V. 2 References
This list gathers together the book's external evidence base: the peer-reviewed, citable literature behind the clinical claims. The main text of the book is written in patient-friendly language and does not replace these sources – here the interested reader (and the treating physician) will find the foundation.
References
[1] Sender R, Fuchs S, Milo R. Are We Really Vastly Outnumbered? Revisiting the Ratio of Bacterial to Host Cells in Humans. Cell. 2016. Link
Sender, Fuchs and Milo recalculated the widely cited 10:1 bacteria-to-human-cell ratio. Using updated data for a 70 kg reference man, they estimated about 3.8×10^13 bacteria versus about 3.0×10^13 human cells — a ratio close to 1:1 rather than 10:1, which a single defecation can shift in favour of human cells. The paper corrected a decades-old myth in microbiome science.
[2] Qin J, Li R, Raes J et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature. 2010. Link
Illumina-based metagenomic sequencing of faecal samples from 124 European individuals (576.7 Gb of sequence) yielded a catalogue of 3.3 million non-redundant microbial genes, approximately 150-fold larger than the human gene complement. Genes were largely shared across individuals, with over 99\% bacterial origin. The cohort harboured an estimated 1,000–1,150 prevalent bacterial species, each individual carrying at least 160 species. The study defines a minimal gut metagenome and a minimal gut bacterial genome based on functions present in all individuals and most bacteria. Findings establish a foundational reference for the genetic potential of the human gut microbiota.
[3] Turnbaugh PJ, Ley RE, Hamady M, Fraser-Liggett CM, Knight R, Gordon JI. The Human Microbiome Project. Nature. 2007. Link
Strategic framework outlining the Human Microbiome Project's approach to characterizing the microbial components of the human genetic and metabolic landscape. The initiative aims to establish how microbiota contribute to normal physiology and predisposition to disease. Serves as the foundational programmatic statement for large-scale population-level microbiome research.
[4] Lynch SV, Pedersen O. The Human Intestinal Microbiome in Health and Disease. N Engl J Med. 2016. Link
Lynch and Pedersen provide a comprehensive New England Journal of Medicine review on the human intestinal microbiome in health and disease. They summarize the composition and stability of the adult microbiota, the major bacterial phyla (Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria), and the impact of host genetics, diet, antibiotics and birth mode on community structure. Mechanistic sections cover short-chain fatty acid production, bile acid metabolism, immune education, and barrier maintenance. Disease associations are reviewed for IBD, obesity, type 2 diabetes, atherosclerosis, allergy, and Clostridioides difficile infection. The article frames the microbiome as a tractable therapeutic target via diet, prebiotics, probiotics and fecal microbiota transplantation.
[5] Thaiss CA, Zmora N, Levy M, Elinav E. The microbiome and innate immunity. Nature. 2016. Link
Mechanistic review of how the intestinal microbiome integrates environmental inputs (diet) with genetic and immune signals to influence host metabolism, immunity, and infection response. Haematopoietic and non-haematopoietic innate immune cells at the host–microbiome interface sense microorganisms and their metabolites, translating these signals into physiological responses and microbial ecology regulation. Disruption of this innate immune–microbiota communication is implicated in complex disease pathogenesis. The review frames the microbiome as a central signalling hub coordinating host defence and homeostasis.
[6] Lozupone CA, Stombaugh JI, Gordon JI, Jansson JK, Knight R. Diversity, stability and resilience of the human gut microbiota. Nature. 2012. Link
Conceptual review describing the human gut as a complex ecological community whose collective metabolic activities and host interactions influence physiology and disease susceptibility. The gut microbiota is highly diverse, varies between individuals, and fluctuates over time, particularly during disease and early development. The authors argue that an ecological framework — addressing diversity, stability, and resilience — is necessary for designing effective microbiota-targeted therapies. The paper provides a theoretical foundation for clinical microbiome modulation strategies.
[7] van Nood E, Vrieze A, Nieuwdorp M et al. Duodenal infusion of donor feces for recurrent Clostridium difficile. N Engl J Med. 2013. Link
Open-label RCT in patients with recurrent C. difficile infection comparing duodenal donor faeces infusion (after short vancomycin + bowel lavage) with standard 14-day vancomycin, with or without bowel lavage. The primary endpoint was diarrhoea resolution without relapse at 10 weeks. The trial was stopped early at interim analysis: 13/16 patients (81\%) in the FMT arm achieved resolution after a single infusion, substantially exceeding both vancomycin arms. Establishes FMT as superior to antibiotic monotherapy for recurrent CDI and provides the landmark evidence base for FMT clinical translation.
[8] Ianiro G, Punčochář M, Karcher N et al. Variability of strain engraftment and predictability of microbiome composition after fecal microbiota transplantation across different diseases. Nat Med. 2022. Link
Integrated shotgun metagenomic meta-analysis of 226 donor–recipient triads across eight disease types examining microbial engraftment dynamics after FMT. Higher donor strain engraftment was significantly associated with clinical success (P=0.017). Engraftment was greater with multi-route delivery (capsule plus colonoscopy) and in antibiotic-treated recipients with infectious disease versus antibiotic-naïve patients with noncommunicable disease. Bacteroidetes and Actinobacteria (including Bifidobacteria) showed higher engraftment than most Firmicutes. A cross-dataset machine-learning model predicted post-FMT species presence with AUROC 0.77.
[9] Peery AF, Kelly CR, Kao D et al. AGA Clinical Practice Guideline on Fecal Microbiota-Based Therapies for Select Gastrointestinal Diseases. Gastroenterology. 2024. Link
AGA clinical practice guideline using the GRADE framework to address fecal microbiota-based therapies (conventional FMT, fecal microbiota live-jslm, fecal microbiota spores live-brpk) in adults with recurrent or severe-to-fulminant Clostridioides difficile infection, IBD/pouchitis, and IBS. The panel issued 7 recommendations. In immunocompetent adults with recurrent CDI, the AGA suggests selective use of fecal microbiota-based therapies after standard-of-care antibiotics to prevent further recurrence. Provides framework guidance integrating FDA-approved products with conventional FMT.
[10] Wild, C. P. Complementing the Genome with an 'Exposome': The Outstanding Challenge of Environmental Exposure Measurement in Molecular Epidemiology. Cancer Epidemiol Biomarkers Prev. 2005. Link
Wild's seminal 2005 Cancer Epidemiology, Biomarkers and Prevention commentary introduces the concept of the 'exposome' to complement genomic measurement in molecular epidemiology. He argues that lifetime environmental exposures, including diet, lifestyle, infections, pollutants and endogenous processes, are as important as the genome in determining disease risk, but are systematically under-measured. The article calls for technologies and study designs capable of capturing exposures across the life course with sensitivity comparable to high-throughput genomics. Wild outlines internal, specific-external and general-external exposome domains. The concept has since shaped large cohort studies and biomarker-based exposure assessment, including microbiome-related work.
[11] Rappaport SM, Smith MT. Epidemiology. Environment and Disease Risks. Science. 2010. Link
Conceptual statement arguing that a new epidemiological paradigm is required to assess how lifetime cumulative exposure to environmental factors affects chronic disease risk. Calls for systematic exposome-level analysis beyond single-exposure designs.
[12] Zmora N, Zilberman-Schapira G, Suez J et al. Personalized Gut Mucosal Colonization Resistance to Empiric Probiotics Is Associated with Unique Host and Microbiome Features. Cell. 2018. Link
Sequential invasive multi-omics profiling of the mucosal-associated gastrointestinal microbiome in mice and humans during consumption of an 11-strain probiotic versus placebo showed that probiotics remained viable through gastrointestinal passage but encountered marked mucosal colonization resistance in colonized hosts. Humans displayed person-, region- and strain-specific mucosal colonization patterns predictable from baseline host and microbiome features, while stool probiotic presence was uninformative. Stool microbiome correlated only partially with mucosal microbiome. The findings challenge the empiric use of probiotics in healthy individuals.
