Literature collection, Microbiome Interpretation

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
?	Belzer et al., 2017, mBio	Akkermansia muciniphila cross-feeds mucin-derived substrates to butyrate producers including Faecalibacterium prausnitzii, the taxa can coexist and support each other ecologically rather than acting as simple opposites.	Co-culture mechanistic study	In vitro co-cultures; relative abundance on consumer reports does not prove cross-feeding activity in vivo	akkermansia, faecalibacterium, cross-feeding, butyrate, synthesis
H	Black et al., 2022, Gut	Network meta-analysis of IBS dietary RCTs ranked low-FODMAP first for global symptom improvement and abdominal bloating/distension vs habitual and several comparator diets.	Network meta-analysis	Mostly short trials; dietitian delivery varies; long-term data limited	bloating, fodmap, ibs, meta-analysis, diet
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	Camilleri et al., 2023, Am J Gastroenterol (ACG constipation guideline)	ACG guidance on chronic idiopathic constipation recommends pathophysiology-based evaluation (transit vs outlet dysfunction) and evidence-supported fibre, osmotic laxatives, and pelvic floor biofeedback rather than unvalidated testing alone.	Guideline	Guideline synthesis; access to manometry and transit tests varies	constipation, motility, guidelines, pelvic-floor
+	Cani et al., 2007, Diabetes	High-fat feeding raises plasma LPS in mice and humans; metabolic endotoxemia via TLR4 signalling links gut barrier permeability to obesity and insulin resistance in models.	Mechanistic human + mouse	Rodent diets and acute human meal challenges; causality in free-living humans incomplete	lps, endotoxemia, metabolic, obesity, barrier
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
H	Duvallet et al., 2017, Nature Communications verified	Re-analysis of 28 case–control 16S studies shows most disease-associated microbiome shifts are shared across conditions, not disease-specific. Alpha diversity falls reliably in diarrhoea and perhaps IBD, but not in obesity or most other diseases. Enrichment of a few pathogens (e.g. CRC) contrasts with depletion of health-associated Clostridiales in IBD; ~51% of genus associations recur in more than one disease.	Meta-analysis	16S amplicon studies only; disease heterogeneity within categories; antibiotic use and symptom overlap (e.g. diarrhoea) confound many associations; genus-level resolution cannot resolve strain-level pathogenic vs commensal roles	alpha-diversity, meta-analysis, dysbiosis, ibd, crc, diarrhea, confounding, methodology, interpretation
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	Ford et al., 2019, Gut (probiotics for IBS network meta-analysis)	Network meta-analysis of probiotics in IBS shows benefit for some endpoints but substantial heterogeneity between strains, no single probiotic class effect.	Meta-analysis	Trial quality varies; strain formulations differ from consumer products	probiotics, ibs, meta-analysis
H	Franzosa et al., 2019, Cell Host & Microbe	Longitudinal metagenomics in adults shows person-specific microbiome signatures that persist over time, supporting individualized baselines rather than one universal healthy template for dysbiosis scoring.	Longitudinal cohort	Relative abundance focus; functional measures add complementary signal	dysbiosis, personalization, longitudinal, interpretation
H	Halmos et al., 2014, Gastroenterology	Crossover trial in IBS: a low-FODMAP diet reduced overall GI symptoms, bloating, pain, and wind vs a typical Australian diet; controls were unaffected.	Randomized crossover feeding trial	Short-term controlled diet; not all real-world FODMAP trials match design	bloating, fodmap, ibs, fermentation, hydrogen
H	Hill et al., 2014, Nat Rev Gastroenterol Hepatol (ISAPP probiotics)	ISAPP consensus defines probiotics as live microorganisms conferring health benefits at adequate doses and stresses that benefits are strain-specific, not genus-level.	Guideline	Consensus definition; does not rate individual commercial products	probiotics, isapp, bifidobacterium, lactobacillus
H	Hooks & O'Malley, 2017, mBio	Commentary arguing that "dysbiosis" is an imprecise ecological descriptor, not a standalone diagnosis, and that microbiome studies need clearer mechanistic hypotheses than deviation from a reference community.	Review	Commentary; does not define vendor scoring algorithms	dysbiosis, interpretation, methodology
