Culturing of a complex gut microbial community in mucin-hydrogel carriers reveals strain- and gene-associated spatial organization

Oregano essential oil-infused mucin microneedle patch for the treatment of hypertrophic scar

Hypertrophic scar (HS) manifests as abnormal dermal myofibroblast proliferation and excessive collagen deposition, leading to raised scars and significant physical, psychological, and financial burdens for patients. HS is difficult to cure in the clinic and current therapies lead to recurrence, pain, and side effects. In this study, a natural amphiphilic polymer mucin is used to prepare a dissolving microneedle (muMN) that is loaded with oregano essential oil (OEO) for HS therapy. muMN exhibits sufficient skin/scar tissue penetration, quick skin recovery time after removal, good loading of natural essential oil, fast dissolution and detachment from the base layer, and good biocompatibility to applied skin. In the rabbit HS model, OEO@muMN shows a significant reduction in scar thickness, epidermal thickness index, and scar elevation index. OEO@muMN also attenuates the mean collagen area fraction and decreases the number of capillaries in scar tissues. Biochemical Assay reveals that OEO@muMN significantly inhibits the expression of transforming growth factor-β1 (TGF-β1) and hydroxyproline (HYP). In summary, this study demonstrates the feasibility and good efficacy of using the anti-proliferative and anti-oxidative OEO for HS treatment. OEO@muMN is an efficient formulation that holds the potential for clinical anti-HS application. muMN is an efficient platform to load and apply essential oils transdermally.

Predicting the first steps of evolution in randomly assembled communities

Microbial communities can self-assemble into highly diverse states with predictable statistical properties. However, these initial states can be disrupted by rapid evolution of the resident strains. When a new mutation arises, it competes for resources with its parent strain and with the other species in the community. This interplay between ecology and evolution is difficult to capture with existing community assembly theory. Here, we introduce a mathematical framework for predicting the first steps of evolution in large randomly assembled communities that compete for substitutable resources. We show how the fitness effects of new mutations and the probability that they coexist with their parent depends on the size of the community, the saturation of its niches, and the metabolic overlap between its members. We find that successful mutations are often able to coexist with their parent strains, even in saturated communities with low niche availability. At the same time, these invading mutants often cause extinctions of metabolically distant species. Our results suggest that even small amounts of evolution can produce distinct genetic signatures in natural microbial communities.

Predicting the First Steps of Evolution in Randomly Assembled Communities

Microbial communities can self-assemble into highly diverse states with predictable statistical properties. However, these initial states can be disrupted by rapid evolution of the resident strains. When a new mutation arises, it competes for resources with its parent strain and with the other species in the community. This interplay between ecology and evolution is difficult to capture with existing community assembly theory. Here, we introduce a mathematical framework for predicting the first steps of evolution in large randomly assembled communities that compete for substitutable resources. We show how the fitness effects of new mutations and the probability that they coexist with their parent depends on the size of the community, the saturation of its niches, and the metabolic overlap between its members. We find that successful mutations are often able to coexist with their parent strains, even in saturated communities with low niche availability. At the same time, these invading mutants often cause extinctions of metabolically distant species. Our results suggest that even small amounts of evolution can produce distinct genetic signatures in natural microbial communities.

Draft genome of Chloroflexus sp. MS-CIW-1, of the Chloroflexus sp. MS-G group from Mushroom Spring, Yellowstone National Park

Chloroflexus sp. MS-CIW-1 was isolated from a phototrophic mat in Mushroom Spring, an alkaline hot spring in Yellowstone National Park, WY, USA. We report the draft genome of 4.8 Mb consisting of 6 contigs with 3755 protein-coding genes and a GC content of 54.45%.

Average Nucleotide Identity based Staphylococcus aureus strain grouping allows identification of strain-specific genes in the pangenome

Staphylococcus aureus causes both hospital and community acquired infections in humans worldwide. Due to the high incidence of infection S. aureus is also one of the most sampled and sequenced pathogens today, providing an outstanding resource to understand variation at the bacterial subspecies level. We processed and downsampled 83,383 public S. aureus Illumina whole genome shotgun sequences and 1,263 complete genomes to produce 7,954 representative substrains. Pairwise comparison of core gene Average Nucleotide Identity (ANI) revealed a natural boundary of 99.5% that could be used to define 145 distinct strains within the species. We found that intermediate frequency genes in the pangenome (present in 10-95% of genomes) could be divided into those closely linked to strain background ("strain-concentrated") and those highly variable within strains ("strain-diffuse"). Non-core genes had different patterns of chromosome location; notably, strain-diffuse associated with prophages, strain-concentrated with the vSaβ genome island and rare genes (<10% frequency) concentrated near the origin of replication. Antibiotic genes were enriched in the strain-diffuse class, while virulence genes were distributed between strain-diffuse, strain-concentrated, core and rare classes. This study shows how different patterns of gene movement help create strains as distinct subspecies entities and provide insight into the diverse histories of important S. aureus functions.

Microbe-cellulose hydrogels as a model system for particulate carbon degradation in soil aggregates

Particulate carbon (C) degradation in soils is a critical process in the global C cycle governing greenhouse gas fluxes and C storage. Millimeter-scale soil aggregates impose strong controls on particulate C degradation by inducing chemical gradients of e.g. oxygen, as well as limiting microbial mobility in pore structures. To date, experimental models of soil aggregates have incorporated porosity and chemical gradients but not particulate C. Here, we demonstrate a proof-of-concept encapsulating microbial cells and particulate C substrates in hydrogel matrices as a novel experimental model for soil aggregates. Ruminiclostridium cellulolyticum was co-encapsulated with cellulose in millimeter-scale polyethyleneglycol-dimethacrylate (PEGDMA) hydrogel beads. Microbial activity was delayed in hydrogel-encapsulated conditions, with cellulose degradation and fermentation activity being observed after 13 days of incubation. Unexpectedly, hydrogel encapsulation shifted product formation of R. cellulolyticum from an ethanol-lactate-acetate mixture to an acetate-dominated product profile. Fluorescence microscopy enabled simultaneous visualization of the PEGDMA matrix, cellulose particles, and individual cells in the matrix, demonstrating growth on cellulose particles during incubation. Together, these microbe-cellulose-PEGDMA hydrogels present a novel, reproducible experimental soil surrogate to connect single cells to process outcomes at the scale of soil aggregates and ecosystems.