Aina Maria Mas Calafell Genomics
METAGENOMICS
Introduction
Microbial communities Primary role in biogeochemical systems
Study of microbial communities
1.- Culture-based methodologies
Only isolated microbes
Phenotypic, biochemical and physiological tests Molecular techniques
o G+C content o DNA-DNA pairing o Targeted sequencing
(Rosselló-Mora & Amann, 2001)
Study of microbial communities 2.- Culture-independent
DNA sequence-based methodologies
Metagenomics
‘Culture-independent and genomic analysis of
microbial communities’
(Tringe & Rubin, 2005)
Low-throughput targeted sequencing
Well-conserved Large enough No horizontal transfer Molecular clock
Sequencing of 16S rRNA genes
2.1.- Sanger sequencing
(Janda & Abott, 2007)
Community structure
2.1.- Sanger sequencing
Low-throughput shotgun sequencing
(Breitbart et al., 2002)
A) Number of sequences from the uncultured shotgun libraries with a significant hit (E < 0.001) to GenBank
Functionallity
Community structure
2.1.- Sanger sequencing
Cost Prohibitive to sequence highly complex communities
Certain microbial and bacteriophague sequences are not carried
stably by E.coli
Study of microbial communities 2.- Culture-independent
DNA sequence-based methodologies
2.2.- SGS and TGS
Higher troughput Lower cost Faster In vitro amplification (SGS) or
lack of amplification (TGS)
(Mardis, 2008)
Whole-metagenome shotgun
Sequence of thousands of organisms at the
same time
Detection of very low abundance members
Increased taxonomic
resolution (Petrosino et al., 2009)
High-throughput shotgun sequencing
2.2.- SGS and TGS
High-throughput targeted
sequencing
Expansion of microbiome studies
(Segata et al., 2013)
2.2.- SGS and TGS
High-throughput shotgun sequencing
(Mardis, 2008)
Comparison of technologies (Luo et al., 2012)
(Barzon et al., 2011)
2.2.- SGS and TGS
High-throughput shotgun sequencing
(Bragg & Tyson 2014)
New view Metagenomics
Human microbiome
Soil
Sea
Deep mine
Honey bee colonies
(Fierer et al., 2007)
(Venter et al., 2004)
Human microbiome
Human microbiome
Humans ~ Superorganisms composed of human and microbial components
(Qin et al., 2010)
(Bäckhed et al., 2006)
Human Microbiome Project
‘To understand the microbial components of our genetic and metabolic landscape’ ‘To highlight how they contribute to our normal physiology and disease predisposition’
(NIH HMP Working group, 2009)
(Turnbaugh et al., 2007)
Human Microbiome Project
(The Human Microbiome Jumpstart Reference Strains Consortium, 2010)
(Cuomo et al., 2014)
(The Human Microbiome Project Consortium, 2012)
Human Microbiome
Future insights
Deeper coverage of the microbiome
Effects of age and
diet?
Effects of pathologic states?
Effect of different
living environments
Human Microbiome
New biomarkers for
defining our health
New ways for optimizing our personal nutrition
New ways to forecast our
predispositions to disorders
Future insights
Deeper coverage of the microbiome
Effects of age and
diet?
Effects of pathologic states?
Effect of different
living environments
A wide view of microbial communities
Meta’omics
(Segata et al., 2013)
Conclusions
The understanding of complex microbial communities can have several applications.
DNA sequence-based methods circumvented the obstacles of culture-based approaches.
Next-generation sequencing technologies have expanded the experimental tools available for studying microbiomes.
The current bottleneck is the downstream analysis of data.
Metagenomic studies are ongoing in several important ecosystems, specially the human body in health and disease.
Metagenomics is complemeted with different approaches to have an overall view of microbial communities, including their functionallity.
References Bäckhed et al. «Host-bacterial mutualism in the human intestine.» Science, 2006 Mar 25; 307(5717):1915-20.
Barzon et al. «Applications of Next-Generation Sequencing Technologies to.» Int. J. Mol. Sci., 2011; 12, 7861-7884.
Bragg andTyson. «Metagenomics using Next-Generation Sequencing.» Methods Mol Biol, 2014; 1096:183-201.
Breitbart et al. «Genomic analysis of uncultured marine viral communities.» Proceedings of the National Academy of Science,
2002 Oct 29; 99(22):14250-5. Cuomo, y otros. «Genome Sequence of the Pathogenic Fungus Sporothrix schenckii (ATCC 58251).» Genome Announc., 201;
May 22;2(3). Fierrer, y otros. «Metagenomic and small-subunit rRNA analyses of the genetic diversity of bacteria, archaea, fungi and
viruses in soil.» Appl Environ Microbiol, 2007; Nov; 73(21):7059-66. Janda, y Abbott. «16S rRNA Gene Sequencing for Bacterial Identification in the Diagnostic Laboratory: Pluses, Perils, and
Pitfalls.» J Clin Microbiol, 2007; Sep 45(9): 2761–2764.
Luo, Tsementzi, Kyrpides, Read, y Konstantinidis. «Direct Comparisons of Illumina vs. Roche 454 Sequencing Technologies on
the Same Microbial Community DNA Sample.» PLoS One, 2012; Feb 7(2).
Mardis. «The impact of next-generation sequencing technology on genetics.» Trends Genet, 2008; Mar; 24(3):133-41.
Petrosino, Highlander, Luna, Gibbs, y Versalovic. «Metagenomic Pyrosequencing and Microbial Identification.» Clin Chem, 2009: May 55(5):856-66.
Qin et. al «A human gut microbial gene catalogue established by metagenomic sequencing.» Nature, 2010; 464, 59-65.
Rosselló-Mora, y Amann. «The species concept for prokaryotes.» FEMS Microbiology reviews 25, 2001: 39-67.
Segata, Boernigen, Tickle, Morgan, Garrett, y Hutternhower. «Computational meta'omics for microbial community studies.»
Molecular Systems Biology, 2013: 9:666.
The Human Microbiome Consortium Jumpstart Reference Strains. «A catalog of reference genomes from the human
microbiome.» Science, 2010; May 21; 328(5981):994-9. Tringe, y Rubin. «Metagenomics: DNA sequencing of environmental samples.» Nature Reviews Genetics, 2005: Nov 6(11): 805-
14.
Turnbaugh, Ley, Hamady, Fraser-Liggett, y Knight. «The human microbiome project: exploring the microbial part of ourselves in a changing world.» Nature , 2007: Oct 449(7164): 804–810.
Venter, y otros. «Environmental Genome Shotgun Sequencing of the Sargasso Sea.» Science, 2004: April Vol. 304 no. 5667 pp. 66-74.