Influence of fecal collection conditions and 16S rRNA gene sequencing at two centers on human gut microbiota analysis

Published online: 12 March 2018To optimise fecal sampling for reproducible analysis of the gut microbiome, we compared different methods of sample collection and sequencing of 16S rRNA genes at two centers. Samples collected from six individuals on three consecutive days were placed in commercial collection tubes (OMNIgeneGut OMR-200) or in sterile screw-top tubes in a home fridge or home freezer for 6-24 h, before transfer and storage at -80 °C. Replicate samples were shipped to centers in Australia and the USA for DNA extraction and sequencing by their respective PCR protocols, and analysed with the same bioinformatic pipeline. Variation in gut microbiome was dominated by differences between individuals. Minor differences in the abundance of taxa were found between collection-processing methods and day of collection, and between the two centers. We conclude that collection with storage and transport at 4 °C within 24 h is adequate for 16S rRNA analysis of the gut microbiome. Other factors including differences in PCR and sequencing methods account for relatively minor variation compared to differences between individuals.Jocelyn Sietsma Penington, Megan A. S. Penno, Katrina M. Ngui, Nadim J. Ajami, Alexandra J. Roth-Schulze, Stephen A. Wilcox, Esther Bandala-Sanchez, John M. Wentworth, Simon C. Barry, Cheryl Y. Brown, Jennifer J. Couper, Joseph F. Petrosino, Anthony T. Papenfuss, Leonard C. Harrison and ENDIA Study Group (Lynne Giles and Rebecca L. Thomson

Pancreas size and exocrine function is decreased in young children with recent-onset Type 1 diabetes

AIMS:To measure pancreatic area and exocrine function in young children with recent-onset Type 1 diabetes to determine whether the exocrine pancreas is also affected in the pathophysiology of early childhood diabetes. METHODS:Thirty-two children (14 boys) aged 5.5 (4.5, 7.3) median (IQR) years presenting with recent-onset Type 1 diabetes and 90 controls (44 boys) of similar age had ultrasound imaging of the pancreas. Children with Type 1 diabetes were receiving insulin and were without ketosis. Transverse and longitudinal areas of the pancreas were measured by digitalized outline. Pancreatic faecal elastase-1 was analysed using an enzyme-linked immunosorbent assay kit in recent-onset Type 1 diabetes and 38 first-degree relative control children. RESULTS:Pancreatic area and exocrine function were reduced in Type 1 diabetes. Mean transverse area (SD) in Type 1 diabetes was 6.82 cm2 (1.61) vs. 8.31 cm2 (1.74) in controls, adjusted estimate (95% CI) 1.45 (-2.12, -0.79), P < 0.001; longitudinal area was 1.28 cm2 (0.44) vs. 1.55 cm2 (0.43), adjusted estimate (95% CI) -0.27 (-0.45, -0.09), P = 0.003. Faecal elastase-1 levels in Type 1 diabetes were 455 (323, 833) ug/g, median (IQR) vs. 1408 μg/g (1031, 1989) in controls, P < 0.001. CONCLUSION:Pancreatic area and accompanying subclinical exocrine function were reduced in very young children with recent-onset Type 1 diabetes. This supports changes in the exocrine pancreas in the pathophysiology of Type 1 diabetes presenting in early life.P. Augustine, R. Gent, J. Louise, M. Taranto, M. Penno, R. Linke and J. J. Couper, on behalf of the ENDIA Study Grou

Cohort profile: the Australia-wide environmental determinants of islet autoimmunity (ENDIA) study

Abstract presented at 55th EASD Annual Meeting of the European Association for the Study of DiabetesA. Haynes, L.C. Giles, M.A.S. Penno, R.L. Thomson , K.J. McGorm, P.G. Colman, M.E. Craig, E.A. Davis, M. Harris, L.C. Harrison, G. Soldatos, J.M. Wentworth, P. Vuillermin, J.J. Couper, the ENDIA Study Grou

Evaluation of protocol amendments to the Environmental Determinants of Islet Autoimmunity (ENDIA) study during the COVID-19 pandemic

