Most humans carry mites in the hair follicles of their skin for their entire lives. Follicular mites are the only metazoans that continuously live on humans. We propose that Demodex folliculorum (Acari) represents a transitional stage from a host-injuring obligate parasite to an obligate symbiont. Here, we describe the profound impact of this transition on the genome and physiology of the mite. Genome sequencing revealed that the permanent host association of D. folliculorum led to an extensive genome reduction through relaxed selection and genetic drift, resulting in the smallest number of protein-coding genes yet identified among panarthropods. Confocal microscopy revealed that this gene loss coincided with an extreme reduction in the number of cells. Single uninucleate muscle cells are sufficient to operate each of the three segments that form each walking leg. While it has been assumed that the reduction of the cell number in parasites starts early in development, we identified a greater total number of cells in the last developmental stage (nymph) than in the terminal adult stage, suggesting that reduction starts at the adult or ultimate stage of development. This is the first evolutionary step in an arthropod species adopting a reductive, parasitic, or endosymbiotic lifestyle. Somatic nuclei show under-replication at the diploid stage. Novel eye structures or photoreceptors as well as a unique human host melatonin-guided day/night rhythm are proposed for the first time. The loss of DNA repair genes coupled with extreme endogamy might have set this mite species on an evolutionary dead-end trajectory.

One of the biggest challenges in microbiome research in environmental and medicalsamples is to better understand functional properties of microbial community membersat a single-cell level. Single-cell isotope probing has become a key tool for this purpose,but the current detection methods for determination of isotope incorporation into singlecells do not allow high-throughput analyses. Here, we report on the development of animaging-based approach termed stimulated Raman scattering–two-photon fluorescencein situ hybridization (SRS-FISH) for high-throughput metabolism and identity analysesof microbial communities with single-cell resolution. SRS-FISH offers an imaging speedof 10 to 100 ms per cell, which is two to three orders of magnitude faster than achievableby state-of-the-art methods. Using this technique, we delineated metabolic responses of 30,000 individual cells to various mucosal sugars in the human gut microbiome viaincorporation of deuterium from heavy water as an activity marker. Application of SRS-FISH to investigate the utilization of host-derived nutrients by two major human gutmicrobiome taxa revealed that response to mucosal sugars tends to be dominated byBacteroidales, with an unexpected finding that Clostridia can outperform Bacteroidalesat foraging fucose. With high sensitivity and speed, SRS-FISH will enable researchers toprobe the fine-scale temporal, spatial, and individual activity patterns of microbial cellsin complex communities with unprecedented detail.

The obligate intracellular bacteria Chlamydia trachomatis store glycogen in the lumen of the vacuoles in which they grow. Glycogen catabolism generates glucose-1-phosphate (Glc1P), while the bacteria can take up only glucose-6-phosphate (Glc6P). We tested whether the conversion of Glc1P into Glc6P could be catalyzed by a phosphoglucomutase (PGM) of host or bacterial origin. We found no evidence for the presence of the host PGM in the vacuole. Two C. trachomatis proteins, CT295 and CT815, are potential PGMs. By reconstituting the reaction using purified proteins, and by complementing PGM deficient fibroblasts, we demonstrated that only CT295 displayed robust PGM activity. Intriguingly, we showed that glycogen accumulation in the lumen of the vacuole of a subset of Chlamydia species (C. trachomatis, C. muridarum, C. suis) correlated with the presence, in CT295 orthologs, of a secretion signal recognized by the type three secretion (T3S) machinery of Shigella. C. caviae and C. pneumoniae do not accumulate glycogen, and their CT295 orthologs lack T3S signals. In conclusion, we established that the conversion of Glc1P into Glc6P was accomplished by a bacterial PGM, through the acquisition of a T3S signal in a “housekeeping” protein. Acquisition of this signal likely contributed to shaping glycogen metabolism within Chlamydiaceae.