Sludge Watch ==> Microbes access large 'arsenal' of novel genes - horizonal gene transmission

[Maureen Reilly]

Sludgewatch admin:

The aerobic and anaerobic (without oxygen) digestion of all the bacteria and 
pathogens together with industrial chemical compounds in every major and 
minor community sewage treatment plant may be driving untold alteration and 
armament of bacteria with novel pathogenic 'weapons' and resistance.

"Vertical" gene flow is the transmission of genes from parents to offspring, 
and of course this means parents within a species. "Horizontal" gene flow is 
the transmission of genes between species, including between highly 
divergent species such as between viruses, bacteria, animals or plants. The 
natural transmission of genes between species is a well established 
phenomenon, the most notable being the transfer of genes between bacteria 
and plants.

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pro·kar·y·ote also pro·car·y·ote (prō-kăr'ē-ōt')
n.
An organism of the kingdom Monera (or Prokaryotae), comprising the bacteria 
and cyanobacteria, characterized by the absence of a distinct, 
membrane-bound nucleus or membrane-bound organelles, and by DNA that is not 
organized into chromosomes. Also called moneran.

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ge·nome (jē'nōm')  also ge·nom (-nŏm)
n.
The total genetic content contained in a haploid set of chromosomes in 
eukaryotes, in a single chromosome in bacteria, or in the DNA or RNA of 
viruses.
An organism's genetic material.

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PLoS Genet. 2005 Nov 18;1 (5):e62 16299586


Evidence of a Large Novel Gene Pool Associated with Prokaryotic Genomic 
Islands.

[My paper] William W L Hsiao , Korine Ung , Dana Aeschliman , Jenny Bryan , 
B Brett Finlay , Fiona S L Brinkman

Microbial genes that are "novel" (no detectable homologs in other species) 
have become of increasing interest as environmental sampling suggests that 
there are many more such novel genes in yet-to-be-cultured microorganisms. 
By analyzing known microbial genomic islands and prophages, we developed 
criteria for systematic identification of putative genomic islands (clusters 
of genes of probable horizontal origin in a prokaryotic genome) in 63 
prokaryotic genomes, and then characterized the distribution of novel genes 
and other features.

All but a few of the genomes examined contained significantly higher 
proportions of novel genes in their predicted genomic islands compared with 
the rest of their genome (Paired t test = 4.43E-14 to 1.27E-18, depending on 
method). Moreover, the reverse observation (i.e., higher proportions of 
novel genes outside of islands) never reached statistical significance in 
any organism examined. We show that this higher proportion of novel genes in 
predicted genomic islands is not due to less accurate gene prediction in 
genomic island regions, but likely reflects a genuine increase in novel 
genes in these regions for both bacteria and archaea.

This represents the first comprehensive analysis of novel genes in 
prokaryotic genomic islands and provides clues regarding the origin of novel 
genes. Our collective results imply that there are different gene pools 
associated with recently horizontally transmitted genomic regions versus 
regions that are primarily vertically inherited. Moreover, there are more 
novel genes within the gene pool associated with genomic islands.

Since genomic islands are frequently associated with a particular microbial 
adaptation, such as antibiotic resistance, pathogen virulence, or metal 
resistance, this suggests that microbes may have access to a larger 
"arsenal" of novel genes for adaptation than previously thought.


http://www.lib.bioinfo.pl/pmid:16299586