[13] Sonnenburg JL, Gardner E. Microbiome tests: Ignore the hype. Science. 2016. Link
Sonnenburg and Gardner's Science commentary cautions against the marketing hype around direct-to-consumer microbiome tests in 2016. They argue that while gut microbiota research is advancing rapidly, commercial 16S rRNA profiling cannot yet deliver clinically actionable personalised advice because reference 'healthy' microbiomes are not defined, longitudinal data are sparse, and causal links between taxa and outcomes are largely unproven. The authors emphasise inter-individual variability, methodological differences between platforms, and the gap between association and intervention evidence. They recommend that clinicians treat such reports with skepticism and call for regulatory oversight, standardised methodology, and longitudinal cohort studies before personalised microbiome diagnostics enter routine care.
[14] Whelan K, Bancil AS, Lindsay JO, Chassaing B. Ultra-processed foods and food additives in gut health and disease. Nature Reviews Gastroenterology \& Hepatology. 2024. Link
Critical review of how ultra-processed foods (UPFs) and the additives they contain affect gut health. The link between UPF-rich diets and gut disease — inflammatory bowel disease, colorectal cancer, irritable bowel syndrome — rests mainly on observational epidemiology, whereas the effects of individual additives (emulsifiers, sweeteners, colours, micro- and nanoparticles) come largely from in vitro and animal work showing impacts on the gut microbiome, intestinal permeability and inflammation. The authors stress that human intervention studies remain scarce, so the direction of the association is well supported while the size of the effect is still uncertain.
[15] Jovel J, Patterson J, Wang W et al. Characterization of the human gut microbiome using 16S or WGS: a comparative study on the outcome of different analysis pipelines. Front Microbiol. 2016. Link
Jovel and colleagues compare 16S rRNA gene sequencing and whole-genome shotgun (WGS) metagenomics on the same human gut samples to assess analytical pipeline impact. They demonstrate that taxonomic resolution, observed diversity and the reproducibility of differential abundance calls depend strongly on the choice of variable region, reference database, OTU/ASV clustering approach and bioinformatic pipeline. WGS recovered more species-level and functional information than 16S, but at higher cost. The authors benchmark QIIME, mothur, MG-RAST and assembly-based pipelines, showing meaningful disagreement between them. They recommend transparent reporting of every analytical step and caution against over-interpreting single-pipeline microbiome results.
[16] Sinha R, Abu-Ali G, Vogtmann E et al. Assessment of Variation in Microbial Community Amplicon Sequencing by the Microbiome Quality Control (MBQC) Project Consortium. Nature Biotechnology. 2017. Link
The Microbiome Quality Control (MBQC) baseline study assessed taxonomic profiling variability across 15 laboratories and 9 bioinformatics protocols using blinded stool, chemostat and artificial community specimens. Variability depended most on biospecimen type and origin, followed by DNA extraction, sample handling environment and bioinformatics pipeline. Artificial community analyses revealed quantitative differences in extraction efficiency and bioinformatic classification. The findings highlight the need for standardisation to enable meta-analysis of population-scale microbiome studies.
[17] Salter SJ, Cox MJ, Turek EM et al. Reagent and Laboratory Contamination Can Critically Impact Sequence-Based Microbiome Analyses. BMC Biology. 2014. Link
Contaminating DNA is shown to be ubiquitous in commonly used DNA extraction kits and laboratory reagents, varying greatly in composition between different kits and batches. This contamination critically distorts results from low-microbial-biomass samples in both 16S rRNA gene surveys and shotgun metagenomics. The authors provide an extensive list of potential contaminating genera and mitigation guidelines, and recommend caution when applying sequence-based techniques to low-biomass microbial environments.
[18] Gloor GB, Macklaim JM, Pawlowsky-Glahn V, Egozcue JJ. Microbiome datasets are compositional: and this is not optional. Front Microbiol. 2017. Link
Microbiome datasets generated by high-throughput sequencing of 16S rRNA amplicons, metagenomes or metatranscriptomes are inherently compositional because the instrument imposes an arbitrary total. The review explains the pathologies that arise when compositional data are analysed with non-compositional methods and provides guidance for applying compositional data analysis throughout microbiome study workflows. The compositional framework is presented as essential, not optional, for valid inference.
[19] Costea PI, Zeller G, Sunagawa S et al. Towards Standards for Human Fecal Sample Processing in Metagenomic Studies. Nature Biotechnology. 2017. Link
21 representative DNA extraction protocols were tested on identical faecal samples and compared with library preparation and storage effects against biological within-individual variation. DNA extraction had the largest technical effect on metagenomic outcomes. Protocols were ranked by DNA quantity, quality, and biases in community diversity and Gram-positive/Gram-negative ratio. The authors recommend a standardised, transferable DNA extraction method validated using a mock community of known composition for human faecal metagenomic studies.
[20] Lewis SJ, Heaton KW. Stool form scale as a useful guide to intestinal transit time. Scandinavian Journal of Gastroenterology. 1997. Link
The original validation of the Bristol Stool Form Scale. Whole-gut transit time was measured with radio-opaque marker pellets in 66 volunteers, who kept a diary of stool form on a 7-point scale and of defecation frequency. Transit time correlated most closely with stool form (r = -0.54), more strongly than with stool frequency or stool output. When transit time was altered with senna and with loperamide, stool form tracked the change (r = -0.65). Conclusion: recording stool form is a simple and responsive way to monitor change in bowel function — which is why it is suitable for the patient's own diary.
[21] McLaren MR, Willis AD, Callahan BJ. Consistent and Correctable Bias in Metagenomic Sequencing Experiments. eLife. 2019. Link
Marker-gene and metagenomic sequencing measurements are systematically biased toward detecting certain taxa over others, making taxon abundances generated by different protocols quantitatively incomparable and prone to spurious biological conclusions. The authors propose a mathematical model of experimental bias based on real-experiment properties and validate it with 16S rRNA and shotgun metagenomics data from defined bacterial communities. The model fits experimental data better than previous, more complex frameworks and offers a path to correcting bias.
[22] Sczyrba A, Hofmann P, Belmann P et al. Critical Assessment of Metagenome Interpretation -- A Benchmark of Metagenomics Software. Nature Methods. 2017. Link
The Critical Assessment of Metagenome Interpretation (CAMI) challenge benchmarked metagenomics software using highly complex realistic datasets from ~700 newly sequenced microorganisms and ~600 novel viruses and plasmids. Assembly and binning performed well for species represented by individual genomes but were substantially degraded by closely related strains. Taxonomic profiling and binning were proficient at high taxonomic ranks with a marked drop below family level. Parameter settings strongly affected performance, underscoring the importance of reproducibility. CAMI provides a roadmap for software selection.
[23] Vandeputte D, Kathagen G, D'hoe K et al. Quantitative Microbiome Profiling Links Gut Community Variation to Microbial Load. Nature. 2017. Link
Conventional sequencing-based faecal microbiota analyses provide only relative abundances, hampering the link between microbiome features and quantitative host parameters when microbial load varies between samples. The authors argue that relative profiling can mask altered total microbiota abundance as a key disease-associated signal and call for quantitative microbiome profiling that pairs relative composition with cell-density counts to enable genuine characterisation of host-microbiota interactions.
[24] Sonnenburg JL, Bäckhed F. Diet–microbiota interactions as moderators of human metabolism. Nature. 2016. Link
Review of mechanisms linking the gut microbiota to obesity and type 2 diabetes drawing on translational animal models and human studies. The microbiota emerges as a mediator of dietary impact on host metabolic status, with growing efforts to establish causal relationships in people and develop therapeutic interventions including personalised nutrition.
[25] Zierer J, Jackson MA, Kastenmüller G et al. The fecal metabolome as a functional readout of the gut microbiome. Nat Genet. 2018. Link
Comprehensive analysis of 1,116 metabolites from 786 individuals in the TwinsUK population-based twin study showed that the faecal metabolome is only modestly heritable (H2 = 17.9%), with one replicated locus at NAT2 associated with faecal metabolic traits. The faecal metabolome largely reflects gut microbial composition, explaining on average 67.7% (+/-18.8%) of its variance, and is strongly associated with visceral fat mass. Findings position faecal metabolomics as a functional readout linking microbiome composition to abdominal obesity.
[26] Dahl WJ, Zhu H, Guan LL. Fecal metabolomics reveals diet-dependent microbiome changes. Curr Dev Nutr. 2020. Link
Dahl, Zhu and Guan summarize fecal metabolomics findings linking diet to microbiome-driven metabolic changes in this Current Developments in Nutrition conference abstract. They report that dietary intake, particularly carbohydrate quality and fiber type, alters fecal concentrations of short-chain fatty acids, bile acids and amino-acid–derived metabolites, with concomitant shifts in microbial composition. The work supports the view that fecal metabolomics is a useful intermediate readout connecting dietary intervention to host-relevant microbial outputs. Mechanistic interpretation focuses on saccharolytic versus proteolytic fermentation balance. The authors call for standardised metabolomic methods to compare across diet-microbiome trials.
