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This Week in Nature: May 30, 2019

In this week's Nature and Nature Medicine, members of the Integrative Human Microbiome Project (IHMP) publish papers revealing new details about how the host-microbiome relationship influences human health. In the first Nature paper, the researchers tracked 132 individuals with inflammatory bowel diseases for one year, creating integrated longitudinal molecular profiles of host and microbial activity. The result is a "comprehensive view of functional dysbiosis in the gut microbiome during inflammatory bowel disease activity" that identifies changes in the composition of the microbiome, host- and microbiome-derived molecules in the gut, and gene expression, the researchers say. The team also pinpoints microbial, biochemical, and host factors central to this dysregulation. In the second Nature paper, IHMP researchers analyze samples from 106 healthy and prediabetic subjects over four years, performing deep profiling of transcriptomes, metabolomes, cytokines, and proteomes, plus changes in the microbiome. Their findings reveal insights into pathways and responses that differ between glucose-dysregulated and healthy individuals during health and disease, and represent a new resource for studying prediabetic and type 2 diabetes states. And in Nature Medicine, the investigators focus on how the vaginal microbiome affects the risk of premature birth, studying samples from roughly 1,500 women of predominantly African ancestry through their pregnancies. They find that those who delivered preterm had significantly different levels of certain bacteria than those who did not, which may provide new opportunities for assessing preterm birth risk.

Also in Nature, a team led by scientists from Johns Hopkins University report a new method for evaluating fragmentation patterns of cell-free DNA genome-wide in patients with cancer. They find that profiles of healthy individuals reflected nucleosomal patterns of white blood cells, whereas patients with cancer had altered fragmentation profiles. When they used the approach to analyze the fragmentation profiles of 236 patients with breast, colorectal, lung, ovarian, pancreatic, gastric, or bile duct cancer and 245 healthy individuals, they found these profiles could be used to narrow down the tissue of origin of the cancers to a limited number of sites in 75 percent of cases. When they combined their approach with  mutation-based cell-free DNA analyses, 91 percent of patients with cancer could be detected. "The results of these analyses highlight important properties of cell-free DNA and provide a proof-of-principle approach for the screening, early detection, and monitoring of human cancer," the authors write.