Literature collection
A structured collection of microbiome-related scientific literature, with one claim per study. Entries are not filtered by certainty or consensus—the point is traceability, not authority.
Collection entries
human mouse mixed
| Paper | One-sentence claim | Study type | Limitation | Tags | |
|---|---|---|---|---|---|
| H | Arumugam et al., 2011, Nature | gut-microbiome, enterotypes, bacteroides, prevotella, ruminococcus | |||
| H | Bulygin et al., 2021, bioRxiv | gut-microbiome, enterotypes, dimensionality-reduction, clustering, 16s-rrna, metagenomics, american-gut-project, human-microbiome-project | |||
| H | Bulygin et al., 2023, PeerJ | Enterotype classifications — such as those reported by consumer gut microbiome tests — are likely artificial labels imposed on what is actually a smooth, continuous spectrum of variation; no matter what your test says, your gut microbiome probably doesn't neatly belong to one distinct biological 'type'. | Computational reanalysis (human metagenomics) | This study only addresses whether gut microbiome 'types' are real as discrete categories — it does not mean that the ratio of certain gut bacteria (like Prevotella vs Bacteroides) is useless. Those ratios may still turn out to be meaningful markers for health and diet, even if the hard boundaries between 'types' are not. | gut-microbiome, enterotypes, dimensionality-reduction, clustering, 16s-rrna, metagenomics, american-gut-project, human-microbiome-project |
| H | Costea et al., 2018, Nature Microbiology | gut-microbiome, enterotypes, gradients, clustering | |||
| H | Depommier et al., 2017, Nature Medicine | Pasteurized A. muciniphila supplementation improved insulin sensitivity in overweight adults. | RCT (human) | Small sample; specific preparation and dose; not a consumer stool test endpoint | akkermansia, intervention, metabolism |
| M | Everard et al., 2013, PNAS | Obese mice had lower A. muciniphila abundance, and restoring it improved metabolic markers. | Preclinical (mouse) | Animal model; not direct evidence for human test interpretation | akkermansia, obesity, metabolism |
| H | Human Microbiome Project Consortium, 2012, Nature | Healthy human gut microbiomes are highly variable between individuals but stable within individuals over time. | Observational cohort | 2012 sequencing depth and methods; limited diversity sampling | diversity, baseline, methodology |
| H | Jeffery et al., 2012, Nature Reviews Microbiology | The neat division of gut microbiomes into distinct enterotypes may be an oversimplification — the data more likely reflects a continuous gradient running from Bacteroides-dominated to Prevotella-dominated communities, with no clean boundaries in between. | Expert commentary / narrative review | This paper questions the discreteness of enterotypes but does not itself provide new experimental data — it is a conceptual reappraisal of existing studies, and the authors acknowledge that linking microbiome composition patterns to clinical outcomes remains a worthwhile and open goal, regardless of whether those patterns are gradients or clusters. | gut-microbiome, enterotypes, bacteroides, prevotella, ruminococcus, microbiome-gradients, 16s-rrna, diet, ageing, co-abundance-groups |
| H | Knights et al., 2014, Cell Host & Microbe | gut-microbiome, enterotypes, clustering, longitudinal, methodology | |||
| + | Valdes et al., 2018, BMJ | Diet influences gut microbiome composition, but causal effects on long-term health outcomes remain incompletely defined. | Review | Heterogeneous primary studies; association-heavy field | diet, interpretation, evidence-limits |
One claim per study. Mixed, uncertain, or conflicting findings sit alongside stronger ones; nothing here is ranked or scored.