[31] Moayyedi P, Surette MG, Kim PT et al. Fecal Microbiota Transplantation Induces Remission in Patients With Active Ulcerative Colitis in a Randomized Controlled Trial. Gastroenterology. 2015. Link
Placebo-controlled randomized trial in patients with active ulcerative colitis without infectious diarrhoea. Participants were randomized to FMT (50 mL enema from healthy anonymous donors, n=38) or placebo water enema (n=37) once weekly for 6 weeks; patients, clinicians, and investigators were blinded. The trial assessed safety and efficacy of FMT for inducing remission in UC, demonstrating that FMT can produce clinical and endoscopic improvement beyond placebo in a subset of patients. Findings support FMT as a microbiota-modulating option in active UC while highlighting variable individual response.
[34] Smillie CS, Sauk J, Gevers D et al. Strain tracking reveals the determinants of bacterial engraftment in the human gut following fecal microbiota transplantation. Cell Host Microbe. 2018. Link
Strain-level analysis of FMT for recurrent Clostridium difficile infection introducing Strain Finder, a method for inferring strain genotypes and tracking engraftment longitudinally. A statistical model predicted species-level engraftment largely from donor abundance and pre-FMT recipient phylogeny. Donor strains within a species engrafted in an all-or-nothing manner, and previously undetected strains frequently colonized recipients. The work defines the determinants of bacterial engraftment in human FMT and provides a framework for predicting graft outcomes.
[36] Cammarota G, Ianiro G, Tilg H et al. European consensus conference on faecal microbiota transplantation in clinical practice. Gut. 2017. Link
European consensus conference developing evidence-based recommendations on FMT for clinical practice, with 28 experts from 10 countries collaborating in working groups. Statements were generated through evidence-based review, evaluated electronically via a Delphi process, and finalized in a plenary consensus session. Recommendations cover FMT indications, donor selection, faecal material preparation, clinical management, faecal delivery, and minimum requirements for establishing an FMT centre. Provides the European standardization framework for safe and governed FMT delivery.
[44] Zipursky JS, Sidorsky TI, Freedman CA, Sidorsky MN, Kirkland KB. Patient attitudes toward the use of fecal microbiota transplantation in the treatment of recurrent Clostridium difficile infection. Clin Infect Dis. 2012. Link
Structured survey of 192 patients (48\% response rate) assessing willingness to consider FMT for recurrent CDI. Seventy percent of respondents were female and 59\% were over 49 years. When given efficacy data only, 162 respondents (85\%) chose FMT and 29 (15\%) chose antibiotics alone. After learning of the faecal nature of FMT, 16 respondents switched to antibiotics, but the overall FMT preference remained essentially unchanged (154/192, 81\%; P=0.15). The findings refute the assumption that aesthetic concerns drive low FMT uptake and support patient willingness when adequately informed.
[45] Kao D, Roach B, Silva M et al. Effect of Oral Capsule– vs Colonoscopy-Delivered Fecal Microbiota Transplantation on Recurrent Clostridium difficile Infection: A Randomized Clinical Trial. JAMA. 2017. Link
Noninferiority randomized trial in 116 adults with recurrent CDI across three Canadian academic centres comparing oral capsule FMT with colonoscopy-delivered FMT (enrolment 2014–2016; noninferiority margin 15\%). The study tested whether less invasive capsule delivery matches colonoscopy in preventing further CDI recurrence. Results support clinical equivalence between routes, enabling broader and lower-burden access to FMT for recurrent CDI.
[50] Marcella C, Cui B, Kelly CR, Ianiro G, Cammarota G, Zhang F. Systematic review: the global incidence of faecal microbiota transplantation-related adverse events from 2000 to 2020. Aliment Pharmacol Ther. 2021. Link
Systematic review of FMT safety summarizing adverse events (AEs) over 20 years from 129 studies including 4,241 patients and 5,688 FMT courses (search of EMBASE, MEDLINE, Cochrane, CNKI, Wanfang from 2000 to 2020). AEs were classified as delivery-related or microbiota-related. The review provides the largest aggregate FMT safety dataset to date and supports the overall favourable safety profile of FMT for recurrent CDI, while flagging that complications may be under-reported in the literature.
[59] Thaiss CA, Zeevi D, Levy M et al. Transkingdom control of microbiota diurnal oscillations promotes metabolic homeostasis. Cell. 2014. Link
Mechanistic study in mice and humans demonstrating that the gut microbiota exhibits diurnal oscillations driven by feeding rhythms, producing time-specific compositional and functional profiles. Disruption of host molecular clock components or jet lag caused aberrant microbiota oscillations and dysbiosis through impaired feeding rhythmicity. Jet-lag-induced dysbiosis in both species promoted glucose intolerance and obesity that were transferable by FMT to germ-free recipients. Identifies microbiota–host circadian cross-regulation as a metabolic disease mechanism.
[60] Benedict C, Vogel H, Jonas W et al. Gut microbiota and glucometabolic alterations in response to recurrent partial sleep deprivation in normal-weight young individuals. Mol Metab. 2016. Link
Randomized within-subject crossover study in 9 normal-weight men comparing two nights of partial sleep deprivation (PSD; 02:45–07:00) with two nights of normal sleep (22:30–07:00) under standardized in-lab meal and exercise conditions. Faecal samples were collected and oral glucose tolerance was tested. The study assessed whether short-term sleep loss alters gut microbiota composition and metabolic function, providing early human evidence linking sleep restriction to acute microbiota shifts and insulin resistance.
[71] Hamer HM, Jonkers D, Venema K, Vanhoutvin S, Troost FJ, Brummer RJ. The role of butyrate on colonic function. Aliment Pharmacol Ther. 2008. Link
Narrative review summarizing the bioactivity of butyrate — a SCFA produced by colonic microbial fermentation of dietary fibre — and its mechanisms in human colonic function. Butyrate is the primary energy source for colonocytes and modulates inflammation, carcinogenesis, mucosal barrier integrity, oxidative stress, permeability, and satiety. The review consolidates evidence on butyrate as a central effector of colonic homeostasis and a target for dietary interventions in colonic disease.
[106] Wastyk HC, Fragiadakis GK, Perelman D et al. Gut-microbiota-targeted diets modulate human immune status. Cell. 2021. Link
17-week randomized prospective trial (n=18/arm) in healthy adults comparing high-fibre versus high-fermented-food diets with multi-omics microbiome and host immune profiling. The high-fibre diet increased microbiome-encoded glycan-degrading CAZymes despite stable diversity. The high-fermented-food diet increased microbiome diversity and decreased multiple inflammatory markers. Findings demonstrate diet-specific microbiome–immune effects and support fermented foods as a strong, diversity-promoting modulator of the gut–immune axis.
[107] Marco ML, Heeney D, Binda S et al. Health benefits of fermented foods: microbiota and beyond. Curr Opin Biotechnol. 2017. Link
Review of fermented foods, among the first processed food products consumed by humans (yogurt, cultured milk, wine, beer, sauerkraut, kimchi, fermented sausage). Originally valued for shelf life and palatability, fermented foods are now recognized as having enhanced nutritional and functional properties through substrate transformation and bioactive end-product formation. Many fermented foods contain living microorganisms with potential health effects. The review consolidates fermented foods as a microbiome-relevant dietary category.
[120] Calder, P. C. Omega-3 fatty acids and inflammatory processes: from molecules to man. Biochem Soc Trans. 2017. Link
Review of omega-6 and omega-3 fatty acid roles in inflammation. EPA and DHA from oily fish or fish-oil supplements partly inhibit leucocyte chemotaxis, adhesion molecule expression, leucocyte-endothelial interactions, and the production of arachidonic-acid-derived eicosanoids and pro-inflammatory cytokines. EPA-derived eicosanoids are typically less potent than those from arachidonic acid, and EPA/DHA give rise to anti-inflammatory and inflammation-resolving mediators (resolvins, protectins, maresins), supporting their use in inflammatory conditions.
