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Quantitative Biology

ISSN 2095-4689

ISSN 2095-4697(Online)

CN 10-1028/TM

邮发代号 80-971

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Quantitative Biology  2016, Vol. 4 Issue (3): 192-206   https://doi.org/10.1007/s40484-016-0078-x
  本期目录
An overview of major metagenomic studies on human microbiomes in health and disease
Hongfei Cui1, Yingxue Li1, Xuegong Zhang1,2()
1. MOE Key Laboratory of Bioinformatics and Bioinformatics Division, TNLIST, Center for Synthetic and Systems Biology/Department of Automation, Tsinghua University, Beijing 100084, China
2. School of Life Sciences, Tsinghua University, Beijing 100084, China
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Abstract：

Many microbes are important symbiotes of human. They form specific microbiota communities, participate in various kinds of biological processes of their host and thus deeply affect human health status. Metagenomic sequencing has been widely used in human microbiota study due to its capacity of studying all genetic materials in an environment as a whole without any extra need of isolation or cultivation of microorganisms. Many efforts have been made by researchers in this area trying to dig out interesting knowledge from various metagenome data. In this review, we go through some prominent studies in the metagenomic area. We summarize them into three categories, constructing taxonomy and gene reference, characterization of microbiome distribution patterns, and detection of microbiome alternations associated with specific human phenotypes or diseases. Some available data resources are also provided. This review can serve as an entrance to this exciting and rapidly developing field for researchers interested in human microbiomes.
Author Summary  

 

Human symbiotic microbes are our important “tiny friends”. They form microbiota communities, participate in multiple types of our biological processes and thus deeply affect our health status. The importance and intricacy of human microbiota studies have attracted extensive attentions. Metagenomic sequencing is one of the most widely used strategies in human microbiota study. Here, we gather the scattered achievements in metagenomic area and comb through their valuable ideas and resources from our perspective. We hope this review can serve as an entrance to this exciting and rapidly developing field for researchers interested in human microbiomes.

