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For next weeks #microtwjc session (8pm BST 23rd July) I thought we would cool things down a little and discuss sequencing bacteria and eukarya in ice taken from a lake in Antarctica. The paper was recently published in PLOS one and is available from the following link http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0067221

Abstract:
Lake Vostok, the 7th largest (by volume) and 4th deepest lake on Earth, is covered by more than 3,700 m of ice, making it the
largest subglacial lake known. The combination of cold, heat (from possible hydrothermal activity), pressure (from the
overriding glacier), limited nutrients and complete darkness presents extreme challenges to life. Here, we report
metagenomic/metatranscriptomic sequence analyses from four accretion ice sections from the Vostok 5G ice core. Two
sections accreted in the vicinity of an embayment on the southwestern end of the lake, and the other two represented part
of the southern main basin. We obtained 3,507 unique gene sequences from concentrates of 500 ml of 0.22 mm-filtered
accretion ice meltwater. Taxonomic classifications (to genus and/or species) were possible for 1,623 of the sequences.
Species determinations in combination with mRNA gene sequence results allowed deduction of the metabolic pathways
represented in the accretion ice and, by extension, in the lake. Approximately 94% of the sequences were from Bacteria and
6% were from Eukarya. Only two sequences were from Archaea. In general, the taxa were similar to organisms previously
described from lakes, brackish water, marine environments, soil, glaciers, ice, lake sediments, deep-sea sediments, deep-sea
thermal vents, animals and plants. Sequences from aerobic, anaerobic, psychrophilic, thermophilic, halophilic, alkaliphilic,
acidophilic, desiccation-resistant, autotrophic and heterotrophic organisms were present, including a number from
multicellular eukaryotes.

Discussion points:

1. Was the paper well written, easy to understand/follow and the data presented well?

2. Were the methods appropriate? Anything else you would have liked the authors to do?

3. Are the results useful? Do they help us to understand microbial communities?

4. What next?

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Brain

Errr so it turns out that our brains might have bacteria in them…

Whilst I expect to read about microbes on our skin, in our gut etc., brain was one place I was not expecting them to be – at least not in healthy people anyway.

This interested me enough that the paper discussing this is going to be our paper for #microtwjc, next week, Tues 9th July at 8pm BST.

The paper is:  Branton WG, Ellestad KK, Maingat F, Wheatley BM, Rud E, et al.  (2013) Brain Microbial Populations in HIV/AIDS: α-Proteobacteria Predominate Independent of Host Immune Status. PLoS ONE 8(1):e54673.doi:10.1371/journal.pone.0054673

and the abstract states:

The brain is assumed to be a sterile organ in the absence of disease although the impact of immune disruption is uncertain in terms of brain microbial diversity or quantity. To investigate microbial diversity and quantity in the brain, the profile of infectious agents was examined in pathologically normal and abnormal brains from persons with HIV/AIDS [HIV] (n = 12), other disease controls [ODC] (n = 14) and in cerebral surgical resections for epilepsy [SURG] (n = 6). Deep sequencing of cerebral white matter-derived RNA from the HIV (n = 4) and ODC (n = 4) patients and SURG (n = 2) groups revealed bacterially-encoded 16 s RNA sequences in all brain specimens with α-proteobacteria representing over 70% of bacterial sequences while the other 30% of bacterial classes varied widely. Bacterial rRNA was detected in white matter glial cells by in situ hybridization and peptidoglycan immunoreactivity was also localized principally in glia in human brains. Analyses of amplified bacterial 16 s rRNA sequences disclosed that Proteobacteria was the principal bacterial phylum in all human brain samples with similar bacterial rRNA quantities in HIV and ODC groups despite increased host neuroimmune responses in the HIV group. Exogenous viruses including bacteriophage and human herpes viruses-4, -5 and -6 were detected variably in autopsied brains from both clinical groups. Brains from SIV- and SHIV-infected macaques displayed a profile of bacterial phyla also dominated by Proteobacteria but bacterial sequences were not detected in experimentally FIV-infected cat or RAG1−/− mouse brains. Intracerebral implantation of human brain homogenates into RAG1−/− mice revealed a preponderance of α-proteobacteria 16 s RNA sequences in the brains of recipient mice at 7 weeks post-implantation, which was abrogated by prior heat-treatment of the brain homogenate. Thus, α-proteobacteria represented the major bacterial component of the primate brain’s microbiome regardless of underlying immune status, which could be transferred into naïve hosts leading to microbial persistence in the brain.

The paper is also discussed on Virology blog and featured on episode #58 of TWiM

Discussion points will follow and, as always, if you write a blog post on the article then please leave a link to it below 🙂

ETA Discussion points

1) Was the paper well written, easy to understand, logical in its presentation etc?

2) Were the methods appropriate?  Was there anything else you would have liked to see the authors do before publishing? Does it matter that they didn’t try to culture the bacteria?

3) Following on from 2), do the results show what the authors say they do?  What is the significance of these results?

4) What experiments would you like to see done next? If you were working on this what avenue/s would you like to now pursue?