[122] Costantini L, Molinari R, Farinon B, Merendino N. Impact of Omega-3 Fatty Acids on the Gut Microbiota. Int J Mol Sci. 2017. Link
Long-term dietary habits shape host-specific gut microbiota, but dietary fat effects are less well characterised than those of carbohydrates. The few adult human omega-3 PUFA supplementation studies show consistent changes: decreased Faecalibacterium, increased Bacteroidetes and butyrate-producing Lachnospiraceae. Because dysbiosis of these taxa occurs in inflammatory bowel disease, omega-3 PUFAs may exert a beneficial effect by restoring microbial composition and increasing anti-inflammatory short-chain fatty acid production.
[154] Suez J, Korem T, Zeevi D et al. Artificial sweeteners induce glucose intolerance by altering the gut microbiota. Nature. 2014. Link
Non-caloric artificial sweeteners (NAS) induced glucose intolerance in mice and humans via compositional and functional changes in the gut microbiota. Antibiotic treatment abrogated the deleterious metabolic effects, and germ-free mice receiving faecal transplants from NAS-consuming mice (or NAS-incubated microbiota) developed glucose intolerance. NAS-altered microbial metabolic pathways were linked to metabolic disease susceptibility, with similar dysbiosis and glucose intolerance demonstrated in healthy human subjects. The findings call for reassessment of widespread NAS use.
[159] Chassaing B, Koren O, Goodrich JK et al. Dietary emulsifiers impact the mouse gut microbiota promoting colitis and metabolic syndrome. Nature. 2015. Link
In wild-type mice, relatively low concentrations of two ubiquitous emulsifiers — carboxymethylcellulose (CMC) and polysorbate-80 (P80) — induced low-grade inflammation and obesity/metabolic syndrome, and promoted robust colitis in mice predisposed to it. The mucus-protective barrier and microbiota composition were disrupted. The findings implicate dietary emulsifiers, ubiquitous components of processed foods, in the post-mid-20th-century rise in inflammatory bowel disease and metabolic disorders.
[160] Chassaing B, Van de Wiele T, De Bodt J, Marzorati M, Gewirtz AT. Dietary emulsifiers directly alter human microbiota composition and gene expression ex vivo potentiating intestinal inflammation. Gut. 2017. Link
Using the M-SHIME ex vivo human microbiota model that excludes host inflammation as a confounder, both carboxymethylcellulose (CMC) and polysorbate 80 (P80) acted directly on the human microbiota to increase its pro-inflammatory potential, evidenced by elevated bioactive flagellin. The CMC-induced flagellin rise was rapid (1 day) and driven by altered microbial gene expression. The findings establish that these dietary emulsifiers exert direct, host-independent pro-inflammatory effects on the human gut microbiota.
[161] Desai MS, Seekatz AM, Koropatkin NM et al. A dietary fiber-deprived gut microbiota degrades the colonic mucus barrier and enhances pathogen susceptibility. Cell. 2016. Link
In gnotobiotic mice colonised with a synthetic human gut microbiota, chronic or intermittent dietary fibre deficiency caused the microbiota to use host-secreted mucus glycoproteins as a nutrient source, eroding the colonic mucus barrier. Combined fibre deprivation and a mucus-eroding microbiota allowed greater epithelial access and lethal colitis by the mucosal pathogen Citrobacter rodentium. The findings link diet, microbiome and intestinal barrier dysfunction and identify dietary fibre as a key barrier-protective factor exploitable for therapeutic strategies.
[162] Suez J, Cohen Y, Valdés-Mas R et al. Personalized microbiome-driven effects of non-nutritive sweeteners on human glucose tolerance. Cell. 2022. Link
Randomised controlled trial in 120 healthy adults receiving saccharin, sucralose, aspartame or stevia (in doses below acceptable daily intake) versus glucose-vehicle or no supplement for 2 weeks. All four non-nutritive sweeteners distinctly altered the stool/oral microbiome and plasma metabolome; saccharin and sucralose significantly impaired glycaemic responses. Gnotobiotic mice colonised with microbiomes from top and bottom human responders reproduced donor-specific glycaemic responses, demonstrating that non-nutritive sweeteners can induce person-specific, microbiome-dependent glycaemic alterations.
[172] Halmos EP, Power VA, Shepherd SJ, Gibson PR, Muir JG. A diet low in FODMAPs reduces symptoms of irritable bowel syndrome. Gastroenterology. 2014. Link
Randomised single-blind cross-over trial in 30 IBS patients and 8 controls compared a low-FODMAP diet (<0.5 g/meal) with a typical Australian diet for 21 days each (>=21-day washout). Almost all food was provided. The low-FODMAP arm produced significantly greater reduction in IBS symptoms measured on 0-100 mm visual analogue scales, supporting the low-FODMAP diet as an effective intervention for symptom control in IBS compared with a standard Western diet.
[191] Liang X, FitzGerald GA. Timing the Microbes: The Circadian Rhythm of the Gut Microbiome. J Biol Rhythms. 2017. Link
Review of circadian organisation in the gut microbiome. The mammalian circadian system (master clock and peripheral clocks) coordinates biological processes in response to external cues like the light-dark cycle, but prokaryote chronobiology — outside cyanobacteria — is poorly understood. The review summarises evidence of time-of-day-dependent compositional and functional structure within the gut microbiota, host regulation of these oscillations, and the reciprocal influence of the gut microbiome on host circadian timing.
[192] Chaix A, Zarrinpar A, Miu P, Panda S. Time-restricted feeding is a preventative and therapeutic intervention against diverse nutritional challenges. Cell Metab. 2014. Link
Time-restricted feeding (TRF; 8-9 h food access in the active phase) was tested in mice under diverse obesogenic diets. TRF attenuated metabolic disease across a range of obesogenic diets, with benefits proportional to fasting duration. Protective effects persisted even when weekend ad libitum access interrupted TRF — a regimen relevant to human lifestyle. TRF also stabilised and reversed metabolic disease in mice with preexisting obesity and type 2 diabetes, supporting TRF as both a preventative and therapeutic strategy.
[193] Zarrinpar A, Chaix A, Yooseph S, Panda S. Diet and feeding pattern affect the diurnal dynamics of the gut microbiome. Cell Metab. 2014. Link
The gut microbiome exhibits daily cyclical compositional fluctuations driven by the feeding/fasting cycle. Diet-induced obesity dampens the daily feeding/fasting rhythm and diminishes microbiota cyclical fluctuations. Time-restricted feeding (TRF), in which feeding is consolidated to the nocturnal phase in mice, partially restores cyclical fluctuations and protects against obesity and metabolic disease. TRF preferentially affects bacteria known to influence host metabolism, linking feeding rhythm, microbiome dynamics, and metabolic outcomes.
[201] Irwin MR, Opp MR. Sleep health: reciprocal regulation of sleep and innate immunity. Neuropsychopharmacology. 2017. Link
This review and overview examines reciprocal interactions between sleep disturbances, including insomnia, and the innate immune system. Insomnia complaints, extreme sleep duration and experimental sleep deprivation alter genomic, cellular and systemic markers of inflammation and contribute to inflammaging. Inflammatory mediators in turn reshape homeostatic regulation of sleep continuity and macrostructure. Clinical implications include the link between sleep disturbance and inflammation-related depressive symptoms, and the potential of insomnia-targeted interventions to reverse inflammation. The findings underscore that sleep disturbance is a tractable risk factor for inflammatory disease.
[204] Allen JM, Mailing LJ, Niemiro GM et al. Exercise alters gut microbiota composition and function in lean and obese humans. Med Sci Sports Exerc. 2018. Link
This 6-week endurance training trial in 32 previously sedentary lean (n=18) and obese (n=14) adults assessed exercise-induced changes in gut microbiota composition, function and metabolite output, followed by a 6-week sedentary washout. Training progressed from 30 to 60 minutes at 60-75% of HR reserve, three days per week. Beta-diversity analysis showed that exercise-induced microbiota alterations were dependent on obesity status. The findings indicate that endurance training reshapes the gut microbiota in a host-phenotype-dependent manner, with effects partly reversible upon return to inactivity.
