Association network analysis identifies enzymatic components of gut microbiota that significantly differ between colorectal cancer patients and healthy controls

PeerJ
Dongmei AiLi C Xia

Abstract

The human gut microbiota plays a major role in maintaining human health and was recently recognized as a promising target for disease prevention and treatment. Many diseases are traceable to microbiota dysbiosis, implicating altered gut microbial ecosystems, or, in many cases, disrupted microbial enzymes carrying out essential physio-biochemical reactions. Thus, the changes of essential microbial enzyme levels may predict human disorders. With the rapid development of high-throughput sequencing technologies, metagenomics analysis has emerged as an important method to explore the microbial communities in the human body, as well as their functionalities. In this study, we analyzed 156 gut metagenomics samples from patients with colorectal cancer (CRC) and adenoma, as well as that from healthy controls. We estimated the abundance of microbial enzymes using the HMP Unified Metabolic Analysis Network method and identified the differentially abundant enzymes between CRCs and controls. We constructed enzymatic association networks using the extended local similarity analysis algorithm. We identified CRC-associated enzymic changes by analyzing the topological features of the enzymatic association networks, including the clustering coef...Continue Reading

References

Apr 16, 1998·Trends in Genetics : TIG·K G Petry, J K Reichardt
Oct 19, 2007·Nature·Peter J TurnbaughJeffrey I Gordon
Feb 4, 2009·Journal of Proteome Research·Hye-Jung KimCheolju Lee
May 30, 2009·Science·Elizabeth A GriceJulia A Segre
Feb 8, 2011·PloS One·Iradj SobhaniJean P Furet
Mar 14, 2012·Nature Reviews. Genetics·Ilseung Cho, Martin J Blaser
May 17, 2012·Briefings in Bioinformatics·Elhanan Borenstein
Jun 16, 2012·Nature·UNKNOWN Human Microbiome Project Consortium
Jun 22, 2012·PLoS Computational Biology·Sahar AbubuckerCurtis Huttenhower
Dec 27, 2012·Nature Reviews. Microbiology·Paul D CotterColin Hill
Aug 27, 2013·PloS One·Vibeke AndersenLotte K Vogel
Jan 11, 2014·Gastroenterology·Maria T Abreu, Richard M Peek
Nov 30, 2014·Molecular Systems Biology·Georg ZellerPeer Bork
Aug 25, 2015·Translational Research : the Journal of Laboratory and Clinical Medicine·Srikanth SanthanamMatthew A Ciorba
Oct 21, 2015·World Journal of Gastrointestinal Oncology·Gokhan CipeHuseyin Bektasoglu
Nov 4, 2015·Frontiers in Oncology·Esther NistalJosé Luis Olcoz
Jan 27, 2016·World Journal of Gastroenterology : WJG·Johan GagnièreMathilde Bonnet
Apr 22, 2016·Genome Medicine·Claire L BoulangéMarc-Emmanuel Dumas
Sep 27, 2016·Applied & Translational Genomics·Jaeyun SungNicholas Chia
Feb 14, 2017·Nature Microbiology·Jonas HalfvarsonJanet K Jansson
Feb 23, 2018·Journal of Environmental Science and Health. Part A, Toxic/hazardous Substances & Environmental Engineering·Bo-Min KiKyung-Suk Cho

❮ Previous
Next ❯

Software Mentioned

HMP Unified Metabolic Analysis Network 2 ( HUMAnN2 )
HUMAnN2
R package plyr
house
ELSA
Cytoscape

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.