Increasing Metagenomic Resolution of Microbiome Interactions Through Functional Phylogenomics and Bacterial Sub-Communities

Frontiers in Genetics
Angélica Cibrián-Jaramillo, Francisco Barona-Gómez

Abstract

The genomic composition of the microbiome and its relationship with the environment is an exciting open question in biology. Metagenomics is a useful tool in the discovery of previously unknown taxa, but its use to understand the functional and ecological capacities of the microbiome is limited until taxonomy and function are understood in the context of the community. We suggest that this can be achieved using a combined functional phylogenomics and co-culture-based experimental strategy that can increase our capacity to measure sub-community interactions. Functional phylogenomics can identify and partition the genome such that hidden gene functions and gene clusters with unique evolutionary signals are revealed. We can test these phylogenomic predictions using an experimental model based on sub-community populations that represent a subset of the diversity directly obtained from environmental samples. These populations increase the detection of mechanisms that drive functional forces in the assembly of the microbiome, in particular the role of metabolites from key taxa in community interactions. Our combined approach leverages the potential of metagenomics to address biological questions from ecological systems.

References

Sep 24, 2004·Proceedings of the National Academy of Sciences of the United States of America·Chris Todd HittingerSean B Carroll
Jul 14, 2005·Systematic Biology·John Gatesy, Richard H Baker
Jan 5, 2006·Applied and Environmental Microbiology·Silke LangenhederLars J Tranvik
Feb 13, 2008·Proceedings of the National Academy of Sciences of the United States of America·Tuo Shi, Paul G Falkowski
Aug 7, 2009·The ISME Journal·Allan Konopka
Mar 27, 2010·Chemistry & Biology·Anthony D'OnofrioKim Lewis
Jul 14, 2010·Genome Biology and Evolution·Angélica Cibrián-JaramilloRob DeSalle
May 20, 2011·Current Opinion in Biotechnology·Niels Klitgord, Daniel Segrè
Oct 22, 2011·Antonie van Leeuwenhoek·Francisco Barona-GómezLianet Noda-García
Dec 24, 2011·PLoS Genetics·Ernest K LeeRob Desalle
Jul 25, 2012·Proceedings of the National Academy of Sciences of the United States of America·B Christopher HoeflerPaul D Straight
Oct 16, 2012·Ecology Letters·Nicolas MouquetVincent Calcagno
Aug 1, 2010·Environmental Microbiology Reports·Eugene RosenbergIlana Zilber-Rosenberg
Aug 6, 2013·FEMS Microbiology Reviews·Eva BoonRobert G Beiko
Aug 30, 2013·The ISME Journal·Eulyn PagalingAndrew Free
Oct 22, 2013·Nature Methods·Shinichi SunagawaPeer Bork
Oct 23, 2013·PLoS Computational Biology·Rogan CarrElhanan Borenstein
Feb 1, 2014·PeerJ·Aaron E DarlingJonathan A Eisen
Feb 11, 2014·Molecular Biology and Evolution·Leonidas SalichosAntonis Rokas
Mar 14, 2014·Frontiers in Microbiology·Stephanie M AmatoMark P Brynildsen
May 21, 2014·Proceedings of the National Academy of Sciences of the United States of America·Eric A FranzosaCurtis Huttenhower
Aug 22, 2014·PLoS Computational Biology·Andries J van TonderAngela B Brueggemann
Sep 15, 2014·Nature Methods·Johannes AlnebergChristopher Quince
Nov 2, 2014·Bioinformatics·Nam-Phuong NguyenTandy Warnow
Jan 7, 2015·Nature·Losee L LingKim Lewis
Jan 20, 2015·ELife·Zachary Charlop-PowersSean F Brady
Jan 21, 2015·PLoS Biology·Matthew K WaldorHamilton Smith
Apr 22, 2015·Trends in Ecology & Evolution·Tom M FayleVojtech Novotny
May 12, 2015·Chemical Society Reviews·Yunzi LuoYing-Jin Yuan
May 23, 2015·Natural Product Reports·Matthew F Traxler, Roberto Kolter
Jun 19, 2015·Nature·Corie Lok
Aug 19, 2015·PLoS Biology·Seth R Bordenstein, Kevin R Theis
Sep 4, 2015·The Journal of Antibiotics·Joshua A V BlodgettWilliam W Metcalf

❮ Previous
Next ❯

Methods Mentioned

BETA
PCR
nuclear magnetic resonance

Software Mentioned

antiSMASH
RADICAL
EvoMining
OrthoMCL

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.