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	Imhann et al., 2016, Science	Population cohort links many non-antibiotic drugs, including PPIs, metformin, and laxatives, to characteristic shifts in gut microbiome composition.	Observational cohort	Association not causation; medication indication confounds	medications, ppi, metformin, drug-microbiome
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
M	Johansson et al., 2011, PNAS	Colon mucus is organized into inner and outer MUC2 layers; the inner layer is largely bacteria-free in health and forms a critical physical barrier.	Observational	Mouse model; human mucus architecture broadly similar but not identical	mucus, muc2, intestinal-barrier, colon
H	Knights et al., 2014, Cell Host & Microbe				gut-microbiome, enterotypes, clustering, longitudinal, methodology
H	Lacy et al., 2021, Am J Gastroenterol (ACG IBS guideline)	ACG guidance on IBS management emphasises identifying alarm features, selective diagnostic testing, and evidence-based dietary and pharmacologic options rather than unvalidated microbiome-based protocols.	Guideline	Guideline synthesis; individual patient workup varies by health system	ibs, red-flags, clinical-care, guidelines
+	Langille et al., 2013, Nature Biotechnology	Metagenomic gene content can predict microbial community metabolic profiles using reference genome databases, supporting pathway inference while highlighting database completeness limits.	Methods / validation	Reference-genome-dependent; human stool validation subset only	metagenomics, pathways, functional-profiling, prediction
H	Lopez-Siles et al., 2018, Front Cell Infect Microbiol	Akkermansia muciniphila and Faecalibacterium prausnitzii co-occur in mucosal microbiota; both can be altered in IBD but are not mutually exclusive markers of health vs disease in individuals.	Observational (mucosal biopsies)	IBD cohort; stool reports may not reflect mucosal co-occurrence	akkermansia, faecalibacterium, ibd, co-occurrence, synthesis
H	Louis & Flint, 2017, Environ Microbiol	Reviews how human colonic bacteria form propionate and butyrate via distinct pathways, including acetate-dependent butyrate production requiring cross-feeding partners.	Review	Pathway focus; does not quantify individual SCFA output from consumer tests	scfa, butyrate, propionate, cross-feeding
H	Lozupone et al., 2012, Nature	Gut microbial communities vary widely between individuals and over time; alpha diversity (within-sample richness/evenness) must be interpreted with ecological context including diet, age, and disease state.	Review	Pre–shotgun-metagenomics era; conceptual framework more than clinical thresholds	alpha-diversity, ecology, beta-diversity, stability
H	Lozupone et al., 2013, Genome Research	Cross-study meta-analysis shows technical variables (16S region, extraction, platform) can bias observed alpha diversity as much as or more than some biological effects.	Meta-analysis	2013 methods; still relevant for interpreting single-lab consumer scores	alpha-diversity, meta-analysis, methodology, 16s
H	Major et al., 2017, Gastroenterology	IBS patients and healthy controls produce similar colonic gas after inulin or fructose challenges; symptom differences reflect colonic hypersensitivity to distension, not excess fermentation alone.	Randomized crossover (MRI + breath hydrogen)	Small cohort; challenge drinks not full dietary patterns	bloating, fodmap, visceral-hypersensitivity, fermentation, ibs
H	Marshall et al., 2019, Nutrients	Systematic review estimates roughly 7–15% of post-gastroenteritis patients develop IBS at 3–12 months, with severity and psychological factors influencing risk.	Systematic review	Heterogeneous primary studies and pathogen definitions	pi-ibs, post-infectious, ibs, gastroenteritis
H	Massier et al., 2021, Gut	Widely used commercial zonulin ELISAs may not measure prehaptoglobin-2 and correlate poorly with gold-standard permeability tests, undermining many ELISA-based leaky-gut claims.	Review	Focuses on assay validity; does not negate all permeability biology	zonulin, intestinal-barrier, permeability, biomarker
H	Moayyedi et al., 2014, Am J Gastroenterol	Meta-analysis of fiber supplementation in IBS found soluble gel-forming fiber (psyllium) beneficial for global symptoms; insoluble wheat bran did not show significant benefit.	Meta-analysis	Heterogeneous trials; fiber types and doses varied	fiber, ibs, psyllium, meta-analysis
H	Oliphant & Allen-Vercoe, 2019, Nat Rev Microbiol	Cross-feeding between gut microbes, acetate and lactate donors feeding butyrate and propionate producers, explains why single-taxon interventions often fail to shift SCFA profiles predictably.	Review	Mechanistic review; human dose-response varies by community	cross-feeding, scfa, butyrate, bifidobacterium
