Cani, P. D. Gut microbiota—at the intersection of everything?. Nat. Rev. Gastroenterol. Hepatol. 14, 321–322 (2017).
Glymenaki, M. et al. Compositional changes in the gut mucus microbiota precede the onset of colitis-induced inflammation. Inflamm. Bowel Dis. 23, 912–922 (2017).
Heinsen, F. A. et al. Dynamic changes of the luminal and mucosa-associated gut microbiota during and after antibiotic therapy with paromomycin. Gut Microbes 6, 243–254 (2015).
Huse, S. M. et al. Comparison of brush and biopsy sampling methods of the ileal pouch for assessment of mucosa-associated microbiota of human subjects. Microbiome 2, 5 (2014).
Galley, J. D. et al. The structures of the colonic mucosa-associated and luminal microbial communities are distinct and differentially affected by a prolonged murine stressor. Gut Microbes 5, 748–760 (2014).
Lavelle, A., et al. Spatial variation of the colonic microbiota in patients with ulcerative colitis and control volunteers. Gut 64, 1553–1561 (2015).
Gevers, D. et al. The treatment-naive microbiome in new-onset Crohn’s disease. Cell Host Microbe 15, 382–392 (2014).
Donaldson, G. P., Lee, S. M. & Mazmanian, S. K. Gut biogeography of the bacterial microbiota. Nat. Rev. Microbiol. 14, 20–32 (2016).
Tang, M. S. et al. Inferred metagenomic comparison of mucosal and fecal microbiota from individuals undergoing routine screening colonoscopy reveals similar differences observed during active inflammation. Gut Microbes 6, 48–56 (2015).
Ringel, Y. et al. High throughput sequencing reveals distinct microbial populations within the mucosal and luminal niches in healthy individuals. Gut Microbes 6, 173–181 (2015).
Yasuda, K. et al. Biogeography of the intestinal mucosal and lumenal microbiome in the Rhesus macaque. Cell Host Microbe 17, 385–391 (2015).
Parthasarathy, G. et al. Relationship between microbiota of the colonic mucosa vs feces and symptoms, colonic transit, and methane production in female patients with chronic constipation. Gastroenterology 150, 367–379.e361 (2016).
Jervis-Bardy, J. et al. Deriving accurate microbiota profiles from human samples with low bacterial content through post-sequencing processing of Illumina MiSeq data. Microbiome 3, 19 (2015).
Salter, S. J. et al. Reagent and laboratory contamination can critically impact sequence-based microbiome analyses. BMC Biol. 12, 87 (2014).
Glassing, A., Dowd, S. E., Galandiuk, S., Davis, B. & Chiodini, R. J. Inherent bacterial DNA contamination of extraction and sequencing reagents may affect interpretation of microbiota in low bacterial biomass samples. Gut Pathog. 8, 24 (2016).
Perez-Munoz, M. E., Arrieta, M. C., Ramer-Tait, A. E. & Walter, J. A critical assessment of the “sterile womb” and “in utero colonization” hypotheses: implications for research on the pioneer infant microbiome. Microbiome 5, 48 (2017).
Watt, E. et al. Extending colonic mucosal microbiome analysis-assessment of colonic lavage as a proxy for endoscopic colonic biopsies. Microbiome 4, 61 (2016).
McHardy, I. H. et al. Integrative analysis of the microbiome and metabolome of the human intestinal mucosal surface reveals exquisite inter-relationships. Microbiome 1, 17 (2013).
Mottawea, W. et al. Altered intestinal microbiota–host mitochondria crosstalk in new onset Crohn’s disease. Nat. Commun. 7, 13419 (2016).
Presley, L. L. et al. Host–microbe relationships in inflammatory bowel disease detected by bacterial and metaproteomic analysis of the mucosal–luminal interface. Inflamm. Bowel Dis. 18, 409–417 (2012).
Li, X. et al. A metaproteomic approach to study human–microbial ecosystems at the mucosal luminal interface. PLoS ONE 6, e26542 (2011).
Zhang, X. et al. MetaPro-IQ: a universal metaproteomic approach to studying human and mouse gut microbiota. Microbiome 4, 31 (2016).
Deeke, S. A. et al. Mucosal–luminal interface proteomics reveals biomarkers of pediatric inflammatory bowel disease-associated colitis. Am. J. Gastroenterol. 113, 713–724 (2018).
Zhang, X. et al. Metaproteomics reveals associations between microbiome and intestinal extracellular vesicle proteins in pediatric inflammatory bowel disease. Nat. Commun. 9, 2873 (2018).
Jimenez-Rivera, C., Haas, D., Boland, M., Barkey, J. L. & Mack, D. R. Comparison of two common outpatient preparations for colonoscopy in children and youth. Gastroenterol. Res. Pract. 2009, 518932 (2009).
Bourne, D. G., Muirhead, A. & Sato, Y. Changes in sulfate-reducing bacterial populations during the onset of black band disease. ISME J. 5, 559–564 (2011).
Caporaso, J. G. et al. QIIME allows analysis of high-throughput community sequencing data. Nat. Methods 7, 335–336 (2010).
McMurdie, P. J. & Holmes, S. phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS ONE 8, e61217 (2013).
Oksanen, J. et al. vegan: Community Ecology Package. R package (2016). https://CRAN.R-project.org/package=vegan, Accessed 31 May 2018.
Segata, N. et al. Metagenomic biomarker discovery and explanation. Genome Biol. 12, R60 (2011).
Momozawa, Y., Deffontaine, V., Louis, E. & Medrano, J. F. Characterization of bacteria in biopsies of colon and stools by high throughput sequencing of the V2 region of bacterial 16S rRNA gene in human. PLoS ONE 6, e16952 (2011).
Hunt, K. M. et al. Characterization of the diversity and temporal stability of bacterial communities in human milk. PLoS ONE 6, e21313 (2011).
Paisse, S. et al. Comprehensive description of blood microbiome from healthy donors assessed by 16S targeted metagenomic sequencing. Transfusion 56, 1138–1147 (2016).
Aagaard, K. et al. The placenta harbors a unique microbiome. Sci. Transl. Med 6, 237ra265 (2014).
Collado, M. C., Rautava, S., Aakko, J., Isolauri, E. & Salminen, S. Human gut colonisation may be initiated in utero by distinct microbial communities in the placenta and amniotic fluid. Sci. Rep. 6, 23129 (2016).
Lauder, A. P. et al. Comparison of placenta samples with contamination controls does not provide evidence for a distinct placenta microbiota. Microbiome 4, 29 (2016).
Kulakov, L. A., McAlister, M. B., Ogden, K. L., Larkin, M. J. & O’Hanlon, J. F. Analysis of bacteria contaminating ultrapure water in industrial systems. Appl. Environ. Microbiol. 68, 1548–1555 (2002).
Eckburg, P. B. et al. Diversity of the human intestinal microbial flora. Science 308, 1635–1638 (2005).
van den Bogert, B., de Vos, W. M., Zoetendal, E. G. & Kleerebezem, M. Microarray analysis and barcoded pyrosequencing provide consistent microbial profiles depending on the source of human intestinal samples. Appl. Environ. Microbiol. 77, 2071–2080 (2011).