宏基因组分析使用编码区注释中的两种方法来组合基因序列末端标签[14]。第一个方法是根据在序列数据库中已公开的同源基因来辨别基因,通常是透过简单的BLAST搜索。这种搜索方法是MEGAN4程式里面就有的[15]。第二个,从头计算,使用序列固有的特点根据从相关物种而来的gene training sets来预测编码区段。GeneMark和GLIMMER等程式就是采用这种方式[16]。从头计算的主要优点是它能够侦测在序列数据库中缺少同源片段的编码区。然而,最准确的时候是用连续的基因组DNA的大片段来比较[12]。
作为另一个项目的一部分进行的一项研究,MetaHit(Metagenomics of the Human Intestinal Tract、人体肠道宏基因组学),对124名丹麦人和西班牙人进行了研究,其中包括健康人、肥胖者和肠易激综合征患者。 这项研究检查了胃肠道菌群的系统多样性。我们正在研究居住在胃肠道的细菌菌群具有什么样的系统多样性。 结果表明,拟杆菌门(Bacteroidetes)和厚壁菌门(Firmicutes)这两个门是构成肠道菌群90%以上的菌株。
Handelsman, J.; Rondon, M. R.; Brady, S. F.; Clardy, J.; Goodman, R. M. (1998) Molecular biological access to the chemistry of unknown soil microbes: A new frontier for natural products. Chemistry & Biology 5 (10): R245. doi:10.1016/S1074-5521(98)90108-9.
Committee on Metagenomics: Challenges and Functional Applications, National Research Council (2007). The New Science of Metagenomics: Revealing the Secrets of Our Microbial Planet. Washington, D.C.: The National Academies Press. ISBN 0-309-10676-1.
Huson, Daniel H; S. Mitra, N. Weber, H. Ruscheweyh and Stephan C. Schuster (2011-06). "Integrative analysis of environmental sequences using MEGAN4". Genome Research 21 (9): 1552–1560.
Hug, Laura A.; Baker, Brett J.; Anantharaman, Karthik; Brown, Christopher T.; Probst, Alexander J.; Castelle, Cindy J.; Butterfield, Cristina N.; Hernsdorf, Alex W.; Amano, Yuki; Ise, Kotaro; Suzuki, Yohey; Dudek, Natasha; Relman, David A.; Finstad, Kari M.; Amundson, Ronald; Thomas, Brian C.; Banfield, Jillian F. A new view of the tree of life. Nature Microbiology. 11 April 2016, 1: 16048 [2017-07-23]. PMID 27572647. doi:10.1038/nmicrobiol.2016.48. (原始内容存档于2019-10-21).
Pagani, Ioanna; Konstantinos Liolios, Jakob Jansson, I-Min A Chen, Tatyana Smirnova, Bahador Nosrat, Victor M Markowitz, Nikos C Kyrpides (1 December 2011). "The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata". Nucleic Acids Research 40 (1): D571–9.
Meyer, F; Paarmann D, D'Souza M, Olson R, Glass EM, Kubal M, Paczian T, Rodriguez A, Stevens R, Wilke A, Wilkening J, Edwards RA (2008). "The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes". BMC Bioinformatics 9: 0.
Markowitz, V. M.; Chen, I. -M. A.; Chu, K.; Szeto, E.; Palaniappan, K.; Grechkin, Y.; Ratner, A.; Jacob, B. et al. (2011). "IMG/M: The integrated metagenome data management and comparative analysis system". Nucleic Acids Research 40 (Database issue): D123–9.
Mitra, Suparna; Paul Rupek, Daniel C Richter, Tim Urich, Jack A Gilbert, Folker Meyer, Andreas Wilke, Daniel H Huson (2011). "Functional analysis of metagenomes and metatranscriptomes using SEED and KEGG". BMC Bioinformatics 12 Suppl 1: S21.
Mitra, Suparna; Paul Rupek, Daniel C Richter, Tim Urich, Jack A Gilbert, Folker Meyer, Andreas Wilke, Daniel H Huson (2011). "Functional analysis of metagenomes and metatranscriptomes using SEED and KEGG". BMC Bioinformatics 12 Suppl 1: S21.
Nelson KE and White BA (2010). "Metagenomics and Its Applications to the Study of the Human Microbiome". Metagenomics: Theory, Methods and Applications. Caister Academic Press.
Li, Luen-Luen; Sean R McCorkle, Sebastien Monchy, Safiyh Taghavi, Daniel van der Lelie (18 May 2009). "Bioprospecting metagenomes: glycosyl hydrolases for converting biomass". Biotechnology for Biofuels 2: 10.
Kakirde, Kavita S.; Larissa C. Parsley, Mark R. Liles (1 November 2010). "Size Does Matter: Application-driven Approaches for Soil Metagenomics". Soil biology & biochemistry 42 (11): 1911–1923.