The investigators have established the "Evaluating the Alimentary and Respiratory Tracts in Health and disease" (EARTH) research program. It provides a structured approach to analysing gastrointestinal and respiratory microbiomes, along with diet and symptomatology, in children with a gastrointestinal and/or respiratory condition with recognised long-term morbidity (e.g. cystic fibrosis, obstructive sleep apnoea, or Hirschsprung's disease). The EARTH program consists of a series of prospective, longitudinal, controlled, observational studies, with each individual study comparing children with a chronic gastrointestinal and/or respiratory condition to healthy controls (HC). It will be conducted in an Australian tertiary paediatric hospital (although the methodology is applicable to other settings). Children with a chronic gastrointestinal and/or respiratory condition will be compared to age and gender matched HC across a 12-month period. The following will be collected at baseline, 6 and 12 months: (i) a stool sample, (ii) an oropharyngeal swab or sputum sample, (iii) a semi-quantitative food frequency questionnaire, (iv) details of disease symptomatology, (v) health-related quality of life, and (vi) psychosocial factors. Data on the intestinal and respiratory microbiomes and diet will be compared between children with a condition and HC. Correlations between dietary intake (energy, macro- and micro-nutrients), intestinal and respiratory microbiomes within each group will be explored. Data on disease symptomatology, quality of life and psychosocial factors will also be compared between children with a condition and HC. The investigators hypothesise that: (i) Children with chronic gastrointestinal and/or respiratory conditions will have altered intestinal and respiratory microbiomes compared to healthy children, and (ii) Diet plays a key role in influencing the intestinal and respiratory microbiomes and this may impact on clinical outcomes, biomarkers of disease, and health-related quality of life.
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1A.i.0 Intestinal Microbiome (Bacteria) - Richness
Timeframe: Baseline
1A.i.6 Intestinal Microbiome (Bacteria) - Richness
Timeframe: Change from baseline at 6 months
1A.i.12 Intestinal Microbiome (Bacteria) - Richness
Timeframe: Change from baseline at 12 months
1A.ii.0 Intestinal Microbiome (Bacteria) - Shannon index
Timeframe: Baseline
1A.ii.6 Intestinal Microbiome (Bacteria) - Shannon index
Timeframe: Change from baseline at 6 months
1A.ii.12 Intestinal Microbiome (Bacteria) - Shannon index
Timeframe: Change from baseline at 12 months
1A.iii.0 Intestinal Microbiome (Bacteria) - UNIFRAC distances
Timeframe: Baseline
1A.iii.6 Intestinal Microbiome (Bacteria) - UNIFRAC distances
Timeframe: 6 months
1A.iii.12 Intestinal Microbiome (Bacteria) - UNIFRAC distances
Timeframe: 12 months
1A.iv.0 Intestinal Microbiome (Bacteria) - relative abundances of bacteria
Timeframe: Baseline
1A.iv.6 Intestinal Microbiome (Bacteria) - relative abundances of bacteria
Timeframe: Change from baseline at 6 months
1A.iv.12 Intestinal Microbiome (Bacteria) - relative abundances of bacteria
Timeframe: Change from baseline at 12 months
1B.i.0 Intestinal Microbiome (Proteome) - normalised abundances of proteins
Timeframe: Baseline
1B.i.6 Intestinal Microbiome (Proteome) - normalised abundances of proteins
Timeframe: Change from baseline at 6 months
1B.i.12 Intestinal Microbiome (Proteome) - normalised abundances of proteins
Timeframe: Change from baseline at 12 months
1C.i.0 Intestinal Microbiome (Metabolome) - normalised abundances of metabolites
Timeframe: Baseline
1C.i.6 Intestinal Microbiome (Metabolome) - normalised abundances of metabolites
Timeframe: Change from baseline at 6 months
1C.i.12 Intestinal Microbiome (Metabolome) - normalised abundances of metabolites
Timeframe: Change from baseline at 12 months
1D.i.0 Intestinal Microbiome (Viruses) - Richness
Timeframe: Baseline
1D.i.6 Intestinal Microbiome (Viruses) - Richness
Timeframe: Change from baseline at 6 months
1D.i.12 Intestinal Microbiome (Viruses) - Richness
Timeframe: Change from baseline at 12 months
1D.ii.0 Intestinal Microbiome (Viruses) - Shannon index
Timeframe: Baseline
1D.ii.6 Intestinal Microbiome (Viruses) - Shannon index
Timeframe: Change from baseline at 6 months
1D.ii.12 Intestinal Microbiome (Viruses) - Shannon index
Timeframe: Change from baseline at 12 months
1D.iii.0 Intestinal Microbiome (Viruses) - Bray-Curtis dissimilarity
Timeframe: Baseline
1D.iii.6 Intestinal Microbiome (Viruses) - Bray-Curtis dissimilarity
Timeframe: 6 months
1D.iii.12 Intestinal Microbiome (Viruses) - Bray-Curtis dissimilarity
Timeframe: 12 months
1D.iv.0 Intestinal Microbiome (Viruses) - relative abundances of viruses.
Timeframe: Baseline
1D.iv.6 Intestinal Microbiome (Viruses) - relative abundances of viruses.
Timeframe: Change from baseline at 6 months
1D.iv.12 Intestinal Microbiome (Viruses) - relative abundances of viruses.
