Reconstruction of ancient microbial genomes from the human gut.

Loss of gut microbial diversity1-6 in industrial populations is associated with chronic diseases7, underscoring the importance of studying our ancestral gut microbiome. However, relatively little is known about the composition of pre-industrial gut microbiomes. Here we performed a large-scale de novo assembly of microbial genomes from palaeofaeces. From eight authenticated human palaeofaeces samples (1,000-2,000 years old) with well-preserved DNA from southwestern USA and Mexico, we reconstructed 498 medium- and high-quality microbial genomes. Among the 181 genomes with the strongest evidence of being ancient and of human gut origin, 39% represent previously undescribed species-level genome bins. Tip dating suggests an approximate diversification timeline for the key human symbiont Methanobrevibacter smithii. In comparison to 789 present-day human gut microbiome samples from eight countries, the palaeofaeces samples are more similar to non-industrialized than industrialized human gut microbiomes. Functional profiling of the palaeofaeces samples reveals a markedly lower abundance of antibiotic-resistance and mucin-degrading genes, as well as enrichment of mobile genetic elements relative to industrial gut microbiomes. This study facilitates the discovery and characterization of previously undescribed gut microorganisms from ancient microbiomes and the investigation of the evolutionary history of the human gut microbiota through genome reconstruction from palaeofaeces.

Parameters affecting the exposure to furfuryl alcohol from coffee.

Recently, furfuryl alcohol (FFA) was labelled a human potential carcinogen (group 2B) by the International Agency for Research on Cancer. Its alimentary exposure is mostly from coffee since in any other foods the concentrations are significantly lower. The various storage conditions of roasted coffee, the different brewing techniques applied and the bioaccessibility after ingestion are potential parameters that might alter the exposure to FFA from coffee. An 8 weeks stability study at varying temperatures showed that FFA is stable in the ground coffee matrix. Moreover, different brewing techniques extracted different amounts of FFA and affected its final concentration. The evaluation of the relative exposure to four furans (FFA, 5-hydroxymethyl-furaldehyde, 2-furoic acid, and 5-hydroxymethyl-2-furoic acid) revealed that FFA amounts were at least 2-fold the amounts of other studied furans in the same brew. A 22-fold variation in the concentration of the four furans in brews prepared using different coffee grounds and brewing techniques could be observed. 90% of the four furans were extracted by the first 25-30% fraction of the filter brew. A significant decrease of FFA is observed after stressing with simulated gastric fluid. However, this decrease could not be reproduced when mimicking a regular coffee ingestion situation.