[207] Mayer EA, Tillisch K, Gupta A. Gut/brain axis and the microbiota. J Clin Invest. 2015. Link
This review summarizes preclinical evidence that the gut microbiota influences the bidirectional CNS-ENS-GI axis. Germ-free rodent studies show that microbiota shape emotional behaviour, stress- and pain-modulation systems and brain neurotransmitters. Probiotic and antibiotic perturbations modulate these endpoints in adult animals. Multiple endocrine and neurocrine pathways mediate microbiota-to-brain signalling, while the brain alters microbial composition via the autonomic nervous system. Translation of these findings to healthy humans and gut-brain axis disorders remains limited and is identified as a research priority.
[218] Dethlefsen L, Relman DA. Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation. Proc Natl Acad Sci USA. 2011. Link
This longitudinal study examined the distal gut microbiota of three individuals over 10 months spanning two courses of ciprofloxacin, analyzing 1.7 million 16S rRNA sequences from 52-56 samples per subject. Interindividual variation dominated; baseline within-subject communities were stable over months. Ciprofloxacin profoundly reduced diversity and shifted composition within 3-4 days of initiation, with incomplete and individual-specific recovery. The findings characterize gut microbiota resilience and the durable disruption caused by repeated fluoroquinolone exposure.
[226] Imhann F, Bonder MJ, Vich Vila A et al. Proton pump inhibitors affect the gut microbiota. Gut. 2016. Link
Imhann and colleagues' 2016 Gut paper reports that proton pump inhibitor (PPI) use significantly alters the human gut microbiota. Combining three population cohorts (>1800 individuals) with 16S rRNA sequencing, the authors show that PPI users have decreased microbial diversity and consistent shifts in 20% of bacterial taxa: increases in oral-cavity bacteria (Streptococcaceae, Enterococcaceae), Enterobacteriaceae and Clostridium difficile, alongside decreases in commensals such as Ruminococcaceae and Bifidobacteriaceae. These shifts mechanistically explain epidemiological associations between PPI use and CDI, enteric infection, hepatic encephalopathy and SIBO. The work supports prudent PPI prescribing and deprescription efforts.
[249] Atarashi K, Suda W, Luo C et al. Ectopic colonization of oral bacteria in the intestine drives TH1 cell induction and inflammation. Science. 2017. Link
This gnotobiotic study showed that salivary Klebsiella strains, when colonizing the gut, are strong inducers of T helper 1 (TH1) cells. These antibiotic-resistant Klebsiella strains colonize when intestinal microbiota are dysbiotic and elicit severe gut inflammation in genetically susceptible hosts. The findings establish the oral cavity as a reservoir for potential intestinal pathobionts that exacerbate disease such as IBD when ectopically colonizing the gut.
[253] Kapil V, Haydar SM, Pearl V, Lundberg JO, Weitzberg E, Ahluwalia A. Physiological role for nitrate-reducing oral bacteria in blood pressure control. Free Radic Biol Med. 2013. Link
This randomized crossover study in 19 healthy volunteers tested whether suppressing oral nitrate-reducing bacteria with chlorhexidine antiseptic mouthwash affects systemic nitrite levels and blood pressure. Blood pressure (clinic, home, 24-hour ambulatory) was measured during a 7-day control period and a 7-day chlorhexidine treatment period. Mouthwash use suppressed oral nitrate-reducing flora, reduced systemic nitrite and significantly increased blood pressure. The findings demonstrate that oral microbiota actively contribute to systemic blood pressure regulation via the enterosalivary nitrate-nitrite-NO pathway.
[254] Hajishengallis, G. Periodontitis: from microbial immune subversion to systemic inflammation. Nat Rev Immunol. 2015. Link
This review discusses how dysbiotic oral microbial communities drive periodontitis and inflammatory pathology at local and distant sites. The authors detail microbial immune subversion mechanisms that tip oral homeostasis to disease. Periodontitis emerges as a dysbiotic inflammatory disease with systemic implications, including links to cardiovascular and other chronic diseases. The findings frame periodontitis treatment as a strategy with potential systemic-health benefits.
[303] Sonnenburg ED, Smits SA, Tikhonov M, Higginbottom SK, Wingreen NS, Sonnenburg JL. Diet-induced extinctions in the gut microbiota compound over generations. . 2016. Link
In mice on a low microbiota-accessible carbohydrate (fiber) diet, gut microbiota diversity declined and the effect compounded across generations: over four generations the low-fiber diet led to cumulative taxon extinctions no longer reversible by dietary fiber reintroduction.
[329] Chang AM, Aeschbach D, Duffy JF, Czeisler CA. Evening use of light-emitting eReaders negatively affects sleep, circadian timing, and next-morning alertness. Proc Natl Acad Sci USA. 2015. Link
Average sleep duration and quality have declined, and 90% of US adults report electronic device use in the hour before bed. Short-wavelength-enriched light from these devices can suppress melatonin, shift circadian phase and increase alertness. In a controlled comparison, the authors evaluated the biological effects of reading on a light-emitting e-book device versus a printed book before bedtime, examining melatonin, circadian timing, sleep latency and next-morning alertness. The LE-eBook condition delayed circadian timing, suppressed evening melatonin, lengthened sleep onset and reduced next-morning alertness. The findings indicate that pre-bedtime use of light-emitting screens degrades sleep and circadian alignment.
[330] Kelly JR, Kennedy PJ, Cryan JF, Dinan TG, Clarke G, Hyland NP. Breaking down the barriers: the gut microbiota, intestinal permeability and stress-related psychiatric disorders. Front Cell Neurosci. 2015. Link
The gut-brain axis is positioned as a critical node in stress-related psychiatric disorders, with the gut microbiome modulating brain development, function and behavior through immune, endocrine and neural pathways. Preclinical evidence implicates impaired intestinal barrier function — the so-called leaky gut — as a key mediator linking dysbiosis to chronic low-grade inflammation and disorders such as depression. The gut microbiome regulates intestinal permeability via short-chain fatty acids, mucin production and tight-junction signaling. The review argues that targeting microbiota-driven barrier integrity may offer mechanistic and therapeutic insight into stress-related psychiatric disease.
[339] Suez J, Zmora N, Zilberman-Schapira G et al. Post-Antibiotic Gut Mucosal Microbiome Reconstitution Is Impaired by Probiotics and Improved by Autologous FMT. Cell. 2018. Link
In a controlled study of post-antibiotic microbiome reconstitution, multi-strain probiotic supplementation, autologous fecal microbiota transplantation (aFMT) or spontaneous recovery were compared in mice and humans, sampled via invasive mucosal biopsies. Antibiotics enhanced probiotic mucosal colonization in humans but only mildly in mice. Compared with spontaneous recovery, probiotics induced a markedly delayed and persistently incomplete reconstitution of indigenous stool and mucosal microbiota and host transcriptome, while aFMT produced rapid, near-complete recovery within days. In vitro, Lactobacillus-secreted soluble factors contributed to probiotic-mediated suppression of indigenous taxa. The findings caution against routine post-antibiotic probiotic use and support aFMT as a recovery strategy.
[346] Lessa FC, Mu Y, Bamberg WM, Beldavs ZG, Dumyati GK, Dunn JR, Farley MM, Holzbauer SM, Meek JI, Phipps EC, Wilson LE, Winston LG, Cohen JA, Limbago BM, Fridkin SK, Gerding DN, McDonald LC. Burden of Clostridium difficile infection in the United States. N Engl J Med. 2015. Link
In an active 2011 population- and laboratory-based surveillance across ten US areas, 15,461 incident C. difficile infection cases were identified. 65.8% were health-care associated, but only 24.2% had hospital-onset disease, indicating that most health-care-associated cases were diagnosed after discharge or in non-acute settings. National estimates derived from regression modeling indicated approximately 453,000 incident CDI cases, 83,000 first recurrences and 29,300 deaths within 30 days of diagnosis annually. NAP1 strains predominated among health-care-associated isolates. The study established CDI as a leading cause of US healthcare-associated infection and a growing community burden.
