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This Week in PNAS: Aug 29, 2017

In the early, online edition of the Proceedings of the National Academy of Sciences, a Stanford University-led team presents a blood-based, cell-free DNA-based approach for getting a glimpse at the microbes in the human body. The researchers did massive shotgun sequencing of cell-free DNA circulating in 1,351 blood samples from 156 heart, lung, or bone marrow transplant patients, or from 32 pregnant women, uncovering thousands of contigs from poorly characterized microbes. "[O]ur approach of using blood effectively enables sampling of the entire body and reveals the colonization of niches which have been previously inaccessible," the authors write, noting that the approach points to "vast and unexpected diversity of microbes" in the human body.

Researchers from Saudi Arabia, Singapore, the US, and Germany characterize giant enteric symbionts living in the guts of a marine algae-feeding surgeonfish using a combination of metagenomics, single-cell genomics, and metatranscriptomics. Using gut samples from four surgeonfish species in the Red Sea, the team came up with seven single-cell amplified genomes and seven genomes established from population samples. Along with 16S ribosomal RNA gene sequences and transcript sequence data, the new draft genomes provided a look at a clade of Candidatus Epulopiscium symbionts from the surgeonfish gut and their contributions to metabolic processes in the host gut. "[T]he genomic blueprint of dominant enteric symbionts belonging to diverse Epulopiscium clades differs according to the host diet," the investigators say. "Thus, the acquisition of a unique enteric microbiota specialized to their diets likely shapes the nutritional ecology of piscine herbivores."

Finally, the Chinese University of Hong Kong's Dennis Lo leads a team using single-cell transcriptomics, and circulating cell-free RNA to track cellular dynamics in the human placenta during pregnancy. The researchers turned to droplet-based single-cell digital transcriptomics to tally up the cellular heterogeneity in placental samples — an approach that led to transcriptional signatures that were subsequently used to follow placenta cell dynamics with cell-free RNA in blood samples from pregnant women with normal pregnancies or preeclampsia. "Analysis of the cellular signature expression in maternal plasma enabled non-invasive delineation of the cellular dynamics of the placenta during pregnancy and the elucidation of extravillous trophoblastic dysfunction in early preeclampsia," the authors explain.