusion criteria; we will refer to them here as ‘healthy’, as defined by the consortium clinical sampling criteria” | |
| research question — evidence | — “This extensive sampling of the human microbiome across many subjects and body habitats provides an initial characterization of the normal microbiota of healthy adults in a Western population.” | |
| contribution — evidence | — “We conclude that most variation in the human microbiome is not well explained by these phenotypic” | |
| mechanism | EACH PERSON'S COMMUNITY IS MORE STABLE THAN THE POPULATION IS UNIFORM: variation within a subject over time is consistently smaller than variation between subjects, in composition and in function alike— “Within-subject variation over time was consistently lower than between-subject variation, both in organismal composition and in metabolic function” | mechanisms[0] |
| mechanism | A DIVERSITY SPLIT THAT REVERSES BY HABITAT: saliva is among the richest within a person and among the most similar across people, while skin is the opposite - so one number for diversity would hide the pattern entirely— “For example, the saliva had among the highest median alpha diversities of operational taxonomic units (OTUs, roughly species level classification, see http://hmpdacc.org/HMQCP), but one of the lowest beta diversities—so although each individual’s saliva was ecologically rich, members of the population shared similar organisms.” | mechanisms[1] |
| sense | healthy - A STIPULATED TERM IN THIS PAPER, flagged as such in the sentence that introduces it: not a clinical judgement but the absence of anything on a list of exclusion criteria, and the authors put the word in quotation marks— “Adult subjects lacking evidence of disease were recruited based on a lengthy list of exclusion criteria; we will refer to them here as ‘healthy’, as defined by the consortium clinical sampling criteria” | senses[0] |
| sense | diversity - ALPHA, within a sample: how many kinds of organism and in what proportions— “The diversity of microbes within a given body habitat can be defined as the number and abundance distribution of distinct types of organisms” | senses[1] |
| sense | diversity - BETA, between samples from the same habitat in different people. The paper's saliva case is the reason the split matters: HIGHEST alpha and one of the LOWEST betas - each mouth is rich, and every mouth is rich in the same way— “For example, the saliva had among the highest median alpha diversities of operational taxonomic units (OTUs, roughly species level classification, see http://hmpdacc.org/HMQCP), but one of the lowest beta diversities—so although each individual’s saliva was ecologically rich, members of the population shared similar organisms.” | senses[2] |
| control | 131 of the subjects sampled again at a second time point, so within-subject change could be measured against between-subject spread — held — rules out mistaking population-level variation for individual instability— “Within-subject variation over time was consistently lower than between-subject variation, both in organismal composition and in metabolic function” | controls[0] |
| edge | alpha diversity —distinct-from→ beta diversity— “This study established that these patterns of alpha diversity (within samples) differed markedly from comparisons between samples from the same habitat among subjects (beta diversity, Fig. 1b).” | concept_edges[0] |
| outcome (stated by the tagger, no quotation) | control — held | controls[0] |
| limitation | THE PAPER'S OWN NEGATIVE RESULT: most variation in the human microbiome is not well explained by the phenotypic metadata collected, and even the strongest associations carry low effect sizes and considerable unexplained variance— “We conclude that most variation in the human microbiome is not well explained by these phenotypic” | limitations[0] |
| limitation | 'Healthy' is defined by an exclusion list rather than by a positive criterion, and the paper marks the word as its own stipulation— “Adult subjects lacking evidence of disease were recruited based on a lengthy list of exclusion criteria; we will refer to them here as ‘healthy’, as defined by the consortium clinical sampling criteria” | limitations[1] |
| limitation | The characterisation is of a WESTERN population, stated in the paper's own first conclusion sentence— “This extensive sampling of the human microbiome across many subjects and body habitats provides an initial characterization of the normal microbiota of healthy adults in a Western population.” | limitations[2] |
| limitation | No taxon was found in every habitat and every individual at this sequencing depth - so the absence is bounded by the depth, not asserted of the biology— “No taxa were observed to be universally present among all body habitats and individuals at the sequencing depth employed here” | limitations[3] |
| limitation | A remarkable fraction of the protein families found are functionally uncharacterised - 58% at the minimum, in the oral cavity— “A remarkable fraction of these families were indeed functionally uncharacterized, including those detected by read mapping, with a minimum in the oral cavity (mean 58% s.d. 6.8%) and maximum in the nares” | limitations[4] |
| limitation | The catalogue does not remove the need for matched internal controls in later clinical studies, and the paper says so— “Clinical studies of the microbiome will be able to leverage the resulting extensive catalogues of taxa, pathways and genes1, although they must also still include carefully matched internal controls.” | limitations[5] |
| concept | alpha diversity— “This study established that these patterns of alpha diversity (within samples) differed markedly from comparisons between samples from the same habitat among subjects (beta diversity, Fig. 1b).” | concepts[0] |
| concept | beta diversity— “This study established that these patterns of alpha diversity (within samples) differed markedly from comparisons between samples from the same habitat among subjects (beta diversity, Fig. 1b).” | concepts[1] |
| concept | diversity— “The diversity of microbes within a given body habitat can be defined as the number and abundance distribution of distinct types of organisms” | concepts[2] |
| concept | microbiome— “The uniqueness of each individual’s microbial community thus seems to be stable over time (relative to the population as a whole), which may be another feature of the human microbiome specifically associated with health.” | concepts[3] |
| concept | operational taxonomic units— “For example, the saliva had among the highest median alpha diversities of operational taxonomic units (OTUs, roughly species level classification, see http://hmpdacc.org/HMQCP), but one of the lowest beta diversities—so although each individual’s saliva was ecologically rich, members of the population shared similar organisms.” | concepts[4] |
| concept | body habitat— “The diversity of microbes within a given body habitat can be defined as the number and abundance distribution of distinct types of organisms” | concepts[5] |
| concept | between-subject variation— “Within-subject variation over time was consistently lower than between-subject variation, both in organismal composition and in metabolic function” | concepts[6] |
| concept | healthy— “Adult subjects lacking evidence of disease were recruited based on a lengthy list of exclusion criteria; we will refer to them here as ‘healthy’, as defined by the consortium clinical sampling criteria” | concepts[7] |
| concept | exclusion criteria— “Adult subjects lacking evidence of disease were recruited based on a lengthy list of exclusion criteria; we will refer to them here as ‘healthy’, as defined by the consortium clinical sampling criteria” | concepts[8] |
| concept | effect sizes— “This lower degree of correlation held for most available biometrics (gender, temperature, blood… | concepts[9] |
| concept | internal controls | concepts[10] |
| concept | Western population | concepts[11] |
| claim type | existence — a second reading reaching the same value; recorded: existence | alternatives.claim_type |
| method | metagenomic-cohort-survey — a second reading DIFFERING from the recorded value; recorded: omics-profiling 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. | alternatives.method |
| phenomenon | the structure, function and diversity of the microbial communities of healthy humans across body habitats — a second reading DIFFERING from the recorded value; recorded: wide variation in the microbiota of healthy people, stable within a person and large between people 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. | alternatives.phenomenon |
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