Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses

被引:144
作者
Perez-Cobas, Ana Elena [1 ,2 ]
Gomez-Valero, Laura [1 ,2 ]
Buchrieser, Carmen [1 ,2 ]
机构
[1] Inst Pasteur, Biol Batteries Intracellulaires, Paris, France
[2] CNRS UMR 3525, F-675724 Paris, France
关键词
metagenomics; whole-genome sequencing; marker genes; sequencing data analyses; 16S RIBOSOMAL-RNA; INTERNAL TRANSCRIBED SPACER; EUKARYOTIC GENOMES; BINNING ALGORITHM; PROTEIN ALIGNMENT; SINGLE-CELL; IDENTIFICATION; ANNOTATION; PREDICTION; NUMBER;
D O I
10.1099/mgen.0.000409
中图分类号
Q3 [遗传学];
学科分类号
071007 ; 090102 ;
摘要
Metagenomics and marker gene approaches, coupled with high-throughput sequencing technologies, have revolutionized the field of microbial ecology. Metagenomics is a culture-independent method that allows the identification and characterization of organisms from all kinds of samples. Whole-genome shotgun sequencing analyses the total DNA of a chosen sample to determine the presence of micro-organisms from all domains of life and their genomic content. Importantly, the whole-genome shotgun sequencing approach reveals the genomic diversity present, but can also give insights into the functional potential of the micro-organisms identified. The marker gene approach is based on the sequencing of a specific gene region. It allows one to describe the microbial composition based on the taxonomic groups present in the sample. It is frequently used to analyse the biodiversity of microbial ecosystems. Despite its importance, the analysis of metagenomic sequencing and marker gene data is quite a challenge. Here we review the primary workflows and software used for both approaches and discuss the current challenges in the field.
引用
收藏
页码:1 / 22
页数:22
相关论文
共 268 条
[1]   Divergence and redundancy of 16S rRNA sequences in genomes with multiple rrn operons [J].
Acinas, SG ;
Marcelino, LA ;
Klepac-Ceraj, V ;
Polz, MF .
JOURNAL OF BACTERIOLOGY, 2004, 186 (09) :2629-2635
[2]  
Afiahayati A., 2015, DNA RES, V22, P69, DOI DOI 10.1093/dnares/dsu041
[3]   CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database [J].
Alcock, Brian P. ;
Raphenya, Amogelang R. ;
Lau, Tammy T. Y. ;
Tsang, Kara K. ;
Bouchard, Megane ;
Edalatmand, Arman ;
Huynh, William ;
Nguyen, Anna-Lisa, V ;
Cheng, Annie A. ;
Liu, Sihan ;
Min, Sally Y. ;
Miroshnichenko, Anatoly ;
Tran, Hiu-Ki ;
Werfalli, Rafik E. ;
Nasir, Jalees A. ;
Oloni, Martins ;
Speicher, David J. ;
Florescu, Alexandra ;
Singh, Bhavya ;
Faltyn, Mateusz ;
Hernandez-Koutoucheva, Anastasia ;
Sharma, Arjun N. ;
Bordeleau, Emily ;
Pawlowski, Andrew C. ;
Zubyk, Haley L. ;
Dooley, Damion ;
Griffiths, Emma ;
Maguire, Finlay ;
Winsor, Geoff L. ;
Beiko, Robert G. ;
Brinkman, Fiona S. L. ;
Hsiao, William W. L. ;
Domselaar, Gary, V ;
McArthur, Andrew G. .
NUCLEIC ACIDS RESEARCH, 2020, 48 (D1) :D517-D525
[4]   A new genomic blueprint of the human gut microbiota [J].
Almeida, Alexandre ;
Mitchell, Alex L. ;
Boland, Miguel ;
Forster, Samuel C. ;
Gloor, Gregory B. ;
Tarkowska, Aleksandra ;
Lawley, Trevor D. ;
Finn, Robert D. .
NATURE, 2019, 568 (7753) :499-+
[5]  
Alneberg J, 2014, NAT METHODS, V11, P1144, DOI [10.1038/NMETH.3103, 10.1038/nmeth.3103]
[6]   BASIC LOCAL ALIGNMENT SEARCH TOOL [J].
ALTSCHUL, SF ;
GISH, W ;
MILLER, W ;
MYERS, EW ;
LIPMAN, DJ .
JOURNAL OF MOLECULAR BIOLOGY, 1990, 215 (03) :403-410
[7]   Differential expression analysis for sequence count data [J].
Anders, Simon ;
Huber, Wolfgang .
GENOME BIOLOGY, 2010, 11 (10)
[8]   PERMANOVA, ANOSIM, and the Mantel test in the face of heterogeneous dispersions: What null hypothesis are you testing? [J].
Anderson, Marti J. ;
Walsh, Daniel C. I. .
ECOLOGICAL MONOGRAPHS, 2013, 83 (04) :557-574
[9]  
Angly FE, 2014, COPYRIGHTER RAPID TO, P1
[10]  
[Anonymous], 2013, Open Bioinforma J, DOI DOI 10.2174/1875036201307010001