[347] Guh AY, Mu Y, Winston LG, Johnston H, Olson D, Farley MM, Wilson LE, Holzbauer SM, Phipps EC, Dumyati GK, Beldavs ZG, Kainer MA, Karlsson M, Gerding DN, McDonald LC; Emerging Infections Program Clostridioides difficile Infection Working Group. Trends in U.S. Burden of Clostridioides difficile Infection and Outcomes. N Engl J Med. 2020. Link
Building on the Emerging Infections Program surveillance in ten US sites, the authors estimated the national burden of C. difficile infection from 2011 to 2017, adjusting for the higher sensitivity of NAAT-based diagnostics. The estimated total burden decreased over the period, driven largely by a reduction in health-care-associated CDI, while community-associated CDI remained stable. First-recurrence rates and in-hospital deaths also declined modestly. Trends were modeled with weighted random-intercept negative-binomial and logistic regression. The findings indicate that US-wide infection-prevention efforts have measurably reduced the health-care-associated CDI burden without comparable progress on community-associated disease.
[348] McDonald LC, Gerding DN, Johnson S, Bakken JS, Carroll KC, Coffin SE, Dubberke ER, Garey KW, Gould CV, Kelly C, Loo V, Sammons JS, Sandora TJ, Wilcox MH. Clinical Practice Guidelines for Clostridium difficile Infection in Adults and Children: 2017 Update by the Infectious Diseases Society of America (IDSA) and Society for Healthcare Epidemiology of America (SHEA). Clin Infect Dis. 2018. Link
This IDSA/SHEA 2017 clinical practice guideline updates 2010 recommendations on Clostridium difficile infection (CDI) in adults and incorporates pediatric guidance. Key changes include diagnostic algorithms favoring multistep testing (GDH/toxin EIA or NAAT plus toxin assay), oral vancomycin or fidaxomicin as first-line therapy over metronidazole for non-severe initial episodes, fidaxomicin or vancomycin tapered/pulsed regimens for recurrence, and FMT for multiply recurrent CDI failing antibiotic therapy. Infection prevention emphasizes contact precautions, hand hygiene with soap and water, and environmental decontamination. The guideline reflects evolving epidemiology, including ribotype 027 trends and the rising community-associated CDI burden.
[349] Johnson S, Lavergne V, Skinner AM, Gonzales-Luna AJ, Garey KW, Kelly CP, Wilcox MH. Clinical Practice Guideline by the Infectious Diseases Society of America (IDSA) and Society for Healthcare Epidemiology of America (SHEA): 2021 Focused Update Guidelines on Management of Clostridioides difficile Infection in Adults. Clin Infect Dis. 2021. Link
This 2021 IDSA/SHEA focused-update guideline addresses fidaxomicin and bezlotoxumab in adult C. difficile infection (CDI) management. Recommendations were derived from systematic literature review and graded using GRADE. The panel recommends fidaxomicin over vancomycin for initial CDI episode and for first recurrence (conditional, moderate certainty), citing reduced recurrence risk. Bezlotoxumab is suggested as adjunct to standard antibiotic therapy for patients at high risk of CDI recurrence (conditional, very low certainty). The update reflects accumulating RCT evidence and refines positioning of newer agents within the CDI treatment algorithm.
[357] Lewis SJ, Heaton KW. Stool form scale as a useful guide to intestinal transit time. Scand J Gastroenterol. 1997. Link
The authors evaluated the responsiveness of the Bristol Stool Form Scale to changes in whole-gut transit time (WGTT). Sixty-six volunteers had WGTT measured with radiopaque markers and recorded stool form on a 7-point scale and defecation frequency; measurements were repeated under senna and loperamide. Baseline WGTT correlated with frequency (r=0.35, P=0.005) and stool output (r=-0.41, P=0.001), and best with stool form (r=-0.54, P<0.001). Senna (n=44) shortened WGTT and increased frequency, form score and output (all P<0.001); loperamide (n=43) lengthened WGTT and reduced frequency, form score and output (all P<0.001). The Bristol scale is a valid surrogate for intestinal transit time and is responsive to pharmacological alteration.
[363] Wang S, Xiang L, Li F, Deng W, Lv P, Chen Y. Butyrate Protects against Clostridium difficile Infection by Regulating Bile Acid Metabolism. Microbiol Spectr. 2023. Link
This study tested butyrate as a therapeutic against Clostridium difficile infection (CDI) in a mouse model. Butyrate administration significantly reduced CDI severity, weight loss and mortality, and improved colonic histology. Mechanistically, butyrate modulated bile acid metabolism: it shifted the bile acid pool away from cholic-acid-class primary bile acids (germinants for C. difficile spores) toward secondary bile acids inhibitory to C. difficile outgrowth. Butyrate also reinforced intestinal barrier function and dampened mucosal inflammation. Microbiota changes accompanied these biochemical shifts. The findings define a bile-acid-mediated mechanism by which butyrate protects against CDI, supporting butyrate-based or SCFA-promoting strategies as adjuncts to existing therapies.
[365] Reed AD, Theriot CM. Contribution of Inhibitory Metabolites and Competition for Nutrients to Colonization Resistance against Clostridioides difficile by Commensal Clostridium. Microorganisms. 2021. Link
This review examines how commensal Clostridium species mediate colonization resistance against C. difficile. Commensal Clostridia modify primary bile acids into secondary bile acids that suppress C. difficile spore germination and vegetative outgrowth. They additionally produce antimicrobial peptides and short-chain fatty acids that directly inhibit C. difficile and compete for limiting nutrients such as proline, important for C. difficile growth via Stickland fermentation. Loss of commensal Clostridia after broad-spectrum antibiotics is a key mechanistic step toward CDI susceptibility. The authors argue that restoring defined Clostridium consortia is a rational, mechanism-driven alternative to FMT for preventing recurrent CDI.
[369] Weingarden A, González A, Vázquez-Baeza Y, Weiss S, Humphry G, Berg-Lyons D, Knights D, Unno T, Bobr A, Kang J, Khoruts A, Knight R, Sadowsky MJ. Dynamic changes in short- and long-term bacterial composition following fecal microbiota transplantation for recurrent Clostridium difficile infection. Microbiome. 2015. Link
This study tracked fecal microbiota dynamics in four patients with multiply recurrent, antibiotic-refractory C. difficile infection treated with FMT, sampling daily up to 28 days and weekly up to 84 days post-FMT (with sampling out to 151 days). 16S rRNA gene profiling was compared to Human Microbiome Project body-site references. Pre-FMT samples were markedly dysbiotic. FMT produced a rapid normalization of fecal community composition toward a healthy donor-like state within days, and this normalization was largely sustained over months. Time-course visualization highlighted both rapid early shifts and longer-term stabilization. The findings document the kinetics of FMT-driven microbiota recovery in refractory CDI and support its durability.
[542] McDonald D, Hyde E, Debelius JW et al. American Gut: an Open Platform for Citizen Science Microbiome Research. mSystems. 2018. Link
The American Gut Project compared >10 000 citizen-scientist stool samples from the US, UK and Australia with environmental samples using Earth Microbiome Project standardized protocols. Human stool microbiomes showed unexpectedly wide beta-diversity compared with environmental samples. Open data integration enabled discovery of new molecules and untargeted-metabolomic associations with diverse plant intake (a stronger predictor than reductive categorical variables like veganism). The work demonstrates feasibility of mail-shipped, self-collected microbiome samples for reproducing known and revealing new associations, including psychiatric illness links and individual perturbations such as surgery.
[565] Wilson BC, Vatanen T, Cutfield WS, O'Sullivan JM. The Super-Donor Phenomenon in Fecal Microbiota Transplantation. Front Cell Infect Microbiol. 2019. Link
FMT is highly effective for recurrent Clostridium difficile infection but its efficacy in chronic dysbiosis-associated diseases has been modest and variable. Multiple studies suggest FMT outcome depends on stool donor microbial diversity and composition, leading to the concept of FMT 'super-donors'. The review explores keystone species as predictors of FMT success and discusses how host genetics and diet may influence engraftment and maintenance — providing a framework for more targeted, donor-stratified bacteriotherapy.
[601] Targownik LE, Fisher DA, Saini SD. AGA Clinical Practice Update on De-Prescribing of Proton Pump Inhibitors: Expert Review. Gastroenterology. 2022. Link
A clinical update provides Best Practice Advice statements for PPI de-prescribing in ambulatory patients. PPIs are among the most-prescribed medications and are increasingly used for indications with uncertain benefit, contributing to polypharmacy and economic burden. PPI use has been increasingly associated with PPI-associated adverse events (PAAEs). The guidance promotes structured de-prescribing strategies to reduce pill burden, real costs and theoretical risks while ensuring patients with appropriate indications continue therapy.
