You are currently browsing Stewart Barker’s articles.
And welcome back to #microTwJC! We took some time off to re-organise our admins, but now we’re back and ready to discuss the latest in microbiology research. I will be tweeting from @Microtwjc, and you can follow the conversation using #microTwJC. All are welcome to join in, at 8pm BST on Tuesday 8th September.
This weeks paper was picked by new admin Frances @ and is being presented by myself – Stewart @stewart_barker, entitled “Distinct soil microbial diversity under long-term organic and conventional farming”. The paper can be accessed for free here!: http://www.nature.com/ismej/journal/v9/n5/full/ismej2014210a.html.
Low-input agricultural systems aim at reducing the use of synthetic fertilizers and pesticides in order to improve sustainable production and ecosystem health. Despite the integral role of the soil microbiome in agricultural production, we still have a limited understanding of the complex response of microbial diversity to organic and conventional farming. Here we report on the structural response of the soil microbiome to more than two decades of different agricultural management in a long-term field experiment using a high-throughput pyrosequencing approach of bacterial and fungal ribosomal markers. Organic farming increased richness, decreased evenness, reduced dispersion and shifted the structure of the soil microbiota when compared with conventionally managed soils under exclusively mineral fertilization. This effect was largely attributed to the use and quality of organic fertilizers, as differences became smaller when conventionally managed soils under an integrated fertilization scheme were examined. The impact of the plant protection regime, characterized by moderate and targeted application of pesticides, was of subordinate importance. Systems not receiving manure harboured a dispersed and functionally versatile community characterized by presumably oligotrophic organisms adapted to nutrient-limited environments. Systems receiving organic fertilizer were characterized by specific microbial guilds known to be involved in degradation of complex organic compounds such as manure and compost. The throughput and resolution of the sequencing approach permitted to detect specific structural shifts at the level of individual microbial taxa that harbours a novel potential for managing the soil environment by means of promoting beneficial and suppressing detrimental organisms.
1. Is this paper well written and easy to understand?
2. Does the introduction set the scene for the research presented?
3. Do the methods appear reliable and are they well explained?
4. Do the results and discussion make sense?
5. What (if any) future work could lead on from this?
Hope to see you at 8 pm BST, Tuesday 8th September! Use #microTwJC to follow the conversation.
Stewart and Frances
Welcome to #MicroTwJC 55, hosted on 14/10/2014 by @_LisaKWilliams_ and @Stewart_Barker.
This week we will be discussing the fascinating world of virophages – that is viruses which attack other viruses. The paper can be found here: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0094923
Following a previous #MicroTwJC discussion on the largest discovered viruses, this fairly recent paper describes a satellite virus (or virophage) named Zamilon that is associated with the giant virus family Mimiviridae. Zamilon is similar to other described virophages which have negative effects on their host – Sputnik virophages, yet does not appear to inhibit it’s host in any way…
“The host-specificity of the Zamilon virophage supports the distinction between satellite viruses (opportunistic entities associated with a virus) and virophages, which target specific hosts.”
Aside from what we think is an interesting paper and concept, the above quote is a crucial point of the paper. We leave you with the abstract and questions to consider below, and look forward to a lively debate!
Virophages, which are potentially important ecological regulators, have been discovered in association with members of the order Megavirales. Sputnik virophages target the Mimiviridae, Mavirus was identified with the Cafeteria roenbergensis virus, and virophage genomes reconstructed by metagenomic analyses may be associated with the Phycodnaviridae. Despite the fact that the Sputnik virophages were isolated with viruses belonging to group A of theMimiviridae, they can grow in amoebae infected by Mimiviridae from groups A, B or C. In this study we describe Zamilon, the first virophage isolated with a member of group C of theMimiviridae family. By co-culturing amoebae with purified Zamilon, we found that the virophage is able to multiply with members of groups B and C of the Mimiviridae family but not with viruses from group A. Zamilon has a 17,276 bp DNA genome that potentially encodes 20 genes. Most of these genes are closely related to genes from the Sputnik virophage, yet two are more related to Megavirus chiliensis genes, a group B Mimiviridae, and one to Moumouvirus monve transpoviron.