Key words： metagenome    human microbiome    taxonomy and gene reference    distribution pattern    microbiome variation
收稿日期: 2016-01-30      出版日期: 2016-09-07
Corresponding Author(s): Xuegong Zhang   
 引用本文:   
. [J]. Quantitative Biology, 2016, 4(3): 192-206.
Hongfei Cui, Yingxue Li, Xuegong Zhang. An overview of major metagenomic studies on human microbiomes in health and disease. Quant. Biol., 2016, 4(3): 192-206.
 链接本文:  
https://academic.hep.com.cn/qb/CN/10.1007/s40484-016-0078-x
https://academic.hep.com.cn/qb/CN/Y2016/V4/I3/192
Fig.1  
Study/Document Reference name Reference type Body site Data provided
Quast et al. 2013 [16] SILVA rRNA Not specific 1,756,783 small subunit and 96,642 large subunit
DeSantis et al. 2006 [17] Greengenes rRNA Not specific 1,262,986 16S rRNAs
Cole et al. 2014 [18] RDP rRNA Not specific 3,224,600 16S rRNAs and 108,901 fungal 28S rRNAs
NCBI Resource Coordinators, 2016 [19] NCBI genome Genome Not specific 8,075 bacteria, 521 archaea, 1,675 eukaryota, 5,428 viruses and 48 viroids
Markowitz et al. 2014 [20] IMG (Genome) Genome Not specific 34,186 bacteria, 675 archaea, 220 eukaryota, 1,193 plasmids and 3,905 viruses and 1,192 assembled genome fragments
Chen et al. 2010 [21] HOMD Genome Oral cavity 1,530 annotated genomes from 406 Human Oral Taxon
Nielsen et al. 2014 [22] – Genome Gut 238
NCBI Resource Coordinators, 2016 [19] NCBI nr Gene Not specific 83,785,854
Kanehisa et al. 2016 [23] KEGG Gene Not specific 17,956,002 genes related to 19,214 KEGG Ortholog groups (KOs)
The UniProt Consortium 2016 [24] UniProt Gene Not specific 550,740 Swiss-Prot sequences and 63,039,659 TrEMBL sequences
The HMP Consortium, 2012 [25] HMP Gene 15 body sites 15,006,602 in Total
Li et al. 2014 [26] IGC Gene Gut 9,879,896
Qin et al. 2014 [27] Liver cirrhosis catalogue Gene Gut 2,688,468
Oh et al. 2014 [28] – Gene Skin 5,922,920
Feng et al. 2015 [29] – Gene Gut ~3.5 million
Meyer et al. 2008 [30] MG-RAST Metagenome Not specific 33,809 samples from 1,159 metagenomic projects
Hunter et al. 2014 [31] EBI metagenomics Metagenome Not specific 7,085 metagenome samples, 884 metatranscriptome samples, 18,820 amplication samples and 69 assemblies from 182 projects
Markowitz et al. 2014 [20] IMG (Metagenome) Metagenome Not specific 4,842 metagenome samples from 244 projects
Tab.1  
Study Body site Aim of study
Qin et al. 2010 [38] Gut General survey
The HMP Consortium, 2012 [25] Multiple sites General survey
Li et al. 2014 [26] Gut General survey
Oh et al. 2014 [28] Skin General survey
Zhou et al. 2007 [61] Vagina Community type
Ravel et al. 2012 [64] Vagina CST
Mehta et al. 2015 [65] Vagina CST
DiGiulio et al. 2015 [67] Vagina CST
Arumugam et al. 2011 [69] Gut Enterotype
Wu et al. 2011 [70] Gut Enterotype
Qin et al. 2012 [41] Gut Enterotype
Moeller et al. 2012 [71] Gut Enterotype
Knights et al. 2014 [73] Gut Rethinking of enterotype
Feng et al. 2015 [29] Gut Enterotype and microbioal community type
Ding et al. 2014 [74] Multiple sites Microbioal community type
Franzosa et al. 2015 [75] Multiple sites Metagenomic code
David et al. 2012 [79] Gut and saliva Dynamics
Lozupone et al. 2012 [78] Gut Dynamics
Sharon et al. 2013 [76] Gut Dynamics
Faith et al. 2013 [77] Gut Dynamics
Tab.2  
Study Main phenotype Body site Number of individuals Main features Main data accession
Single phenotype
Smith et al. 2013 [80] Kwashiorkor Gut 317 pairs Taxa, functions EBI accessions ERP001928 and ERP001911
Le Chatelier et al. 2013 [55] Obesity Gut 292 Genes EBI accession ERP003612
Dewulf et al. 2013 [81] Obesity Gut 30 Taxa
Cotillard et al. 2013 [82] Diet, Obesity Gut 49 Genes EBI accession ERP003699
Adler et al. 2013 [83] Diet of ancient Ancient dental calculus 34 Taxa EBI or SRA accession ERP002107
David et al. 2014 [84] Diet Gut 10 Taxa, functions GEO accession GSE46761 and MG-RAST accession 6248
Qin et al. 2012 [41] Diabetes Gut 345 Taxa(MLGs), functions SRA accession SRA045646 and SRA050230
Karlsson et al. 2013 [85] Diabetes Gut 145 Taxa(MGCs), functions EBI or SRA accession ERP002469
Rajilic-Stojanovic et al. 2011 [86] IBS Gut 108 Taxa
Saulnier et al. 2011 [87] IBS Gut 44 Taxa SRA accession SRP002457
Qin et al. 2010 [38] IBD Gut 124 Taxa, functions EBI accession ERA000116, http://www.bork.embl.de/~arumugam/Qin_et_al_2010/
Gevers et al. 2014 [88] IBD Gut 668 Taxa BioProjects accessions PRJNA237362 and PRJNA205152
Zhu et al. 2013 [89] Fatty liver Gut 63 Taxa MG-RAST accession 1195
Qin et al. 2014 [27] Cirrhosis Gut 181 Taxa(MGS), functions EBI accession ERP005860
Karlsson et al. 2012 [90] Atherosclerosis Gut 27 Taxa, functions SRA accession SRA059451
Kostic et al. 2012 [91] Cancer Colorectal carcinoma tumors and adjacent non-affected tissues 18+190 Taxa SRA accession SRP000383
Yu et al. 2015 [92] Cancer Gut 168+40 Taxa(MLGs), functions EBI accession PRJEB10878
Feng et al. 2015 [29] Cancer Gut 156 Taxa(MLGs), functions EBI accession ERP008729
Tyakht et al. 2013 [93] Urban/countryside Gut 96 Taxa, functions SRA accession SRA059011, http://www.metagenome.ru/files/rus_met/
Koren et al. 2012 [94] Pregnant Gut 91 Taxa
DiGiulio et al. 2015 [67] Pregnant Vagina, gut, saliva, and tooth/gum 49 Taxa SRA accession SRP288562 (Not available now)
Belda-Ferre et al. 2012 [95] Oral diseases Supragingival plaque 25 Taxa, functions MG-RAST accessions 4447192.3, 4447102.3, 4447103.3, 4447101.3, 4447943.3, 4447903.3, 4447971.3 and 4447970.3
Wang et al. 2013 [96] Oral diseases Dental surface and plaque 16 Taxa, functions
Duran-Pinedo et al. 2014 [97] Oral diseases Subgingival plaque 13 Taxa, functions ftp://ftp.homd.org/publication_data/20130522/
Yang et al. 2009 [98] Distal esophagus diseases Biopsy samples of the distal esophagus 34 Taxa GEO accessions DQ537536-DQ537935 and DQ632752-DQ639751
Tunney et al. 2013 [99] Bronchiectasis Sputum 40 Taxa EBI or SRA accession ERP002060
Marri et al. 2013 [100] Asthma Sputum 20 Taxa
Morris et al. 2013 [101] Smoke Upper and lower respiratory tract 45 Taxa
Multiple phenotypes
Yatsunenko et al. 2012 [102] Country, age Gut 531 Taxa, genes MG-RAST accession ‘qiime:850’ and ‘qiime:621’
Claesson et al. 2012 [103] Diet, health Gut 178 Taxa, genes MG-RAST accession 154
Stahringer et al. 2012 [104] Host gene, age Saliva 107 Taxa EBI or SRA accession ERP001346
Lozupone et al. 2013 [105] Body sites, studies Multiple sites Public data Taxa Public data
Lax et al. 2014 [106] Family, indoor environment, time Skin 15+3+3+1 Taxa EBI accession ERP005806
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