BackgroundSubstantial efforts have been made to link the gut bacterial community to many complex human diseases. Nevertheless, the gut phages are often neglected.ResultsIn this study, we used multiple bioinformatic methods to catalog gut phages from whole-community metagenomic sequencing data of fecal samples collected from both type II diabetes (T2D) patients (n = 71) and normal Chinese adults (n = 74). The definition of phage operational taxonomic units (pOTUs) and identification of large phage scaffolds (n = 2567, ≥ 10 k) revealed a comprehensive human gut phageome with a substantial number of novel sequences encoding genes that were unrelated to those in known phages. Interestingly, we observed a significant increase in the number of gut phages in the T2D group and, in particular, identified 7 pOTUs specific to T2D. This finding was further validated in an independent dataset of 116 T2D and 109 control samples. Co-occurrence/exclusion analysis of the bacterial genera and pOTUs identified a complex core interaction between bacteria and phages in the human gut ecosystem, suggesting that the significant alterations of the gut phageome cannot be explained simply by co-variation with the altered bacterial hosts.ConclusionsAlterations in the gut bacterial community have been linked to the chronic disease T2D, but the role of gut phages therein is not well understood. This is the first study to identify a T2D-specific gut phageome, indicating the existence of other mechanisms that might govern the gut phageome in T2D patients. These findings suggest the importance of the phageome in T2D risk, which warrants further investigation.Electronic supplementary materialThe online version of this article (10.1186/s40168-018-0410-y) contains supplementary material, which is available to authorized users.

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A novel acidothermophilic archaeon, strain Ar-4 T , was isolated from a sulfuric hot spring in Tengchong, Yunnan, China. Cells of strain T were Gram-staining-negative, irregular cocci and motile by means of flagella. Strain Ar-4 T grew over a temperature range of 55-75 6C(optimum, 65 6C), a pH range of 2.5-5.5 (optimum, pH 3.5) and a NaCl concentration range of 0-1 % (w/v). The novel strain was aerobic and facultatively chemolithoautotrophic. The strain could extract metal ions from sulfidic ore. It was also able to oxidize reduced sulfur compounds. In addition, it was able to use heterogeneous organic materials for organotrophic growth. , respectively. The differences in cell motility, the temperature and pH ranges for growth, the ability to utilize carbon sources, the DNA G+C content, and the low DNA-DNA relatedness values distinguished strain T from recognized species of the genus Metallosphaera. On the basis of these results, it was concluded that strain Ar-4 T represents a novel species of the genus Metallosphaera, for which the name Metallosphaera cuprina is proposed. The type strain is Ar-4