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Unpublished but public microbial genomes with biotechnological relevance.

Siezen RJ, Wilson G - Microb Biotechnol (2008)

View Article: PubMed Central - PubMed

Affiliation: Kluyver Centre for Genomics of Industrial Fermentation, TI Food and Nutrition, 6700AN Wageningen, The Netherlands. r.siezen@cmbi.ru.nl

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In the past few years, the number of microbial genome sequencing projects worldwide has rapidly increased, both of single species and microbial consortia (metagenomes)... The development of several new high‐throughput sequencing platforms, and an enormous reduction in costs, means we can expect to have thousands of complete and incomplete genomes sequences available to us in the coming years... The entry page links to the GOLD tables, each containing a summary of different kinds of sequencing projects: completed genomes, ongoing genomes (archaeal, bacterial or eukaryote) or metagenomes... After 2004, the number of newly published public genomes has remained rather steady at 60–70 per year, while the number of ‘unpublished public’ genomes has increased rapidly... Last year, over 200 new genomes were released to public databases, but two‐thirds of those did not appear in scientific publications... The comparative analysis may also help to explain the differences that occur during biofilm formation with these organisms, as the formation of biofilms may have dramatic effects on subsequent cellulose decomposition... It is possible that in some (Clostridium phytofermentans) it will increase ethanol production and in others (Clostridium cellulolyticum) reduce ethanol formation... The genome and a genome‐scale metabolic model are also available for another succinate producer, Mannheimia succiniciproducens, and it should be interesting to compare their metabolic capacities... This family of bacteria is considered as having great value for bioremediation... They have the ability to reduce metals and so could be used to remove contamination from sites with heavy metals... The challenge for the comparative genomics field and not just the comparative biotech consortia is to explain what all this sequencing has accomplished, to tell us what it means and what it predicts for the future... There is also great concern that in the push to cut dependence upon fossil fuels, that the means of producing the biofuel may be even more damaging on the environment... Surely, the comparative analysis of all these biotechnologically relevant micro‐organisms can produce new leads, cleaner methods, less energy demanding processes and sustainable production of biobased products – something which all the world requires.

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Number of microbial genomes made public annually from 2003–2007 (source GOLD On‐line Database v 2.0; http://www.genomesonline.org).
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f1: Number of microbial genomes made public annually from 2003–2007 (source GOLD On‐line Database v 2.0; http://www.genomesonline.org).

Mentions: At the end of 2007, over 700 completed genomes were listed that can be accessed in public databases, and the large majority of those were of bacterial and archaeal origin. ‘Complete’ means single complete sequences for each chromosome. Up to 2004, nearly all of these complete genomes were also reported in scientific journals, and these are referred to as ‘published public’ genomes (Figure 1). After 2004, the number of newly published public genomes has remained rather steady at 60–70 per year, while the number of ‘unpublished public’ genomes has increased rapidly. Last year, over 200 new genomes were released to public databases, but two‐thirds of those did not appear in scientific publications. These are the genomes that remain ‘invisible’ to the general reader who relies only on PubMed searches or other literature alert services. One way of getting a quick insight into recent ‘unpublished public’ genomes is to read Michael Galperin's two‐monthly brief summaries in the Genomics Update section of Environmental Microbiology (Galperin, 2007a,b).


Unpublished but public microbial genomes with biotechnological relevance.

Siezen RJ, Wilson G - Microb Biotechnol (2008)

Number of microbial genomes made public annually from 2003–2007 (source GOLD On‐line Database v 2.0; http://www.genomesonline.org).
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3815881&req=5

f1: Number of microbial genomes made public annually from 2003–2007 (source GOLD On‐line Database v 2.0; http://www.genomesonline.org).
Mentions: At the end of 2007, over 700 completed genomes were listed that can be accessed in public databases, and the large majority of those were of bacterial and archaeal origin. ‘Complete’ means single complete sequences for each chromosome. Up to 2004, nearly all of these complete genomes were also reported in scientific journals, and these are referred to as ‘published public’ genomes (Figure 1). After 2004, the number of newly published public genomes has remained rather steady at 60–70 per year, while the number of ‘unpublished public’ genomes has increased rapidly. Last year, over 200 new genomes were released to public databases, but two‐thirds of those did not appear in scientific publications. These are the genomes that remain ‘invisible’ to the general reader who relies only on PubMed searches or other literature alert services. One way of getting a quick insight into recent ‘unpublished public’ genomes is to read Michael Galperin's two‐monthly brief summaries in the Genomics Update section of Environmental Microbiology (Galperin, 2007a,b).

View Article: PubMed Central - PubMed

Affiliation: Kluyver Centre for Genomics of Industrial Fermentation, TI Food and Nutrition, 6700AN Wageningen, The Netherlands. r.siezen@cmbi.ru.nl

AUTOMATICALLY GENERATED EXCERPT
Please rate it.

In the past few years, the number of microbial genome sequencing projects worldwide has rapidly increased, both of single species and microbial consortia (metagenomes)... The development of several new high‐throughput sequencing platforms, and an enormous reduction in costs, means we can expect to have thousands of complete and incomplete genomes sequences available to us in the coming years... The entry page links to the GOLD tables, each containing a summary of different kinds of sequencing projects: completed genomes, ongoing genomes (archaeal, bacterial or eukaryote) or metagenomes... After 2004, the number of newly published public genomes has remained rather steady at 60–70 per year, while the number of ‘unpublished public’ genomes has increased rapidly... Last year, over 200 new genomes were released to public databases, but two‐thirds of those did not appear in scientific publications... The comparative analysis may also help to explain the differences that occur during biofilm formation with these organisms, as the formation of biofilms may have dramatic effects on subsequent cellulose decomposition... It is possible that in some (Clostridium phytofermentans) it will increase ethanol production and in others (Clostridium cellulolyticum) reduce ethanol formation... The genome and a genome‐scale metabolic model are also available for another succinate producer, Mannheimia succiniciproducens, and it should be interesting to compare their metabolic capacities... This family of bacteria is considered as having great value for bioremediation... They have the ability to reduce metals and so could be used to remove contamination from sites with heavy metals... The challenge for the comparative genomics field and not just the comparative biotech consortia is to explain what all this sequencing has accomplished, to tell us what it means and what it predicts for the future... There is also great concern that in the push to cut dependence upon fossil fuels, that the means of producing the biofuel may be even more damaging on the environment... Surely, the comparative analysis of all these biotechnologically relevant micro‐organisms can produce new leads, cleaner methods, less energy demanding processes and sustainable production of biobased products – something which all the world requires.

Show MeSH