Insights into early evolutionary adaptations of the Akkermansia genus to the vertebrate gut.

Akkermansia, a relevant mucin degrader from the vertebrate gut microbiota, is a member of the deeply branched Verrucomicrobiota, as well as the only known member of this phylum to be described as inhabitants of the gut. Only a few Akkermansia species have been officially described so far, although there is genomic evidence addressing the existence of more species-level variants for this genus. This niche specialization makes Akkermansia an interesting model for studying the evolution of microorganisms to their adaptation to the gastrointestinal tract environment, including which kind of functions were gained when the Akkermansia genus originated or how the evolutionary pressure functions over those genes. In order to gain more insight into Akkermansia adaptations to the gastrointestinal tract niche, we performed a phylogenomic analysis of 367 high-quality Akkermansia isolates and metagenome-assembled genomes, in addition to other members of Verrucomicrobiota. This work was focused on three aspects: the definition of Akkermansia genomic species clusters and the calculation and functional characterization of the pangenome for the most represented species; the evolutionary relationship between Akkermansia and their closest relatives from Verrucomicrobiota, defining the gene families which were gained or lost during the emergence of the last Akkermansia common ancestor (LAkkCA) and; the evaluation of the evolutionary pressure metrics for each relevant gene family of main Akkermansia species. This analysis found 25 Akkermansia genomic species clusters distributed in two main clades, divergent from their non-Akkermansia relatives. Pangenome analyses suggest that Akkermansia species have open pangenomes, and the gene gain/loss model indicates that genes associated with mucin degradation (both glycoside hydrolases and peptidases), (micro)aerobic metabolism, surface interaction, and adhesion were part of LAkkCA. Specifically, mucin degradation is a very ancestral innovation involved in the origin of Akkermansia. Horizontal gene transfer detection suggests that Akkermansia could receive genes mostly from unknown sources or from other Gram-negative gut bacteria. Evolutionary metrics suggest that Akkemansia species evolved differently, and even some conserved genes suffered different evolutionary pressures among clades. These results suggest a complex evolutionary landscape of the genus and indicate that mucin degradation could be an essential feature in Akkermansia evolution as a symbiotic species.

Phylogenomic analysis of the Porphyromonas gingivalis - Porphyromonas gulae duo: approaches to the origin of periodontitis.

Porphyromonas gingivalis is an oral human pathogen associated with the onset and progression of periodontitis, a chronic immune-inflammatory disease characterized by the destruction of the teeth-supporting tissue. P. gingivalis belongs to the genus Porphyromonas, which is characterized by being composed of Gram-negative, asaccharolytic, non-spore-forming, non-motile, obligatory anaerobic species, inhabiting niches such as the oral cavity, urogenital tract, gastrointestinal tract and infected wound from different mammals including humans. Among the Porphyromonas genus, P. gingivalis stands out for its specificity in colonizing the human oral cavity and its keystone pathogen role in periodontitis pathogenesis. To understand the evolutionary process behind P. gingivalis in the context of the Pophyoromonas genus, in this study, we performed a comparative genomics study with publicly available Porphyromonas genomes, focused on four main objectives: (A) to confirm the phylogenetic position of P. gingivalis in the Porphyromonas genus by phylogenomic analysis; (B) the definition and comparison of the pangenomes of P. gingivalis and its relative P. gulae; and (C) the evaluation of the gene family gain/loss events during the divergence of P. gingivalis and P. gulae; (D) the evaluation of the evolutionary pressure (represented by the calculation of Tajima-D values and dN/dS ratios) comparing gene families of P. gingivalis and P. gulae. Our analysis found 84 high-quality assemblies representing P. gingivalis and 14 P. gulae strains (from a total of 233 Porphyromonas genomes). Phylogenomic analysis confirmed that P. gingivalis and P. gulae are highly related lineages, close to P. loveana. Both organisms harbored open pangenomes, with a strong core-to-accessory ratio for housekeeping genes and a negative ratio for unknown function genes. Our analyses also characterized the gene set differentiating P. gulae from P. gingivalis, mainly associated with unknown functions. Relevant virulence factors, such as the FimA, Mfa1, and the hemagglutinins, are conserved in P. gulae, P. gingivalis, and P. loveana, suggesting that the origin of those factors occurred previous to the P. gulae - P. gingivalis divergence. These results suggest an unexpected evolutionary relationship between the P. gulae - P. gingivalis duo and P. loveana, showing more clues about the origin of the role of those organisms in periodontitis.

Microbiota Profile of the Nasal Cavity According to Lifestyles in Healthy Adults in Santiago, Chile.

BACKGROUND: The respiratory microbiome is dynamic, varying between anatomical niches, and it is affected by various host and environmental factors, one of which is lifestyle. Few studies have characterized the upper respiratory tract microbiome profile according to lifestyle. We explored the association between lifestyles and microbiota profiles in the upper respiratory tract of healthy adults. METHODS: We analyzed nasal samples from 110 healthy adults who were living in Santiago, Chile, using 16S ribosomal RNA gene-sequencing methods. Volunteers completed a structured questionnaire about lifestyle. RESULTS: The composition and abundance of taxonomic groups varied across lifestyle attributes. Additionally, multivariate models suggested that alpha diversity varied in the function of physical activity, nutritional status, smoking, and the interaction between nutritional status and smoking, although the significant impact of those variables varied between women and men. Although physical activity and nutritional status were significantly associated with all indexes of alpha diversity among women, the diversity of microbiota among men was associated with smoking and the interaction between nutritional status and smoking. CONCLUSIONS: The alpha diversity of nasal microbiota is associated with lifestyle attributes, but these associations depend on sex and nutritional status. Our results suggest that future studies of the airway microbiome may provide a better resolution if data are stratified for differences in sex and nutritional status.

Role of microbial secreted proteins in gut microbiota-host interactions.

The mammalian gut microbiota comprises a variety of commensals including potential probiotics and pathobionts, influencing the host itself. Members of the microbiota can intervene with host physiology by several mechanisms, including the secretion of a relatively well-reported set of metabolic products. Another microbiota influence mechanism is the use of secreted proteins (i.e., the secretome), impacting both the host and other community members. While widely reported and studied in pathogens, this mechanism remains understood to a lesser extent in commensals, and this knowledge is increasing in recent years. In the following minireview, we assess the current literature covering different studies, concerning the functions of secretable proteins from members of the gut microbiota (including commensals, pathobionts, and probiotics). Their effect on host physiology and health, and how these effects can be harnessed by postbiotic products, are also discussed.