Additional file 6: Figure S4. of Effect of room temperature transport vials on DNA quality and phylogenetic composition of faecal microbiota of elderly adults and infants

Microbiota composition of each sample of four subjects after all conditions of storage. L = Fresh extraction 0.2 g stool; M = Fresh extraction 0.1 g stool; N = storage for 1 week in DNA Genotek storage vial and extracted with 4 % SDS RBB lysis buffer; O = storage for 1 week in DNA Genotek storage vial and extracted with 6 % SDS RBB lysis buffer; P = storage in regular stool collection tube at 4 °C for 1 week; Q = storage for 2 weeks in DNA Genotek storage vial and extracted with 4 % SDS RBB lysis buffer; R = storage for 2 weeks in DNA Genotek storage vial and extracted with 6 % SDS RBB lysis buffer; S = Frozen at−80 °C for a week prior to extraction; T = 0.2 g of stool fixed overnight in 700 μl of RNAlater before freezing at−80 °C for a week. (PDF 54 kb

Additional file 2: Figure S1. of Effect of room temperature transport vials on DNA quality and phylogenetic composition of faecal microbiota of elderly adults and infants

Microbiota composition of each sample for every infant subject in the study. A = Fresh, B = 1 week’s storage, C = 2 weeks’ storage. Numbers indicate subject IDs. (PDF 120 kb

<i>Helicobacter pylori</i>, HIV and Gastric Hypochlorhydria in the Malawian Population

<div><p>Background</p><p>HIV and <i>Helicobacter pylori</i> are common chronic infections in sub-Saharan Africa. Both conditions can predispose to gastric hypochlorhydria that may be a risk factor for enteric infections and reduced drug absorption. We have investigated to what extent HIV and <i>H</i>. <i>pylori</i> infections are associated with hypochlorhydria in a Malawian cohort of patients undergoing endoscopy.</p><p>Methods</p><p>104 sequential symptomatic adults referred for gastroscopy at Queen Elizabeth Central Hospital, Blantyre, Malawi, had blood taken for rapid HIV testing and fasting serum gastrin analysis. Gastric fluid was aspirated for pH testing, and gastric biopsies were taken.</p><p>Results</p><p>After 9/104 HIV-infected patients who were already established on anti-retroviral therapy were excluded, 17/95 (25.0%) were seropositive for untreated HIV, and 68/95 (71.6%) patients were <i>H</i>. <i>pylori</i> positive by histology. Hypochlorhydria (fasting gastric pH>4.0) was present in 55.8% (53/95) of patients. <i>H</i>. <i>pylori</i> infection was significantly associated with hypochlorhydria (OR 2.91, [1.02-7.75], p=0.046). While single infection with HIV was not significantly independently associated with hypochlorhydria. <i>H</i>. <i>pylori</i> and HIV co-infection was more strongly associated with hypochlorhydria (OR 6.25, [1.33-29.43], p=0.020) than either infection alone, suggesting an additive effect of co-infection. HIV infection was associated with higher serum gastrin levels (91.3pM vs. 53.1pM, p=0.040), while <i>H</i>. <i>pylori</i> infection was not (63.1pM vs. 55.1pM, p=0.610). Irrespective of <i>H</i>. <i>pylori</i> and HIV status, most patients (>90%) exhibited pangastritis. Only three patients had histological evidence of gastric atrophy, of which only one was HIV-infected.</p><p>Conclusion</p><p><i>H</i>. <i>pylori</i> infection was associated with fasting hypochlorhydria, while HIV was not independently associated. HIV and <i>H</i>. <i>pylori</i> co-infection, however, was more strongly associated with hypochlorhydria than <i>H</i>. <i>pylori</i> infection alone. The mechanism of this apparent additive effect between HIV and <i>H</i>. <i>pylori</i> remains unclear, but appears to be related to chronic pangastritis rather than gastric atrophy, and associated with hypergastrinaemia in HIV-infected individuals.</p></div

The scatterplot displays the serum gastrin (pM) levels for the four groups in relation to <i>H</i>.<i>pylori</i> and HIV infection status.

<p>The scatterplot displays the serum gastrin (pM) levels for the four groups in relation to <i>H</i>.<i>pylori</i> and HIV infection status.</p

The scatterplot displays the absolute pH values for the four groups in relation to <i>H</i>.<i>pylori</i> and HIV infection status.

<p>The scatterplot displays the absolute pH values for the four groups in relation to <i>H</i>.<i>pylori</i> and HIV infection status.</p

Univariate and binary logistic regression by factors potentially associated with hypochlorhydria.

<p>Univariate and binary logistic regression by factors potentially associated with hypochlorhydria.</p

Histological assessment of antral and corpus (body) biopsies from all subjects.

<p>Histological assessment of antral and corpus (body) biopsies from all subjects.</p

Mean gastric pH values by age, gender, <i>H</i>. <i>pylori</i> and HIV status.

<p>Mean gastric pH values by age, gender, <i>H</i>. <i>pylori</i> and HIV status.</p

Findings at gastroscopy; the examination was entirely normal in 27 (26%) patients.

<p>Findings at gastroscopy; the examination was entirely normal in 27 (26%) patients.</p

Binary logistic regression analysis investigating the impact of single infection or co-infection with <i>H</i>. <i>pylori</i> (HP) and HIV on the odds of having hypochlorhydria.

<p>Binary logistic regression analysis investigating the impact of single infection or co-infection with <i>H</i>. <i>pylori</i> (HP) and HIV on the odds of having hypochlorhydria.</p