From bag-of-genes to bag-of-genomes: metabolic modelling of communities in the era of metagenome-assembled genomes.

Computational and Structural Biotechnology Journal
Clémence FriouxFalk Hildebrand

Abstract

Metagenomic sequencing of complete microbial communities has greatly enhanced our understanding of the taxonomic composition of microbiotas. This has led to breakthrough developments in bioinformatic disciplines such as assembly, gene clustering, metagenomic binning of species genomes and the discovery of an incredible, so far undiscovered, taxonomic diversity. However, functional annotations and estimating metabolic processes from single species - or communities - is still challenging. Earlier approaches relied mostly on inferring the presence of key enzymes for metabolic pathways in the whole metagenome, ignoring the genomic context of such enzymes, resulting in the 'bag-of-genes' approach to estimate functional capacities of microbiotas. Here, we review recent developments in metagenomic bioinformatics, with a special focus on emerging technologies to simulate and estimate metabolic information, that can be derived from metagenomic assembled genomes. Genome-scale metabolic models can be used to model the emergent properties of microbial consortia and whole communities, and the progress in this area is reviewed. While this subfield of metagenomics is still in its infancy, it is becoming evident that there is a dire need for f...Continue Reading

References

Sep 15, 1986·The Biochemical Journal·D A Fell, J R Small
Jun 11, 1999·The Journal of Biological Chemistry·J S Edwards, B O Palsson
Dec 11, 1999·Nucleic Acids Research·M Kanehisa, S Goto
Dec 11, 1999·Nucleic Acids Research·R L TatusovE V Koonin
Mar 2, 2002·Science·Hiroaki Kitano
Aug 10, 2002·Bioinformatics·Peter D KarpPedro Romero
Oct 18, 2002·Proceedings of the National Academy of Sciences of the United States of America·Mya BreitbartForest Rohwer
May 7, 2004·Nature·Markus W CovertBernhard O Palsson
Oct 20, 2004·Metabolic Engineering·Mats AkessonJens Nielsen
Aug 20, 2005·PLoS Computational Biology·Kevin Chen, Lior Pachter
Jan 5, 2007·Nucleic Acids Research·Jens BarthelmesDietmar Schomburg
Mar 14, 2007·Molecular Systems Biology·Sergey StolyarDavid A Stahl
Apr 28, 2007·BMC Bioinformatics·Matthew DeJonghAaron Best
Jun 15, 2007·Proceedings of the National Academy of Sciences of the United States of America·Buck S SamuelJeffrey I Gordon
Oct 16, 2007·Current Opinion in Microbiology·Jeroen RaesPeer Bork
Jul 1, 2008·Bioinformatics·Thomas J LeePeter Karp
Jul 1, 2008·Nature Reviews. Microbiology·Jeroen Raes, Peer Bork
Aug 14, 2008·Bioinformatics·Albert GevorgyanDavid A Fell
Aug 20, 2008·Nature Biotechnology·Tomer ShlomiEytan Ruppin
Oct 8, 2008·Nucleic Acids Research·Brandi L CantarelBernard Henrissat
Jan 9, 2010·Nature Protocols·Ines Thiele, Bernhard Ø Palsson
Apr 28, 2010·FEBS Letters·Liming LiuJens Nielsen
May 1, 2010·Current Opinion in Microbiology·Adam M Feist, Bernhard O Palsson
Jun 11, 2010·Proceedings of the National Academy of Sciences of the United States of America·Gabriel Cuevas-RamosJean-Philippe Nougayrède
Dec 3, 2010·PLoS Computational Biology·Niels Klitgord, Daniel Segrè
Dec 21, 1993·Journal of Theoretical Biology·A Varma, B O Palsson
Jun 24, 2011·The New England Journal of Medicine·Christina FrankUNKNOWN HUS Investigation Team
Nov 3, 2011·BMC Genomics·Aline MetrisArnoud H M van Vliet
Dec 21, 2011·Proceedings of the National Academy of Sciences of the United States of America·Sharon GreenblumElhanan Borenstein
Feb 10, 2012·PLoS Computational Biology·Ali R Zomorrodi, Costas D Maranas
Jul 17, 2012·Nature Reviews. Microbiology·Karoline Faust, Jeroen Raes
Dec 14, 2012·BMC Systems Biology·Yuliang WangNathan D Price
Feb 19, 2013·Methods in Molecular Biology·Scott DevoidChristopher Henry
Mar 5, 2013·Nature Biotechnology·Ines ThieleBernhard Ø Palsson
Mar 16, 2013·Human Molecular Genetics·Swagatika Sahoo, Ines Thiele
Aug 27, 2013·Nature Biotechnology·Morgan G I LangilleCurtis Huttenhower
Aug 30, 2013·Nature·Emmanuelle Le ChatelierOluf Pedersen

❮ Previous
Next ❯

Citations

Oct 4, 2020·Journal of Veterinary Pharmacology and Therapeutics·Patrick F McDermott, James J Davis
Dec 29, 2020·Computational and Structural Biotechnology Journal·Johan Bengtsson-Palme
Dec 19, 2020·Computational and Structural Biotechnology Journal·Álvaro AltamiranoDaniel Garrido
Nov 14, 2020·Current Opinion in Biotechnology·Michela Gambino, Lone Brøndsted
Mar 9, 2021·Frontiers in Molecular Biosciences·Fabrice Jean-PierreGeorge A O'Toole
Mar 18, 2021·MBio·Fabrice Jean-PierreGeorge A O'Toole
Sep 1, 2021·MSystems·Falk Hildebrand
Oct 7, 2021·Nucleic Acids Research·Francisco ZorrillaAleksej Zelezniak

❮ Previous
Next ❯

Methods Mentioned

BETA
amplicon sequencing
PCR
interaction prediction

Software Mentioned

eggNOG
LotuS
FAPROTAX
MetaBAT2
AGORA
PATRIC
mapper
DMMM
NetSeed
Flux Balance Analysis ( FBA )

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.