Points to consider
- Is the paper well written?
- Do the methods fully investigate whether the Zamilon virophage has a disruptive effect on its host?
- Are the results and discussion appropriate?
- Is Zamilon a virophage, or a satellite virus? Is there actually a difference between the two terms?
@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: http://www.plosone.org/article/fetchObject.action?uri=info%3Adoi%2F10.1371%2Fjournal.pone.0098514&representation=PDF
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!:
- Is the paper easy to understand?
- Are the methods used suitable and correct?
- Is the data well presented and analysed?
- Does the paper achieve what the authors set out to do?
- 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
Hi again everyone, @Stewart_Barker here with #microtwjc 37.
This week’s paper can be accessed here: http://www.unomaha.edu/toxoplasma/docs/jc20130906.pdf
In 2011 Scientists believed they had finally found the largest virus in existence, Megavirus chilensis (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3198346/). This relative behemoth stands at 1.259 megabases, encoding 1120 proteins. For comparison, one of the smallest known bacteria Hodgkinia cicadicola (a symbiont of Cicadas) has a genome of only 144 kb (read the PLOS paper here: http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000565). Viruses of this size were an unprecedented find – one that many thought would never be topped.
For today’s session, we will be looking at one of this year’s most interesting microbiology discoveries – the Pandoravirus. Two isolates are described in this paper, Pandoravirus salinus (2.5-2.77 mb genome) and Pandoravirus dulcis (1.9 mb) – from saltwater and freshwater respectively. The two Pandovirus genomes are the largest known to date, with P. salinus being at least double the size of M. chilensis. Further to this, most viruses are measured at the nanometre scale, whereas Pandoraviruses measure 1 um long.
These statistics aren’t even the most shocking. The biggest revelation comes with the similarity of Pandoravirus to other organisms. A shocking 93% of Pandoravirus genes resemble nothing currently known, making them practically alien in nature. Their lineage has not yet been traced, but their DNA polymerase can be grouped with other giant viruses. There is even controversial talk about a fourth domain of life! This paper opens a ‘Pandora’s Box’ of possibilities, with exciting future work possible.
- Is the paper easy to understand?
- Are the methods used suitable and correct?
- Do you think any larger viruses are possible?
- What is the impact of the ‘alien’ genome?
- What further work can be carried out?
For those of you who don’t know me already, my name is Stewart (@Stewart_Barker on Twitter), and i am a final year Biology BSc student at Sheffield Hallam University. I have been active with #microtwjc for a few months now, and it is my turn to lead a discussion session!
This week’s paper –
Correlation between virulence gene expression and proton pump inhibitors and ambient pH in C. difficile: Results of an in vitro study
The paper has very kindly been made open access by the Society for General Microbiology from 27th September to 2nd October here: http://jmm.sgmjournals.org/content/early/2013/06/25/jmm.0.059709-0.full.pdf+html
Proton pump inhibitors (PPIs), such as Omeprazole and Lansoprazole are frequently prescribed as outpatient medication and are even prescribed over the counter. They produce an antacid effect in the stomach, used to treat diseases caused by excess acid, like Peptic ulcers. As gut microorganisms are highly adapted to survive in the low pH, a change in the environment will alter their physiology and virulence. This has long been thought to be a secondary cause of Clostridium difficile infections, after the use of broad spectrum antibiotics.
The authors look beyond just the manipulation of stomach pH – at the direct effect of PPIs on the expression of toxins and their regulators. Considering the growing issue with antibiotic resistance, and the continuous use of orally administered broad-spectrum antibiotics, it is crucial to investigate other options to inhibit C. difficile infections.
- Is the paper well written, easy to understand and thoroughly explained?
- Are the methods appropriate?
- What do the results tell us – how significant is the impact of this research?
- What research can and should this follow on to?