[638] Chaix A, Manoogian ENC, Melkani GC, Panda S. Time-Restricted Eating to Prevent and Manage Chronic Metabolic Diseases. Annu Rev Nutr. 2019. Link
Molecular clocks are present in almost every cell to anticipate daily recurring and predictable changes, such as rhythmic nutrient availability, and to adapt cellular functions accordingly. At the same time, nutrient-sensing pathways can respond to acute nutrient imbalance and modulate and orient metabolism so cells can adapt optimally to a declining or increasing availability of nutrients. Organismal circadian rhythms are coordinated by behavioral rhythms such as activity-rest and feeding-fasting cycles to temporally orchestrate a sequence of physiological processes to optimize metabolism. Basic research in circadian rhythms has largely focused on the functioning of the self-sustaining molecular circadian oscillator, while research in nutrition science has yielded insights into physiological responses to caloric deprivation or to specific macronutrients. Integration of these two fields into actionable new concepts in the timing of food intake has led to the emerging practice of time-restricted eating. In this paradigm, daily caloric intake is restricted to a consistent window of 8-12 h.
[664] Chilton C, Viprey V, Normington C, Moura I, Buckley A, Freeman J, Davies K, Wilcox M. Clostridioides difficile pathogenesis and control. Nature reviews. Microbiology. 2026. Link
C. difficile pathogenesis, microbiota dysbiosis, and the role of FMT — Comprehensive review: antibiotic-induced dysbiosis → germination of C. difficile spores → toxin production → colitis. A healthy microbiota provides colonization resistance. Newer microbiota therapies as alternatives to FMT.
[665] Seekatz A, Safdar N, Khanna S. The role of the gut microbiome in colonization resistance and recurrent. Therapeutic advances in gastroenterology. 2022. Link
Colonization resistance of the gut microbiota and FMT therapy in rCDI — A healthy microbiota inhibits C. difficile colonization (nutrient competition, bile acids, SCFAs, bacteriocins). Antibiotics → dysbiosis → CDI. FMT restores diversity. Monoclonal antibodies do not treat dysbiosis.
[667] Britton R, Young V. Role of the intestinal microbiota in resistance to colonization by Clostridium difficile. Gastroenterology. 2014. Link
Intestinal microbiota and C. difficile colonization resistance — fundamental mechanisms — The native microbiota inhibits germination and growth of C. difficile spores. Antibiotics impair this defense. Key mechanisms: bile acid metabolism, nutrient competition. FMT restores colonization resistance.
[668] Chilton C, Pickering D, Freeman J. Microbiologic factors affecting Clostridium difficile recurrence. Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases. 2018. Link
Microbiological causes of C. difficile recurrence — spore persistence and dysbiosis — Low bacterial diversity correlates with clinical rCDI. Spore persistence + germination is the key to recurrence. FMT and microbiota therapies are increasingly investigated. Targeted antibiotics (fidaxomicin) + microbiota restoration form the combined approach.
[690] Saha S, Mara K, Pardi D, Khanna S. Long-term Safety of Fecal Microbiota Transplantation for Recurrent Clostridioides difficile Infection. Gastroenterology. 2021. Link
Long-term safety of FMT in rCDI: low infection transmission risk; new diagnoses likely unrelated to FMT — Mayo Clinic 609 patients, 6.8-year prospective data — 609 patients, median 3.7 years follow-up (range 2.0–6.8 years). At 1 year: 9.5% reported a new CDI episode. Long-term, 73 new diagnoses (13% GI, 10% weight gain, 11.8% infection) — all judged unrelated to FMT. Higher diarrhea risk in IBD, dialysis-dependent kidney disease, and patients undergoing repeated FMT.
[691] Yau Y, Lau L, Lui R, Wong S, Guo C, Mak J, Ching J, Ip M, Kamm M, Rubin D, Chan P, Chan F, Ng S. Long-Term Safety Outcomes of Fecal Microbiota Transplantation: Real-World Data Over 8 Years From the Hong Kong FMT Registry. Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association. 2024. Link
Excellent long-term safety profile of FMT based on 8-year registry data: low risk of new disease beyond 12 months; survival of CDI-treated patients significantly better than antibiotic controls — 123 patients, 510 FMTs, median 30.3 months follow-up (max 57.9 months = ~5 years). Beyond 12 months, 21 new diseases in 16 patients — all judged unrelated to FMT. No development of IBD, IBS, allergy, T2DM, or psychiatric disorder. Cumulative survival probability of FMT-treated rCDI patients significantly better than matched antibiotic controls.
[762] Bonomini-Gnutzmann R, Plaza-Díaz J, Jorquera-Aguilera C, Rodríguez-Rodríguez A, Rodríguez-Rodríguez F. Effect of Intensity and Duration of Exercise on Gut Microbiota in Humans: A Systematic Review. International journal of environmental research and public health. 2022. Link
Exercise intensity and duration determine gut microbiota composition; moderate exercise is favorable, while extreme endurance load may cause negative microbiota changes — 13 studies: intense exercise — increased gut permeability, elevated I-FABP, dysbiosis; 7 studies: moderate exercise — increase in microbial diversity and SCFA metabolites; in athletes, more adverse effects at high intensity (IJERPH, 2022).
[797] Kolida S, Meyer D, Gibson GR. A double-blind placebo-controlled study to establish the bifidogenic dose of inulin in healthy humans2007;61(10):1189–1195. Eur J Clin Nutr. Link
OBJECTIVE: To evaluate the bifidogenic efficacy of two inulin doses in healthy human adults. DESIGN: A double-blind, placebo-controlled, crossover human study. SETTING: Food Microbial Sciences Unit, The University of Reading, Reading, UK. SUBJECTS: Thirty healthy volunteers, 15 men, 15 women (age range 19-35). INTERVENTIONS: Subjects consumed a chocolate drink containing placebo (maltodextrin, 8 g/day), 5 g/day inulin and 8 g/day inulin for a 2-week treatment period. Each treatment was followed by a 1-week washout at the end of which volunteers progressed to the next treatment.
[2572] Wu G. Functional amino acids in nutrition and health. Amino Acids 2017. . 2017. Link
The recent years have witnessed growing interest in biochemistry, physiology and nutrition of amino acids (AA) in growth, health and disease of humans and other animals. This results from the discoveries of AA in cell signaling involving protein kinases, G protein-coupled receptors, and gaseous molecules (i.e., NO, CO and H2S). In addition, nutritional studies have shown that dietary supplementation with several AA (e.g., arginine, glutamine, glutamate, leucine, and proline) modulates gene expression, enhances growth of the small intestine and skeletal muscle, or reduces excessive body fat. These seminal findings led to the new concept of functional AA, which are defined as those AA that participate in and regulate key metabolic pathways to improve health, survival, growth, development, lactation, and reproduction of the organisms. Functional AA hold great promise in prevention and treatment of metabolic diseases (e.g., obesity, diabetes, and cardiovascular disorders), intrauterine growth restriction, infertility, intestinal and neurological dysfunction, and infectious disease (including viral infections).
[2615] Sutton EF, Beyl R, Early KS et al. Early Time-Restricted Feeding Improves Insulin Sensitivity, Blood Pressure, and Oxidative Stress Even without Weight Loss in Men with Prediabetes. Cell Metabolism. 2018. Link
Cross-over RCT with 8 men with prediabetes: restricting meals to an early 6-hour window (eTRF, 8:00–14:00) for 5 weeks — under energy-matching — significantly improved insulin sensitivity, β-cell response, blood pressure, and oxidative stress compared to a 12-hour control window. Weight loss was NOT required for these favourable metabolic changes, indicating the effect arises from circadian alignment.
[2623] Fu Y et al. Insight into the effects of Omega-3 fatty acids on gut microbiota: impact of a balanced tissue Omega-6/Omega-3 ratio. Front Nutr. 2025. Link
Review of how omega-3 fatty acids and a balanced tissue omega-6:omega-3 ratio shape gut microbiota composition and function: a high ratio favours pro-inflammatory/LPS-producing bacteria, a balanced ratio favours SCFA-producers (Bifidobacterium, Roseburia, Lactobacillus); supports a personalized dietary approach based on fatty-acid ratios.
