Sequence errors in GenBank sequence of strain E (DOW) of <i>R. prowazekii</i>.

<p>Sequence errors in GenBank sequence of strain E (DOW) of <i>R. prowazekii</i>.</p

Body weight changes after infection with <i>R. prowazekii</i> strain E strain (DHW) and strain Evir at 10⁴, 10⁵, or 10⁶ organisms.

<p>L929 cell suspension was used as control.</p

Mutation in Madrid E strains of <i>R. prowazekii</i>.

<p>Mutation position was referred to the nucleotide position with the open reading frame of the gene.</p><p>Mutation in Madrid E strains of <i>R. prowazekii</i>.</p

Body temperature changes after infection with <i>R. prowazekii</i> strain E (DHW) and strain Evir at 10⁶ (E or Evir), 10⁵ (E1:10 and Evir 1:10), or 10⁴ (E1:100 and Evir 1:100) organisms.

<p>L929 cell suspension was used as control.</p

Premature gut microbiota variation in the first two month of life.

<p>The gut microbiota variation at class level over 0–60 days of life from all the samples is visualized by NMDS plot. The color gradient from red to blue represents the day of life of the babies. The microbiota from early day of life is distinguished from the elder days.</p

Anellovirus DNA was more prevalent in specimens from febrile children by high-throughput sequencing.

<p><b>A–B</b>. High-throughput sequencing analysis of plasma (<b>A</b>) and NP (<b>B</b>) specimens showed that a higher percentage of specimens from febrile children contained anellovirus DNA compared to specimens from afebrile children (plasma, p = 0.034; NP, p = 0.002). <b>C</b>. The trend was the same, but not statistically significant at the patient level of analysis. <b>D–E</b>. Afebrile and febrile patients had a similar median number of anellovirus sequence reads in their plasma (10.2 vs. 15.6) (<b>D</b>) and NP (2.9 vs. 1.7) (<b>E</b>) specimens. <b>F</b>. Anellovirus sequences detected by high-throughput sequencing were more prevalent in plasma compared to NP specimens (p<0.0001; Chi-squared test).</p

NMDS of early and late onset NEC and controls at the genus level.

<p>The difference between NEC and controls is displayed for early onset NEC (Fig. 2A) and late onset NEC (Fig. 2B) with their controls by NMDS plot. Each dot represents one sample. Green dots represent the controls and red dots represent the NEC samples. Early NEC subjects and control subjects have a clear separation at second week of the life. The distinction between late onset NEC and controls is less obvious except at the third week of life.</p

Microbiota progression before early onset NEC and late onset NEC at class and genus level.

<p>The relative abundances of four most dominant classes (Fig. 3A-early onset at class level, 3B-late onset at class level) and the genera (Fig. 3C-early onset at genus level, 3D-late onset at genus level) that are significantly different between NEC and controls are plotted at 7–9 days, 4–6 days and 1–3 days prior to NEC onset. In early onset NEC category, 3,6, 8 NEC samples were included at 7–9 days, 4–6 days and 1–3 days; 8, 5, 6 control samples were included in the above time points. In late onset NEC category, 7, 7,10 NEC samples and 6, 8, 4 control samples were included in the above time points. Red and green of the boxplots indicate NEC and control samples, respectively. The asterisks indicate the significant difference between NEC and control.</p

PCR analysis showed that DNA from human anellovirus species TTV and TTMDV, but not TTMV, were more prevalent in febrile patient specimens compared to afebrile controls.

<p><b>A–C</b>. PCR identified TTV (<b>A</b>) and TTMDV (<b>B</b>) in a higher percentage of febrile patients compared to afebrile controls while TTMV (<b>C</b>) was present in equivalent percentages (plasma TTV, p = 0.0567; NP TTV, p = 0.0182; patient TTV, p = 0.0026). <b>D</b>. The majority of patients were either positive or negative for TTV, TTMDV, and TTMV DNA in both their plasma and NP specimens. P-values determined by chi-squared test.</p

Many patient specimens contained DNA from multiple human anellovirus species.

<p><b>A–B</b>. Patient plasma (<b>A</b>) and NP (<b>B</b>) specimens were assayed for TTV, TTMDV, and TTV DNA by PCR and the percentage of specimens with 3, 2, 1, or no anellovirus species were determined.</p