Quantitative metagenomic analyses based on average genome size normalization

Applied and Environmental Microbiology
Jeremy A Frank, Søren J Sørensen

Abstract

Over the past quarter-century, microbiologists have used DNA sequence information to aid in the characterization of microbial communities. During the last decade, this has expanded from single genes to microbial community genomics, or metagenomics, in which the gene content of an environment can provide not just a census of the community members but direct information on metabolic capabilities and potential interactions among community members. Here we introduce a method for the quantitative characterization and comparison of microbial communities based on the normalization of metagenomic data by estimating average genome sizes. This normalization can relieve comparative biases introduced by differences in community structure, number of sequencing reads, and sequencing read lengths between different metagenomes. We demonstrate the utility of this approach by comparing metagenomes from two different marine sources using both conventional small-subunit (SSU) rRNA gene analyses and our quantitative method to calculate the proportion of genomes in each sample that are capable of a particular metabolic trait. With both environments, to determine what proportion of each community they make up and how differences in environment affect...Continue Reading

References

Aug 1, 1976·Archives of Microbiology·B B Buchanan, R Sirevåg
Oct 5, 1990·Journal of Molecular Biology·S F AltschulDavid J Lipman
Apr 15, 1988·European Journal of Biochemistry·B GonteroJ Ricard
Nov 1, 1987·Journal of Bacteriology·J S Shieh, W B Whitman
Nov 1, 1970·The Biochemical Journal·R Sirevåg, J G Ormerod
Jul 1, 1993·Nucleic Acids Research·N LarsenC R Woese
Apr 1, 2000·Applied and Environmental Microbiology·J A KlappenbachThomas M Schmidt
Jul 19, 2001·Nature·O BéjàEdward F DeLong
Jul 3, 2002·Proceedings of the National Academy of Sciences of the United States of America·Jonathan A EisenClaire M Fraser
Aug 15, 2003·Proceedings of the National Academy of Sciences of the United States of America·Alexis DufresneWolfgang R Hess
Dec 19, 2003·Nucleic Acids Research·David L WheelerLukas Wagner
Apr 7, 2004·Science·J Craig VenterHamilton O Smith
Sep 18, 2004·Journal of Bacteriology·Michael W Finn, F Robert Tabita
Nov 6, 2004·Applied and Environmental Microbiology·Bradley S Stevenson, Thomas M Schmidt
Oct 11, 2005·Nucleic Acids Research·Ross OverbeekVeronika Vonstein
Nov 4, 2005·Nature·Stephen J GiovannoniDouglas F Barofsky
Feb 17, 2006·Nature·Niels-Ulrik FrigaardEdward F DeLong
Oct 31, 2006·Applied and Environmental Microbiology·Rebecca J CaseStaffan Kjelleberg
Dec 16, 2006·Nucleic Acids Research·David L WheelerEugene Yaschenko
Jan 17, 2007·Genome Biology·Jeroen RaesPeer Bork
Jul 11, 2007·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Oliver Mueller-Cajar, Murray Ronald Badger
Sep 11, 2007·Nature Reviews. Microbiology·Mary Ann Moran, William L Miller
Oct 10, 2007·Environmental Microbiology·Linda WegleyForest Rohwer
Jan 29, 2008·Nature·Xiaozhen MouMary Ann Moran
Feb 26, 2008·Applied and Environmental Microbiology·Jeremy A FrankGary J Olsen
Sep 25, 2008·Proceedings of the National Academy of Sciences of the United States of America·Eric A WelshHimadri B Pakrasi
Mar 26, 2010·The ISME Journal·Bánk BeszteriStephen J Giovannoni

Citations

Jun 24, 2011·The ISME Journal·Joseph J Grzymski, Alex M Dussaq
Nov 24, 2012·Briefings in Bioinformatics·Carlotta De FilippoDuccio Cavalieri
Jun 26, 2012·Applied and Environmental Microbiology·Vicente Gomez-AlvarezJorge W Santo Domingo
Jun 26, 2012·BMC Microbiology·Vicente Gomez-AlvarezJorge W Santo Domingo
Apr 18, 2014·The ISME Journal·Stephen J GiovannoniBen Temperton
Jan 7, 2016·Frontiers in Microbiology·Thea Van RossumFiona S L Brinkman
Dec 24, 2015·Microbiome·Aaron J Prussin, Linsey C Marr
Sep 3, 2011·Environmental Microbiology·Nof Atamna-IsmaeelShimshon Belkin
Mar 21, 2016·Journal of Microbiological Methods·Antony T VincentSteve J Charette
Apr 1, 2012·Environmental Microbiology Reports·Nof Atamna-IsmaeelO Béjà
Jun 18, 2016·Health Security·Norman A DoggettSegaran Pillai
Dec 20, 2016·PLoS Computational Biology·Renaud Berlemont, Adam C Martiny
May 30, 2020·Molecular Biology and Evolution·Jaelle C BrealeyKaterina Guschanski

Related Concepts

Cyanobacteria
Environmental Microbiology
Microbiological Techniques
RNA, Ribosomal, 16S
Chlorobiaceae
Deltaproteobacteria
Microbiome
Metagenomics
Bacterial Count Measurement
Carbon

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.

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.

Systemic Juvenile Idiopathic Arthritis

Systemic juvenile idiopathic arthritis is a rare rheumatic disease that affects children. Symptoms include joint pain, but also fevers and skin rashes. Here is the latest on this disease.

Chromatin Regulation and Circadian Clocks

The circadian clock plays an important role in regulating transcriptional dynamics through changes in chromatin folding and remodelling. Discover the latest research on Chromatin Regulation and Circadian Clocks here.

Central Pontine Myelinolysis

Central Pontine Myelinolysis is a neurologic disorder caused most frequently by rapid correction of hyponatremia and is characterized by demyelination that affects the central portion of the base of the pons. Here is the latest research on this disease.

Myocardial Stunning

Myocardial stunning is a mechanical dysfunction that persists after reperfusion of previously ischemic tissue in the absence of irreversible damage including myocardial necrosis. Here is the latest research.

Pontocerebellar Hypoplasia

Pontocerebellar hypoplasias are a group of neurodegenerative autosomal recessive disorders with prenatal onset, atrophy or hypoplasia of the cerebellum, hypoplasia of the ventral pons, microcephaly, variable neocortical atrophy and severe mental and motor impairments. Here is the latest research on pontocerebellar hypoplasia.

Cell Atlas Along the Gut-Brain Axis

Profiling cells along the gut-brain axis at the single cell level will provide unique information for each cell type, a three-dimensional map of how cell types work together to form tissues, and insights into how changes in the map underlie health and disease of the GI system and its crosstalk with the brain. Disocver the latest research on single cell analysis of the gut-brain axis here.

Chronic Traumatic Encephalopathy

Chronic Traumatic Encephalopathy (CTE) is a progressive degenerative disease that occurs in individuals that suffer repetitive brain trauma. Discover the latest research on traumatic encephalopathy here.