Sunday, 3 July 2016

Gut microbes is it reproducible?

Alterations of the human gut microbiome in multiple sclerosis.
Jangi S, Gandhi R, Cox LM, Li N, von Glehn F, Yan R, Patel B, Mazzola MA, Liu S, Glanz BL, Cook S, Tankou S, Stuart F, Melo K, Nejad P, Smith K, Topçuolu BD, Holden J, Kivisäkk P, Chitnis T, De Jager PL, Quintana FJ, Gerber GK, Bry L, Weiner HL.
Nat Commun. 2016 Jun 28;7:12015. doi: 10.1038/ncomms12015.

The gut microbiome plays an important role in immune function and has been implicated in several autoimmune disorders. Here we use 16S rRNA sequencing to investigate the gut microbiome in subjects with multiple sclerosis (MS, n=60) and healthy controls (n=43). Microbiome alterations in MS include increases in Methanobrevibacter and Akkermansia and decreases in Butyricimonas, and correlate with variations in the expression of genes involved in dendritic cell maturation, interferon signalling and NF-kB signalling pathways in circulating T cells and monocytes. Patients on disease-modifying treatment show increased abundances of Prevotella and Sutterella, and decreased Sarcina, compared with untreated patients. MS patients of a second cohort show elevated breath methane compared with controls, consistent with our observation of increased gut Methanobrevibacter in MS in the first cohort. Further study is required to assess whether the observed alterations in the gut microbiome play a role in, or are a consequence of, MS pathogenesis.



In this study the poor old researchers or more likely the poor young researchers had to collect stool samples..yep pooh, to determine what microbes were present.

These were

The microbes were changed in response to treatment, but what does it mean?

In another study of 20 MS patients versus 40 healthy controls, FaecalibacteriumPrevotella and Anaerostipes were decreased in MS

In this study the faecal microbiota of both people with MS and controls was dominated by Firmicutes and Bacteroidetes, with smaller contributions of Euryarchaeota, Verrucomicrobia and Proteobacteria. People with MS patients had a significantly increased relative abundance of the phyla Euryarchaeota and Verrucomicrobia compared to healthy controls.

They investigated potential associations between the MS-related microbiota and immune changes and found some.

The gut microbiome is made up of a wide range of (chiefly) bacterial species that colonize the small and large intestine. The human gut microbiome contains a subset of thousands of bacterial species, with up to 10(14)- (a 100 million million) total bacteria. Studies examining this bacterial content have shown wide variations in which species are present between individuals.

However, within a week we have had two papers doing essentially the same experiment using the same technique and what do we get?....Simply lack of reproducibility, so who do you want to believe the Harvard group or Iowa group or neither?


http://multiple-sclerosis-research.blogspot.com/2016/06/gut-microbiota-is-different-in-ms.html

They observed an increased abundance of Psuedomonas, Mycoplana, Haemophilus, Blautia, and Dorea genera in MS patients, whereas control group showed increased abundance of Parabacteroides, Adlercreutzia and Prevotella genera.






People in different places are going to get different gut flora as they eat and drink differently. 

However, it seems to me that presence of this or that microrobe is not giving clear cut answers. However I must admit I know nothing about microbes and maybe we can find some one with an interest in microbiomones to compare these two papers and deterine whether there is liquid gold in there that complement each other or whether they are poles apart more work is needed to get a consensus of the reality of the data, before we place significance to each bacteria.

3 comments:

  1. Although there's a large number of different species present in the gut, the number of metabolic pathways they use are limited.
    Comparing composition of species can easily give you conflicting results just because the number is so huge.
    Grouping them by their metabolic pathways could narrow this down.
    E.g. According to the Harvard paper Butyricimonas is decreased in MS patients. It produces butyric acid which, besides propionic acid and other SCFA, was shown to have positive effects in MS models. But it's not just Butyricimonas that produces butyric acid in the gut, there are quite a few others. A different study might find that Faecalibacteria or certain Clostridia are decreased because they also produce butyric acid.
    So maybe in the end it's not one species missing or causing trouble but "a lack of a metabolic pathway" or just a wrong composition.

    All of this microbiome stuff is way too complex to determine cause and effect - yet :) Exciting times for researchers!

    ReplyDelete
  2. Thanks for this. Nice comments made

    I have sent to the two papers to a microbiome researcher to see if they can decifer this.

    Exciting times...Sorry...Bacteria in Pooh is not my thang:-)

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  3. Anon 11:44 again.
    To answer your question:
    The Harvard paper says Akkermansia and Methanobrevibacter is increased, the other one says Euryarchaeota and Verrucomicrobiota are increased.
    In fact, this fits very well because Akkermansia=Verrucomicrobiota and Methanobrevibacter=Eryarchaeota :)

    ReplyDelete

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