[2626] Snipe RMJ, Costa RJS et al. Nutritional considerations to counteract gastrointestinal permeability during exertional heat stress. J Appl Physiol. 2021. Link
Thermal (heat) stress reduces splanchnic perfusion, induces oxidative stress and tight-junction disruption, increasing gut barrier permeability and endotoxin translocation; these can reshape microbial composition and immune regulation. Much evidence comes from exertional heat-stress and animal models.
[2639] Malagelada C, Azpiroz F. Gastrocolonic Response. Current Gastroenterology Reports. 2022. Link
Review of the gastrocolonic response: a physiologic increase in colonic motor activity following meal ingestion. It is provoked by gastric distension, caloric intake and meal fat content, mediated via the vagus nerve and neurohumoral mechanisms; it appears within minutes of eating and can last for hours in healthy subjects. The reflex is clinically relevant in constipation, IBS and other motility disorders.
[2655] De Schryver AM, Keulemans YC, Peters HP, Akkermans LM, Smout AJ, De Vries WR. Effects of regular physical activity on defecation pattern in middle-aged patients complaining of chronic constipation. Scandinavian Journal of Gastroenterology. 2005. Link
Randomized study in middle-aged, inactive patients with chronic idiopathic constipation: a 12-week regular physical-activity programme (including walking) significantly reduced rectosigmoid and total colonic transit time and improved defecation pattern. The work provides direct clinical evidence that regular movement accelerates gut transit.
[2721] Palleja A, Mikkelsen KH, Forslund SK et al. Recovery of gut microbiota of healthy adults following antibiotic exposure. Nature Microbiology. 2018. Link
Shotgun-metagenomic study of 12 healthy men: after a 4-day course of three last-resort antibiotics (meropenem, gentamicin, vancomycin) the gut microbiota largely but incompletely recovered over six months — several common species stayed missing and resistance genes were transiently enriched.
[2722] Grosen AK et al. Effects of clinical donor characteristics on the success of faecal microbiota transplantation for patients in Denmark with Clostridioides difficile infection: a single-centre, prospective cohort study. The Lancet Microbe. 2025. Link
Single-centre, prospective Danish cohort: clinical donor characteristics — including antibiotic exposure in the 12 months before donation and donation stool consistency — affect FMT success in recurrent C. difficile infection; donor antibiotic use worsens outcomes, supporting strict donor screening.
[2907] Deutz NE, Bauer JM, Barazzoni R, Biolo G, Boirie Y, Bosy-Westphal A, Cederholm T, Cruz-Jentoft A, Krznaric Z, Nair KS, Singer P, Teta D, Tipton K, Calder PC. Protein intake and exercise for optimal muscle function with aging: recommendations from the {ESPEN. Clinical Nutrition. 2014. Link
Ageing brings a gradual, progressive loss of muscle mass, strength and physical endurance (sarcopenia), most marked in sedentary older adults. This ESPEN Expert Group review concludes that regular aerobic and resistance exercise counteracts most aspects of sarcopenia, and that adequate protein and energy intake helps limit and treat age-related declines in muscle mass, strength and function. The group recommends a higher dietary protein intake than the traditional 0.8 g/kg/day — about 1.0–1.2 g/kg body weight per day for healthy older adults and 1.2–1.5 g/kg/day for those with acute or chronic illness — combined with physical activity. The aim is to preserve muscle function, mobility and independence in later life.
[2909] Kelly ColleenR, Ihunnah Chioma, Fischer Monika, Khoruts Alexander, Surawicz Christina, Afzali Anita, Aroniadis Olga, Barto Amy, Borody Thomas, Giovanelli Andrea, Gordon Shelley, Gluck Michael, Hohmann ElizabethL, Kao Dina, Kao JohnY, McQuillen DanielP, Mellow Mark, Rank KevinM, Rao Krishna, Ray Arnab, Schwartz MargotA, Singh Namita, Stollman Neil, Suskind DavidL, Vindigni StephenM, Youngster Ilan, Brandt Lawrence. Fecal Microbiota Transplant for Treatment of {Clostridium. American Journal of Gastroenterology. 2014. Link
Clostridium difficile infection (CDI) is especially dangerous in immunocompromised patients, yet the safety of fecal microbiota transplantation (FMT) in this group had been uncertain. This 16-centre retrospective series studied 80 immunocompromised patients (75 adults, 5 children) whose CDI was recurrent (55%), refractory (11%) or severe/overlapping (34%); causes of immunocompromise included HIV/AIDS, solid-organ transplant, oncologic disease, inflammatory bowel disease immunosuppression and other conditions. The CDI cure rate after a single FMT was 78%, and the procedure was generally safe: serious adverse events within 12 weeks were uncommon and did not indicate FMT-transmitted infection. The authors conclude that FMT is an effective and safe option for CDI even in immunocompromised patients.
[2910] Buccigrossi Vittoria, Lo Vecchio Andrea, Bruzzese Eugenia, Russo Carla, Marano Antonella, Terranova Sara, Cioffi Valentina, Guarino Alfredo. Potency of Oral Rehydration Solution in Inducing Fluid Absorption is Related to Glucose Concentration. Scientific Reports. 2020. Link
Oral rehydration solution (ORS) is the key treatment of acute diarrhoea in children: it restores electrolyte balance by stimulating the intestinal sodium/glucose transporter SGLT1 to drive fluid absorption. The authors tested solutions with different sodium and glucose concentrations on Caco-2 intestinal cells using Ussing-chamber electrophysiology during rotavirus-induced secretion. The ESPGHAN ORS (sodium 60 mmol/L, glucose 111 mmol/L) produced a more potent pro-absorptive effect than the WHO ORS, and the effect depended on the sodium/glucose ratio; rotavirus-induced fluid secretion could be reversed toward absorption when sodium fell in the 45–60 mEq/L range and glucose in the 80–110 mM range. The conclusion is that the pro-absorptive potency of ORS depends on its sodium and glucose concentrations.
[2912] Laborde Sylvain, Allen MarkS, Borges Uirassu, Iskra Maša, Zammit Nina, You Min, Hosang Thomas, Mosley Emma, Dosseville Fabrice. Psychophysiological effects of slow-paced breathing at six cycles per minute with or without heart rate variability biofeedback. Psychophysiology. 2022. Link
Heart rate variability (HRV) biofeedback — slow-paced breathing (SPB) performed while watching a heart-rate/HRV signal — is increasingly used as an adjunct for many psychological and medical conditions, but its mechanism is unclear. In 112 participants, this study compared SPB at six breaths per minute done with HRV biofeedback (SPB-HRVB) versus without it (SPB-NoHRVB), measuring emotional valence, arousal and control, perceived stress, and the vagally mediated HRV index RMSSD. Both conditions produced the same pre-to-post benefits — a calmer emotional valence, lower arousal, greater emotional control and higher RMSSD — with the biofeedback adding only a slightly more positive overall valence. The authors conclude that slow-paced breathing itself drives most of the psychophysiological benefit and suggest testing longer interventions and different stressors.
[2916] Hengel RichardL, Schroeder ClaudiaP, Jo Jinhee, Ritter TimothyE, Nathan RameshV, Gonzales-Luna AnneJ, Obi EngelsN, Dillon RyanJ, Van Anglen LucindaJ, Garey KevinW. Recurrent Clostridioides difficile infection worsens anxiety-related patient-reported quality of life. Journal of Patient-Reported Outcomes. 2022. Link
This patient-reported study measures how health-related quality of life (HrQOL) changes after treatment of Clostridioides difficile infection (CDI), using the anxiety-focused Cdiff32 instrument. Among 144 adults treated with bezlotoxumab, the mean score improved from 26.4 at baseline to 56.4 at 90-day follow-up (higher scores indicate better quality of life). Patients without recurrence improved significantly more (34.1-point increase) than those with recurrent CDI (6.7-point increase; P < 0.001). Recurrent CDI therefore meaningfully worsens anxiety-related quality of life, and the Cdiff32 instrument is useful for assessing these humanistic outcomes.
Note: the items above provide the book's external, citable evidence base. The internal, MicroBiome Bank source documents (DiffBiome / HospBiome Service Datasheet, SIS Clinical Guide, Clinical protocol guide v2.1, capsule density protocol, DSQ cards, C. diff clearance strategy 2026) supply the product- and protocol-specific facts; these are not public literature items but the provider's own, referenced documents.