This list contains references from the content that can be linked to their source. For a full set of references and notes please see the PDF or HTML where available.
1M Rajilic-Stojanovic , H Smidt & WM de Vos (2007) Diversity of the human gastrointestinal tract microbiota revisited. Environ Microbiol 9, 2125–2136.
2PJ Turnbaugh , M Hamady , T Yatsunenko , (2008) A core gut microbiome in obese and lean twins. Nature 457, 480–484.
3EG Zoetendal , EE Vaughan & WM de Vos (2006) A microbial world within us. Mol Microbiol 59, 1639–1650.
4J Maukonen , J Matto , R Satokari , (2006) PCR DGGE and RT-PCR DGGE show diversity and short-term temporal stability in the Clostridium coccoides-Eubacterium rectale group in the human intestinal microbiota. FEMS Microbiol Ecol 58, 517–528.
5T Vanhoutte , G Huys , E De brandt , (2004) Temporal stability analysis of the microbiota in human feces by denaturing gradient gel electrophoresis using universal and group-specific 16S rRNA gene primers. FEMS Microbiol Ecol 48, 437–446.
7EG Zoetendal , M Rajilic-Stojanovic & WM de Vos (2008) High-throughput diversity and functionality analysis of the gastrointestinal tract microbiota. Gut 57, 1605–1615.
8L Dethlefsen , S Huse , ML Sogin , (2008) The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing. PLoS Biol 6, e280.
9C Jernberg , S Lofmark , C Edlund , (2007) Long-term ecological impacts of antibiotic administration on the human intestinal microbiota. ISME J 1, 56–66.
11PJ Barnes (2000) Mechanisms in COPD: differences from asthma. Chest 117, 10S–14S.
12G Turato , R Zuin & M Saetta (2001) Pathogenesis and pathology of COPD. Respiration 68, 117–128.
14GC Donaldson , TA Seemungal , IS Patel , (2003) Longitudinal changes in the nature, severity and frequency of COPD exacerbations. Eur Respir J 22, 931–936.
16C Hogenauer , HF Hammer , GJ Krejs , (1998) Mechanisms and management of antibiotic-associated diarrhea. Clin Infect Dis 27, 702–710.
17AJ Macpherson & T Uhr (2004) Induction of protective IgA by intestinal dendritic cells carrying commensal bacteria. Science 303, 1662–1665.
18MC Noverr & GB Huffnagle (2004) Does the microbiota regulate immune responses outside the gut? Trends Microbiol 12, 562–568.
19F Cremonini , S Di Caro , EC Nista , (2002) Meta-analysis: the effect of probiotic administration on antibiotic-associated diarrhoea. Aliment Pharmacol Ther 16, 1461–1467.
20AL D'Souza , C Rajkumar , J Cooke , (2002) Probiotics in prevention of antibiotic associated diarrhoea: meta-analysis. BMJ 324, 1361.
21M Hickson , AL D'Souza , N Muthu , (2007) Use of probiotic Lactobacillus preparation to prevent diarrhoea associated with antibiotics: randomised double blind placebo controlled trial. BMJ 335, 80.
22LV McFarland (2006) Meta-analysis of probiotics for the prevention of antibiotic associated diarrhea and the treatment of Clostridium difficile disease. Am J Gastroenterol 101, 812–822.
23HM Timmerman , LE Niers , BU Ridwan , (2007) Design of a multispecies probiotic mixture to prevent infectious complications in critically ill patients. Clin Nutr 26, 450–459.
24NR Anthonisen , J Manfreda , CP Warren , (1987) Antibiotic therapy in exacerbations of chronic obstructive pulmonary disease. Ann Intern Med 106, 196–204.
25T van der Molen , BW Willemse , S Schokker , (2003) Development, validity and responsiveness of the clinical COPD questionnaire. Health Qual Life Outcomes 1, 13.
26LJ O'Donnell , J Virjee & KW Heaton (1990) Detection of pseudodiarrhoea by simple clinical assessment of intestinal transit rate. BMJ 300, 439–440.
28DZ Sousa , MA Pereira , AJ Stams , (2007) Microbial communities involved in anaerobic degradation of unsaturated or saturated long-chain fatty acids. Appl Environ Microbiol 73, 1054–1064.