H	Palleja et al., 2018, Nature Microbiology	In healthy adults, common antibiotics acutely reduce gut microbiome diversity; species richness often returns toward baseline within weeks to months, but compositional and functional differences can persist for at least six months.	Longitudinal intervention	Healthy volunteers, not patients; antibiotic regimens differ from all clinical use	alpha-diversity, antibiotics, recovery, longitudinal
H	Pimentel et al., 2014, Gastroenterology	Methane on breath testing associates with constipation-predominant IBS and slower transit; methanogenesis acts as a hydrogen sink altering colonic fermentation.	Review / mechanistic synthesis	Breath-test populations; not all constipation is methane-driven	methane, ibs-c, constipation, breath-testing, methanogens
H	Rinninella et al., 2019, Microorganisms	There is no single "healthy" gut microbiome template; diversity and composition vary widely among asymptomatic people by diet, geography, and lifestyle.	Review	Narrative review; does not define consumer-test optimal ranges	alpha-diversity, dysbiosis, healthy-microbiome, interpretation
M	Schroeder et al., 2018, Cell Host & Microbe	In mice, low microbiota-accessible carbohydrates erode colonic mucus; dietary fiber or Bifidobacterium supplementation protected mucus thickness.	Intervention	Mouse diet model; human dose and community differ	fiber, mucus, bifidobacterium, intestinal-barrier, mac
H	Sokol et al., 2008, PNAS	Faecalibacterium prausnitzii produces anti-inflammatory metabolites and is reduced in some IBD cohorts, an association, not a diagnostic threshold for individuals.	Observational	Cohort associations; abundance varies with diet and sequencing method	faecalibacterium, ibd, inflammation, scfa
H	Sonnenburg & Sonnenburg, 2014, Cell Metabolism	Diets low in microbiota-accessible carbohydrates deplete fiber-degrading taxa and reduce fermentation capacity, framing the long-term cost of low-fiber Western diets.	Review	Narrative synthesis; MAC availability is person-specific	fiber, mac, dysbiosis, scfa
H	Sperber et al., 2017, Neurogastroenterol Motil (Rome IV overview)	Rome IV defines functional GI disorders by symptom-based criteria and distinguishes them from organic disease when alarm features are absent or adequately investigated.	Guideline	Symptom-based criteria; does not replace endoscopy or serology when indicated	rome-iv, ibs, functional-gut, red-flags
H	Spiller & Garsed, 2009, Postgrad Med J	Post-infectious IBS involves persistent motility, immune, and sensory changes after gastroenteritis; many patients improve over 12–24 months without targeted microbiome therapy.	Review	Mechanistic synthesis; treatment trials limited at time of publication	pi-ibs, post-infectious, motility, mechanisms
H	Su et al., 2020, Gastroenterology (AGA probiotics guideline)	AGA guidance provides conditional recommendations for specific probiotic strains in selected indications and cautions against indiscriminate use.	Guideline	Conditional recommendations; evidence base evolving	probiotics, guidelines, aga
H	Suez et al., 2018, Cell	After antibiotics, autologous fecal microbiota transplant accelerated gut microbiome and mucosal gene expression reconstitution in this trial, whereas a multi-strain probiotic regimen delayed full recovery compared with spontaneous recovery.	RCT	Single trial design; probiotic formulation and timing may not generalize to all products	antibiotics, probiotics, fmt, recovery, post-antibiotic
+	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
H	Villoria et al., 2011, Am J Gastroenterol	Visible abdominal distension in functional gut disorders often reflects abdominophrenic dyssynergia (diaphragmatic descent + abdominal wall relaxation), not necessarily increased intra-abdominal gas volume.	Physiology / imaging cohort	Specialist centre; not all bloating is APD	bloating, distension, abdominophrenic-dyssynergia, motility
+	Windey et al., 2012, Molecular Nutrition & Food Research	Colonic protein fermentation yields branched-chain fatty acids, ammonia, and phenolic compounds distinct from saccharolytic SCFA production on fermentable carbohydrate.	Review	Mostly in vitro and animal dose data; human clinical thresholds sparse	protein, bcfas, fermentation, scfa

One claim per study. Mixed, uncertain, or conflicting findings sit alongside stronger ones; nothing here is ranked or scored.