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Hi everyone, in our next session on Tuesday, the 24th of June at 8 pm (BST) we will look at the following paper:

“Circulating Avian Influenza Viruses Closely Related to the 1918 VirusHave Pandemic Potential” by Watanabe et al from Japan & the US published on the 11th of June 2014 in cell Host&Microbe available here:


Wild birds harbor a large gene pool of influenza A viruses that have the potential to cause influenza pandemics. Foreseeing and understanding this potentialis important for effective surveillance. Our phylogenetic and geographic analyses revealed the global prevalence of avian influenza virus genes whose proteins differ only a few amino acids from the 1918 pandemic influenza virus, suggesting that 1918-like pandemic viruses may emerge in the future. To assess this risk, we generated and characterized a virus composed of avian influenza viral segments with high homology to the 1918 virus. This virus exhibited pathogenicity in mice and ferrets higher than that in an authentic avian influenza virus. Further, acquisition of seven amino acid substitutions in the viral polymerases and the hemagglutinin surface glycoprotein conferred respiratory droplet transmission to the 1918-like avian virus in ferrets, demonstrating that contemporary avian influenza viruses with 1918 virus-like proteins may have pandemic potential.

The paper also got some news coverage, some examples can be found here:

Discussion points:

1. Was the publication written for an easy understanding?

2. Are the methods chosen appropiately?

3. Is the data well presented?

4. Does the paper achieve what the authors set it out?

5. What do you think of this research? Is it ethically to perform this high-risk research? Or would it be better to study it only theoretically? (to include the public discussion aspect)

Hope to see many of you there,



@Stewart_Barker here, very happy to be running the 50th meeting of the #MicroTwJC!

I will be tweeting from @MicroTwJC on the night (10th June, 8pm GMT), please remember to use #MicroTwJC on all tweets!

I stuck with the paper’s original title (I mean how can you re-word that?!), which can be found here:

Although some may flinch at the term ‘vaginal microbiome’, it is an important area of cross-interdisciplinary study that has implications for infections during pregnancy. This study looks at n=12 caucasian women, and compares to a ‘complementary study’ on african-american women.

The usual questions apply!:

  1. Is the paper easy to understand?
  2. Are the methods used suitable and correct?
  3. Is the data well presented and analysed?
  4. Does the paper achieve what the authors set out to do?
  5. What further work can be carried out?



Objective: To assess the vaginal microbiome throughout full-term uncomplicated pregnancy.

Methods: Vaginal swabs were obtained from twelve pregnant women at 8-week intervals throughout their uncomplicated
pregnancies. Patients with symptoms of vaginal infection or with recent antibiotic use were excluded. Swabs were obtained
from the posterior fornix and cervix at 8–12, 17–21, 27–31, and 36–38 weeks of gestation. The microbial community was
profiled using hypervariable tag sequencing of the V3–V5 region of the 16S rRNA gene, producing approximately 8 million
reads on the Illumina MiSeq.

Results: Samples were dominated by a single genus, Lactobacillus, and exhibited low species diversity. For a majority of the
patients (n = 8), the vaginal microbiome was dominated by Lactobacillus crispatus throughout pregnancy. Two patients
showed Lactobacillus iners dominance during the course of pregnancy, and two showed a shift between the first and
second trimester from L. crispatus to L. iners dominance. In all of the samples only these two species were identified, and
were found at an abundance of higher than 1% in this study. Comparative analyses also showed that the vaginal
microbiome during pregnancy is characterized by a marked dominance of Lactobacillus species in both Caucasian and
African-American subjects. In addition, our Caucasian subject population clustered by trimester and progressed towards a
common attractor while African-American women clustered by subject instead and did not progress towards a common

Conclusion: Our analyses indicate normal pregnancy is characterized by a microbiome that has low diversity and high
stability. While Lactobacillus species strongly dominate the vaginal environment during pregnancy across the two studied
ethnicities, observed differences between the longitudinal dynamics of the analyzed populations may contribute to
divergent risk for pregnancy complications. This helps establish a baseline for investigating the role of the microbiome in
complications of pregnancy such as preterm labor and preterm delivery