Timeframe: Change from baseline at 12 months
2A.i.0 Respiratory Microbiome (Bacteria) - Richness
Timeframe: Baseline
2A.i.6 Respiratory Microbiome (Bacteria) - Richness
Timeframe: Change from baseline at 6 months
2A.i.12 Respiratory Microbiome (Bacteria) - Richness
Timeframe: Change from baseline at 12 months
2A.ii.0 Respiratory Microbiome (Bacteria) - Shannon index
Timeframe: Baseline
2A.ii.6 Respiratory Microbiome (Bacteria) - Shannon index
Timeframe: Change from baseline at 6 months
2A.ii.12 Respiratory Microbiome (Bacteria) - Shannon index
Timeframe: Change from baseline at 12 months
2A.iii.0 Respiratory Microbiome (Bacteria) - UNIFRAC distances
Timeframe: Baseline
2A.iii.6 Respiratory Microbiome (Bacteria) - UNIFRAC distances
Timeframe: Change from baseline at 6 months
2A.iii.12 Respiratory Microbiome (Bacteria) - UNIFRAC distances
Timeframe: Change from baseline at 12 months
2A.iv.0 Respiratory Microbiome (Bacteria) - relative abundances of bacteria
Timeframe: Baseline
2A.iv.6 Respiratory Microbiome (Bacteria) - relative abundances of bacteria
Timeframe: Change from baseline at 6 months
2A.iv.12 Respiratory Microbiome (Bacteria) - relative abundances of bacteria
Timeframe: Change from baseline at 12 months
2B.i.0 Respiratory Microbiome (Proteome) - normalised abundances of proteins
Timeframe: Baseline
2B.i.6 Respiratory Microbiome (Proteome) - normalised abundances of proteins
Timeframe: Change from baseline at 6 months
2B.i.12 Respiratory Microbiome (Proteome) - normalised abundances of proteins
Timeframe: Change from baseline at 12 months
2C.i.0 Respiratory Microbiome (Metabolome) - normalised abundances of metabolites
Timeframe: Baseline
2C.i.6 Respiratory Microbiome (Metabolome) - normalised abundances of metabolites
Timeframe: Change from baseline at 6 months
2C.i.12 Respiratory Microbiome (Metabolome) - normalised abundances of metabolites
Timeframe: Change from baseline at 12 months
2D.i.0 Respiratory Microbiome (Viruses) - Richness
Timeframe: Baseline
2D.i.6 Respiratory Microbiome (Viruses) - Richness
Timeframe: Change from baseline at 6 months
2D.i.12 Respiratory Microbiome (Viruses) - Richness
Timeframe: Change from baseline at 12 months
2D.ii.0 Respiratory Microbiome (Viruses) - Shannon index
Timeframe: Baseline
2D.ii.6 Respiratory Microbiome (Viruses) - Shannon index
Timeframe: Change from baseline at 6 months
2D.ii.12 Respiratory Microbiome (Viruses) - Shannon index
Timeframe: Change from baseline at 12 months
2D.iii.0 Respiratory Microbiome (Viruses) - Bray-Curtis dissimilarity
Timeframe: Baseline
2D.iii.6 Respiratory Microbiome (Viruses) - Bray-Curtis dissimilarity
Timeframe: 6 months
2D.iii.12 Respiratory Microbiome (Viruses) - Bray-Curtis dissimilarity
Timeframe: 12 months
2D.iv.0 Respiratory Microbiome (Viruses) - relative abundances of viruses
Timeframe: Baseline
2D.iv.6 Respiratory Microbiome (Viruses) - relative abundances of viruses
Timeframe: Change from baseline at 6 months
2D.iv.12 Respiratory Microbiome (Viruses) - relative abundances of viruses
Timeframe: Change from baseline at 12 months
3A.i.0 Diet - total energy intake
Timeframe: Baseline
3A.i.6 Diet - total energy intake
Timeframe: Change from baseline at 6 months
3A.i.12 Diet - total energy intake
Timeframe: Change from baseline at 12 months
3B.i.0 Diet - percentage energy from core foods
Timeframe: Baseline
3B.i.6 Diet - percentage energy from core foods
Timeframe: Change from baseline at 6 months
3B.i.12 Diet - percentage energy from core foods
Timeframe: Change from baseline at 12 months
3C.i.0 Diet - total macronutrients intake
Timeframe: Baseline
3C.i.6 Diet - total macronutrients intake
Timeframe: Change from baseline at 6 months
3C.i.12 Diet - total macronutrients intake
Timeframe: Change from baseline at 12 months
3C.ii.0 Diet - macronutrients proportion of total energy intake
Timeframe: Baseline
3C.ii.6 Diet - macronutrients proportion of total energy intake
Timeframe: Change from baseline at 6 months
3C.ii.12 Diet - macronutrients proportion of total energy intake
Timeframe: Change from baseline at 12 months
3D.i.0 Diet - total micronutrients intake
Timeframe: Baseline
3D.i.6 Diet - total micronutrients intake
Timeframe: Change from baseline at 6 months
3D.i.12 Diet - total micronutrients intake
Timeframe: Change from baseline at 12 months
3D.ii.0 Diet - micronutrients proportion of total energy intake
Timeframe: Baseline
3D.ii.6 Diet - micronutrients proportion of total energy intake
Timeframe: Change from baseline at 6 months
3D.ii.12 Diet - micronutrients proportion of total energy intake
Timeframe: Change from baseline at 12 months
3E.i.0 Diet - diet quality score
Timeframe: Baseline
3E.i.6 Diet - diet quality score
Timeframe: Change from baseline at 6 months
3E.i.12 Diet - diet quality score
Timeframe: Change from baseline at 12 months