We provide data from the sequenced and analyzed gut metagenome of 368 Chinese individuals with Type 2 Diabetes (T2D) and healthy controls used in a newly developed two stage Metagenome-Wide Association Study (MWAS) aimed at identifying associations between gut microbiota and Type 2 Diabetes. The data here include the an updated metagenome gene catalog, metagenome assemblies, genetic and functional markers associated with T2D, and a novel form of marker- a Metagenomic Linkage Marker (MGL), that allows taxonomic species-level analyses without the need to identify, isolate, and culture novel bacterial species.Bacterial DNA was extracted from faecal samples and subjected to unbiased, whole-genome shotgun (WGS) sequencing using the Illumina GAIIx and HiSeq2000. In summary, 145 samples were sequenced in stage I and 378.4 Gb of paired-end (PE) sequence data were generated; 200 samples were sequenced in stage II and 830.8 Gb of PE sequence data were generated, as well as 23 additional samples for a validation study on gut-microbiota-based T2D classification. By combining MetaHIT data and our sequence data in stage I we constructed an updated human gut microbial gene catalogue, which contained 4.3 million genes suitable for studies on Chinese individuals. In this updated gene catalogue, 21.3%, 47.1% and 60.9% of genes could be assigned to known genera, KEGG and eggNOG database respectively. Taking this gene catalogue as a reference, we identified gene, KO and OG markers, respectively, which seemed to be strongly associated with T2D in our two-stage case-control study, and 47 Metagenomic Linkage Groups (MLGs). These MLGs were further assembled into different contig sets, which could provide useful genetic, functional, and taxonomic information for the relevant bacterium.

Chinese hamster ovary (CHO) K1 cells are a cell line cultured from the ovary of the Chinese hamster (Cricetulus griseus). CHO cells are often used in biological and medical studies and commercially in the production of therapeutic proteins, which contribute significantly to the $100 billion biopharmaceutical market.BGI sequenced the CHO K1 genome genome using next-generation sequencing technology, assembling a 2.45G genome with 24,383 predicted genes.