Understanding how microbial communities develop is essential for predicting and directing their future states. Ecological theory suggests that community development is often influenced by priority effects, in which the order and timing of species arrival determine how species affect one another. Priority effects can have long-lasting consequences, particularly if species arrival history varies during the early stage of community development, but their importance to the human gut microbiota and host health remains largely unknown. Here, we explore how priority effects might influence microbial communities in the gastrointestinal tract during early childhood and how the strength of priority effects can be estimated from the composition of the microbial species pool. We also discuss factors that alter microbial transmission, such as delivery mode, diet and parenting behaviours such as breastfeeding, which can influence the likelihood of priority effects. An improved knowledge of priority effects has the potential to inform microorganism-based therapies, such as prebiotics and probiotics, which are aimed at guiding the microbiota towards a healthy state.

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The circadian input kinase A (cikA) gene encodes a protein relaying environmental signal to the central circadian oscillator in cyanobacteria. The CikA protein has a variable architecture and usually consists of four tandemly arrayed domains: GAF, histidine kinase (HisKA), histidine kinase-like ATPase (HATPase_c), and a pseudo-receiver (REC). Among them, HisKA and HATPase_c are the least polymorphic, and REC is not present in heterocystic filamentous cyanobacteria. CikA contains several conserved motifs that are likely important for circadian function. There are at least three types of circadian systems, each of which possesses a different set of circadian genes. The originally described circadian system (kaiABC system) possesses both cikA and kaiA, while the others lack either only cikA (kaiABC (Delta)) or both (kaiBC). The results we obtained allowed us to approximate the time of the cikA origin to be about 2600-2200 MYA and the time of its loss in the species with the kaiABC (Delta) or kaiBC system between 1100 and 600 MYA. Circadian specialization of CikA, as opposed to its non-circadian homologs, is a result of several factors, including the unique conserved domain architecture and high evolutionary constraints of some domains and regions, which were previously identified as critical for the circadian function of the gene.

Endogenous intestinal microbiota have wide-ranging and largely uncharacterized effects on host physiology. Here, we used reverse-phase liquid chromatography-coupled tandem mass spectrometry to define the mouse intestinal proteome in the stomach, jejunum, ileum, cecum and proximal colon under three colonization states: germ-free (GF), monocolonized with Bacteroides thetaiotaomicron and conventionally raised (CR). Our analysis revealed distinct proteomic abundance profiles along the gastrointestinal (GI) tract. Unsupervised clustering showed that host protein abundance primarily depended on GI location rather than colonization state and specific proteins and functions that defined these locations were identified by random forest classifications. K-means clustering of protein abundance across locations revealed substantial differences in host protein production between CR mice relative to GF and monocolonized mice. Finally, comparison with fecal proteomic data sets suggested that the identities of stool proteins are not biased to any region of the GI tract, but are substantially impacted by the microbiota in the distal colon.

Previously, we determined that genetic and environmental factors contributed equally towards rosacea in twins. To assess an environmental factor, we characterized the malar cheek bacterial microbiome from twins discordant for rosacea. We found no significant difference in facial microbiome alpha and beta diversity between related twins discordant for rosacea. However, the relative percentage abundance of Gordonia and Geobacillus, low-abundant genera, was positively and negatively associated with rosacea severity, respectively. Our data demonstrate a significant correlation between facial microbiome and severity of rosacea in genetically matched twins and importantly that overall microbiome composition is largely unchanged. | BACKG ROU N DRosacea is a chronic inflammatory disease of the facial skin and eyes that affects ~16 million individuals in the United States alone.Although its aetiology is unknown, we previously determined that both genetic and environmental factors contribute equally towards disease using identical (monozygotic) and fraternal (dizygotic) twins. [1] Previous studies have implicated microbial colonization and the cognate immune response as the critical driver of rosacea. [2,3] Increased levels of Demodex mites and associated bacteria (bacillus), antimicrobial peptides (eg cathelicidin/LL37), host immune variables (eg Tolllike receptor (TLR)-2) and nutrients (eg vitamin D3) are reported to alter the innate immune response and cause chronic inflammation and the facial skin sensitivity in rosacea. [2,3] In addition, the recent studies suggest significant associations between the severity of rosacea and systemic comorbidities (eg cardiovascular, allergic, respiratory, metabolic and gastrointestinal diseases) that are linked with chronic inflammation. [4,5] Rosacea and its reported comorbidities share involvement with barrier tissues that are colonized with a wide variety of microflora that constitute the microbiome. | QUE S TION ADDRE SS EDThe beneficial use of therapeutic drugs for rosacea including oral and topical antibiotics, sulphur compounds and ivermectin that alter the facial microbiome, [6] suggests that altering the resident skin microbiome may play a role in the disease. However, no conclusive evidence has been established.Microbial dysbiosis could be one of the factors associated with the pathogenesis of rosacea as well as its comorbidities. Harnessing the genetic and environmental control inherent in a twin study, we performed next-generation sequencing of the 16S rRNA gene to evaluate the hypothesis that facial bacterial microbiome dysbiosis will associate with the severity of rosacea in twins discordant for rosacea. | E XPERIMENTAL DE S I G NSee Appendix S1. | RE SULTS | Comparable overall facial skin microbiome composition across subjectsWe estimated the relative percentage abundance (RPA) of facial bacterial microbiome at the phylum level in twins with and without rosacea. The top four abundant phyla were Firmicutes (mean ± SD; 42.98% ± 1.05%), Proteobacteria (39.29% ± 1...