31SR Konstantinov , W-Y Zhu , BA Williams , (2003) Effect of fermentable carbohydrates on faecal bacterial communities as revealed by DGGE analysis of 16S rDNA. FEMS Microbiol Ecol 43, 225–235.
32S Possemiers , K Verthe , S Uyttendaele , (2004) PCR-DGGE-based quantification of stability of the microbial community in a stimulator of the human intestinal microbial ecosystem. FEMS Microbiol Ecol 49, 495–507.
33MT Suzuki , LT Taylor & EF DeLong (2000) Quantitative analysis of small-subunit rRNA genes in mixed microbial populations via 5′-nuclease assays. Appl Environ Microbiol 66, 4605–4614.
34R Byun , MA Nadkarni , KL Chhour , (2004) Quantitative analysis of diverse Lactobacillus species present in advanced dental caries. J Clin Microbiol 42, 3128–3136.
35RM Satokari , EE Vaughan , AD Akkermans , (2001) Bifidobacterial diversity in human feces detected by genus-specific PCR and denaturing gradient gel electrophoresis. Appl Environ Microbiol 67, 504–513.
36S Fuentes , M Egert , M Jimenez-Valera , (2008) A strain of Lactobacillus plantarum affects segmented filamentous bacteria in the intestine of immunosuppressed mice. FEMS Microbiol Ecol 63, 65–72.
38R Hartemink , VR Domenech & FM Rombouts (1997) LAMVAB – a new selective medium for the isolation of lactobacilli from faeces. J Microbiol Methods 29, 77–84.
39N Bruinsma , JM Hutchinson , AE van den Bogaard , (2003) Influence of population density on antibiotic resistance. J Antimicrob Chemother 51, 385–390.
40S Nys , IN Okeke , S Kariuki , (2004) Antibiotic resistance of faecal Escherichia coli from healthy volunteers from eight developing countries. J Antimicrob Chemother 54, 952–955.
41MF De La Cochetiere , T Durand , P Lepage , (2005) Resilience of the dominant human fecal microbiota upon short-course antibiotic challenge. J Clin Microbiol 43, 5588–5592.
42A Sullivan , C Edlund & CE Nord (2001) Effect of antimicrobial agents on the ecological balance of human microflora. Lancet Infect Dis 1, 101–114.
43EJ Woodmansey (2007) Intestinal bacteria and ageing. J Appl Microbiol 102, 1178–1186.
44H Goris , F de Boer & D van der Waaij (1988) Kinetics of endotoxin release by gram-negative bacteria in the intestinal tract of mice during oral administration of bacitracin and during in vitro growth. Scand J Infect Dis 20, 213–219.
45RG Holzheimer (2001) Antibiotic induced endotoxin release and clinical sepsis: a review. J Chemother 13, Spec No. 1, 159–172.
47JC Hurley (1995) Antibiotic-induced release of endotoxin. A therapeutic paradox. Drug Saf 12, 183–195.
48MS Ammor , AB Florez & B Mayo (2007) Antibiotic resistance in non-enterococcal lactic acid bacteria and bifidobacteria. Food Microbiol 24, 559–570.
49B Brismar , C Edlund & CE Nord (1993) Impact of cefpodoxime proxetil and amoxicillin on the normal oral and intestinal microflora. Eur J Clin Microbiol Infect Dis 12, 714–719.
51EJ Woodmansey , ME McMurdo , GT Macfarlane , (2004) Comparison of compositions and metabolic activities of fecal microbiotas in young adults and in antibiotic-treated and non-antibiotic-treated elderly subjects. Appl Environ Microbiol 70, 6113–6122.
52D Goossens , D Jonkers , M Russel , (2003) The effect of Lactobacillus plantarum 299v on the bacterial composition and metabolic activity in faeces of healthy volunteers: a placebo-controlled study on the onset and duration of effects. Aliment Pharmacol Ther 18, 495–505.
54GW Tannock , K Munro , HJ Harmsen , (2000) Analysis of the fecal microflora of human subjects consuming a probiotic product containing Lactobacillus rhamnosus DR20. Appl Environ Microbiol 66, 2578–2588.
55K Kajander , E Myllyluoma , M Rajilic-Stojanovic , (2007) Clinical trial: multispecies probiotic supplementation alleviates the symptoms of IBS and stabilises intestinal microbiota. Aliment Pharmacol Ther 27, 48–57.