A human gut microbial gene catalogue established by metagenomic sequencing

[lansbergen]

Dr Vernon talking about metagenome and forum members talking about bowel maybe this can come in handy.

http://www.nature.com/nature/journal/v464/n7285/full/nature08821.html

> Full Text Article

Nature 464, 59-65 (4 March 2010) | doi:10.1038/nature08821; Received 14 August 2009; Accepted 23 December 2009

A human gut microbial gene catalogue established by metagenomic sequencing

 

[xchocoholic]

Thanks ... I'm still waking up but I pulled this in from that article. Does this say that ATP production is the result of bacteria ?

Bacterial functions important for life in the gut


The extensive non-redundant catalogue of the bacterial genes from the human intestinal tract provides an opportunity to identify bacterial functions important for life in this environment.

There are functions necessary for a bacterium to thrive in a gut context (that is, the ‘minimal gut genome’) and those involved in the homeostasis of the whole ecosystem, encoded across many species (the ‘minimal gut metagenome’). The first set of functions is expected to be present in most or all gut bacterial species; the second set in most or all individuals’ gut samples.






To identify the functions encoded by the minimal gut genome we use the fact that they should be present in most or all gut bacterial species and therefore appear in the gene catalogue at a frequency above that of the functions present in only some of the gut bacterial species.

The relative frequency of different functions can be deduced from the number of genes recruited to different eggNOG clusters, after normalization for gene length and copy number (Supplementary Fig. 10a, b).

We ranked all the clusters by gene frequencies and determined the range that included the clusters specifying well-known essential bacterial functions, such as those determined experimentally for a well-studied firmicute, Bacillus subtilis27, hypothesizing that additional clusters in this range are equally important.

As expected, the range that included most of B. subtilis essential clusters (86%) was at the very top of the ranking order (Fig. 5). Some 76% of the clusters with essential genes of Escherichia coli28 were within this range, confirming the validity of our approach.

This suggests that 1,244 metagenomic clusters found within the range (Supplementary Table 10; termed ‘range clusters’ hereafter) specify functions important for life in the gut.







We found two types of functions among the range clusters: those required in all bacteria (housekeeping) and those potentially specific for the gut.

Among many examples of the first category are the functions that are part of main metabolic pathways (for example, central carbon metabolism, amino acid synthesis), and important protein complexes (RNA and DNA polymerase, ATP synthase, general secretory apparatus).

Not surprisingly, projection of the range clusters on the KEGG metabolic pathways gives a highly integrated picture of the global gut cell metabolism (Fig. 6a).

 

[lansbergen]

Thanks ... I'm still waking up but I pulled this in from that article. Does this say that ATP production is the result of bacteria ?

"We found two types of functions among the range clusters: those required in all bacteria (housekeeping) and those potentially specific for the gut. Among many examples of the first category are the functions that are part of main metabolic pathways (for example, central carbon metabolism, amino acid synthesis), and important protein complexes (RNA and DNA polymerase, ATP synthase, general secretory apparatus). Not surprisingly, projection of the range clusters on the KEGG metabolic pathways gives a highly integrated picture of the global gut cell metabolism (Fig. 6a)."

No, I think they say ATP synthese is a function of the main metabolic pathways of the bacteria.

Do you know that:
It is generally agreed that certain organelles of the eukaryotic cell, especially mitochondria and plastids such as chloroplasts, originated as bacterial endosymbionts.

Mitochondria have many features in common with prokaryotes. As a result, they are believed to be originally derived from endosymbiotic prokaryotes.

 

[xchocoholic]

I actually saw that the other day. You may be interested in this thread where parasites and worms are discussed.

http://www.glutenfreeandbeyond.org/forum/viewtopic.php?t=4230&highlight=

FWIW. The idea that certain bacteria were necessary for certain bodily functions first caught my attention when I learned that people with kidney stones were lacking in the bacteria o.forminges. Later, I learned that this isn't something that labs can produce so it has to be happening in our bodies. I think there's a link to lactobaccillus but can't swear to it.

 

[lansbergen]

Of the known fraction, about 5% codes for (pro)phage-related proteins, implying a universal presence and possible important ecological role of bacteriophages in gut homeostasis.


A bacteriophage is any one of a number of viruses that infect bacteria.
Bacteriophages are among the most common biological entities on Earth.

Bacteriophage (phage) are obligate intracellular parasites that multiply inside bacteria by making use of some or all of the host biosynthetic machinery (i.e., viruses that infect bacteria.).

There are many similarities between bacteriophages and animal cell viruses. Thus, bacteriophage can be viewed as model systems for animal cell viruses. In addition a knowledge of the life cycle of bacteriophage is necessary to understand one of the mechanisms by which bacterial genes can be transferred from one bacterium to another.

General Information about Bacteriophages http://www.phages.org/PhageInfo.html

 

[xchocoholic]

Of the known fraction, about 5% codes for (pro)phage-related proteins, implying a universal presence and possible important ecological role of bacteriophages in gut homeostasis.


A bacteriophage is any one of a number of viruses that infect bacteria.
Bacteriophages are among the most common biological entities on Earth.

Bacteriophage (phage) are obligate intracellular parasites that multiply inside bacteria by making use of some or all of the host biosynthetic machinery (i.e., viruses that infect bacteria.).

There are many similarities between bacteriophages and animal cell viruses. Thus, bacteriophage can be viewed as model systems for animal cell viruses. In addition a knowledge of the life cycle of bacteriophage is necessary to understand one of the mechanisms by which bacterial genes can be transferred from one bacterium to another.

General Information about Bacteriophages http://www.phages.org/PhageInfo.html

Does this mean that when we kill off certain bacteria that those viruses are killed off too ? Or do they move on to another host ?

 

[lansbergen]

Does this mean that when we kill off certain bacteria that those viruses are killed off too ? Or do they move on to another host ?

Bacteriophages are very specific, targeting only one or a few strains of bacteria.

Most phages are cleared very rapidly by the reticuloendothelial system if they don't quickly find a bacterial host in which to multiply

http://en.wikipedia.org/wiki/Reticuloendothelial_system

http://www.nature.com/nbt/journal/v22/n1/full/nbt0104-31.html

http://www.bbc.co.uk/dna/h2g2/A471575

http://textbookofbacteriology.net/phage.html