LetterThe Environmental Determinants of Islet Autoimmunity (ENDIA) Study is an Australia-wide observational pregnancy-birth cohort of children at genetic risk on account of a first-degree relative with type 1 diabetes (1). 1511 participants were recruited from all Australian States and Territories from 2013-2019 with 1473 live-born infants in follow-up. The standard protocol involves 3-monthly face-to-face visits from pregnancy until the child is 2 years of age, then 6-monthly visits. Study staff across nine centres in five States collect biospecimens (blood, urine, stool, swabs) and administer lifestyle and dietary questionnaires. Approximately 10% of the cohort are engaged in a Regional Participant Program (2) that requires self-collection of sample types except for venepuncture performed at local pathology services.Megan A. S. Penno, Amanda J. Anderson, Rebecca L. Thomson, Kelly McGorm, Simon C. Barry, Peter G. Colman, Maria E. Craig, Elizabeth A. Davis, Mark Harris, Aveni Haynes, Grant Morahan, Helena Oakey, William D. Rawlinson, Richard O. Sinnott, Georgia Soldatos, Peter J. Vuillermin, John M. Wentworth, Leonard C. Harrison, Jennifer J. Couper, the ENDIA Study Grou

Mental Health During Late Pregnancy and Postpartum in Mothers With and Without Type 1 Diabetes: The ENDIA Study

This article contains supplementary material online at https://doi.org/10.2337/figshare.18551261.Objective: Pregnancy and type 1 diabetes are each associated with increased anxiety and depression, but the combined impact on well-being is unresolved. We compared the mental health of women with and without type 1 diabetes during pregnancy and postpartum and examined the relationship between mental health and glycemic control. Research Design and Methods: Participants were women enrolled from 2016 to 2020 in the Environmental Determinants of Islet Autoimmunity (ENDIA) study, a pregnancy to birth prospective cohort following children with a first-degree relative with type 1 diabetes. Edinburgh Postnatal Depression Scale (EPDS) and Perceived Stress Scale (PSS) were completed during the third trimester (T3) (median [interquartile range] 34 [32, 36] weeks) and postpartum (14 [13, 16] weeks) by 737 women (800 pregnancies) with (n = 518) and without (n = 282) type 1 diabetes. Results: EPDS and PSS scores did not differ between women with and without type 1 diabetes during T3 and postpartum. EPDS scores were marginally higher in T3: predicted mean (95% CI) 5.7 (5.4, 6.1) than postpartum: 5.3 (5.0, 5.6), independent of type 1 diabetes status (P = 0.01). HbA1c levels in type 1 diabetes were 6.3% [5.8, 6.9%] in T3 and did not correlate with EPDS or PSS scores. Reported use of psychotropic medications was similar in women with (n = 44 of 518 [8%]) and without type 1 diabetes (n = 17 of 282 [6%]), as was their amount of physical activity. Conclusions: Overall, mental health in late pregnancy and postpartum did not differ between women with and without type 1 diabetes, and mental health scores were not correlated with glycemic control.Madeleine Hall, Helena Oakey, Megan A.S. Penno, Kelly McGorm, Amanda J. Anderson, Pat Ashwood, Peter G. Colman, Maria E. Craig, Elizabeth A. Davis, Mark Harris, Leonard C. Harrison, Aveni Haynes, Claire Morbey, Richard O. Sinnott, Georgia Soldatos, Peter J. Vuillermin, John M. Wentworth, Rebecca L. Thomson, Jennifer J. Couper on behalf of the ENDIA Study Grou

A surge in serum mucosal cytokines associated with seroconversion in children at risk for type 1 diabetes

ABSTRACT Aims/Introduction Autoantibodies to pancreatic islet antigens identify young children at high risk of type 1 diabetes. On a background of genetic susceptibility, islet autoimmunity is thought to be driven by environmental factors, of which enteric viruses are prime candidates. We sought evidence for enteric pathology in children genetically at‐risk for type 1 diabetes followed from birth who had developed islet autoantibodies (“seroconverted”), by measuring mucosa‐associated cytokines in their sera. Materials and Methods Sera were collected 3 monthly from birth from children with a first‐degree type 1 diabetes relative, in the Environmental Determinants of Islet Autoimmunity (ENDIA) study. Children who seroconverted were matched for sex, age, and sample availability with seronegative children. Luminex xMap technology was used to measure serum cytokines. Results Of eight children who seroconverted, for whom serum samples were available at least 6 months before and after seroconversion, the serum concentrations of mucosa‐associated cytokines IL‐21, IL‐22, IL‐25, and IL‐10, the Th17‐related cytokines IL‐17F and IL‐23, as well as IL‐33, IFN‐γ, and IL‐4, peaked from a low baseline in seven around the time of seroconversion and in one preceding seroconversion. These changes were not detected in eight sex‐ and age‐matched seronegative controls, or in a separate cohort of 11 unmatched seronegative children. Conclusions In a cohort of children at risk for type 1 diabetes followed from birth, a transient, systemic increase in mucosa‐associated cytokines around the time of seroconversion lends support to the view that mucosal infection, e.g., by an enteric virus, may drive the development of islet autoimmunity