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Additional file 5. a Table showing mutations in evolved strains. A representative strain is displayed per lineage. b Overall outgrowth statistics of the stated antibiotics from all the mice used in the project.

Additional file 6. a Primer sequences. b Bacterial strains.

Additional file 2. a Male mice were orally gavaged with 105 CFU of K. pneumoniae at day 0. Ampicillin was given from day 7 to day 21. CFU of K. pneumoniae in stool at day 0, 7, 14, and 21. N=14. The dotted line marks the limit of detection. b Mice were orally gavaged with 105 CFU of KPNIH1 K. pneumoniae at day 0. Ampicillin was given from day 7 to day 21. Levels of K. pneumoniae in stool at day 0, 7, 14, and 21 were determined by plating on antibiotic cocktail agar or qPCR using primers at blaKPC gene. N=6. c KPC-producing strains of K. pneumoniae, E. cloacae and E.coli occultly colonize the gut until robust outgrowth by ampicillin. Mice were orally gavaged with 105 CFU of each strain or PBS at day 0. Ampicillin was given from day 7 to day 21. Levels of Enterobacteriaceae in stool at the stated time-points. Measurement was done by qPCR using primers at blaKPC gene. N=4-9. d Levels of K. pneumoniae were also measured using primers that bind to a chromosomal gene at the Klebsiella capsular polysaccharide synthesis gene cluster. For (c), statistics was performed using Fisher���s exact test with Hommel correction comparing each strain to PBS control on each time-point. *p-value < 0.05, **p-value < 0.01, ***p-value < 0.001.

Additional file 4. a Percentage of reads with a Kraken2 taxonomic classification using standard RefSeq or GTDB databases. Error bars denote SEM. b Relative abundance of the only significant genus Akkermansia between susceptible and nonsusceptible microbiota. c Top 5 species that show a trend between susceptible and nonsusceptible microbiota. d Percentage of reads with an eggNOG functional annotation. For (a), p-value is calculated by a two-tailed t-test. For (b) and (c), p-value is calculated using the linear model in MaAsLin2 and adjusted by Benjamini-Hochberg. *p-value < 0.05, ***p-value < 0.001.

Additional file 3. a, b Volcano plots showing adjusted p-value versus fold change of relative abundances of taxa at (a) family level and (b) genus level between day 0 and day 7. c, d Relative abundances of (c) Erysipelotrichaceae and (d) component genus Dubosiella. Bars show mean abundance. N=64. For (a-d), p-value is calculated by paired Wilcoxon signed-rank test with Benjamini-Hochberg correction. ***p-value < 0.001.

Additional file 1. a Table showing minimum inhibitory concentration (MIC) of antibiotics on wild-type KPNIH1 derivative (MKP103), evolved strain (xylR-L4) and transposon strain (xylR-Tn1). ND, not determined. b Mice were orally gavaged with 105 CFU of K. pneumoniae at day 0. Antibiotic cocktail was given from day 7 to day 21. CFU of K. pneumoniae in the stated samples at day 21. N=6. c Table showing antibiotics used in study, their drug class, mechanisms of actions and target bacteria.

The aim of regenerative engineering is to restore complex tissues and biological systems through convergence in the fields of advanced biomaterials, stem cell science, and developmental biology. Hydrogels are one of the most attractive biomaterials for regenerative engineering, since they can be engineered into tissue mimetic 3D scaffolds to support cell growth due to their similarity to native extracellular matrix. Advanced nano- and micro-technologies have dramatically increased the ability to control properties and functionalities of hydrogel materials by facilitating biomimetic fabrication of more sophisticated compositions and architectures, thus extending our understanding of cell-matrix interactions at the nanoscale. With this perspective, this review discusses the most commonly used hydrogel materials and their fabrication strategies for regenerative engineering. We highlight the physical, chemical, and functional modulation of hydrogels to design and engineer biomimetic tissues based on recent achievements in nano- and micro-technologies. In addition, current hydrogel-based regenerative engineering strategies for treating multiple tissues, such as musculoskeletal, nervous and cardiac tissue, are also covered in this review. The interaction of multiple disciplines including materials science, cell biology, and chemistry, will further play an important role in the design of functional hydrogels for the regeneration of complex tissues.

Nanotechnology offers significant potential in regenerative medicine, specifically with the ability to mimic tissue architecture at the nanoscale. In this perspective, we highlight key achievements in the nanotechnology field for successfully mimicking the composition and structure of different tissues, and the development of bio-inspired nanotechnologies and functional nanomaterials to improve tissue regeneration. Numerous nanomaterials fabricated by electrospinning, nanolithography and self-assembly have been successfully applied to regenerate bone, cartilage, muscle, blood vessel, heart and bladder tissue. We also discuss nanotechnology-based regenerative medicine products in the clinic for tissue engineering applications, although so far most of them are focused on bone implants and fillers. We believe that recent advances in nanotechnologies will enable new applications for tissue regeneration in the near future.

Human skin is stably colonized by a distinct microbiota that functions together with epidermal cells to maintain a protective physical barrier. Staphylococcus , a prominent genus of the skin microbiota, participates in colonization resistance, tissue repair, and host immune regulation in strain specific manners. To unlock the potential of engineering skin microbial communities, we aim to fully characterize the functional diversity of this genus within the context of the skin environment. We conducted metagenome and pan-genome analyses of isolates obtained from distinct body sites of healthy volunteers, providing a detailed biogeographic depiction of staphylococcal species that colonize our skin. S. epidermidis , S. capitis, and S. hominis were the most abundant species present in all volunteers and were detected at all body sites. Pan-genome analysis of these three species revealed that the genus-core was dominated by central metabolism genes. Species-specific core genes were enriched in host colonization functions. The majority (~68%) of genes were detected only in a fraction of isolate genomes, underscoring the immense strain-specific gene diversity. Conspecific genomes grouped into phylogenetic clades, exhibiting body site preference. Each clade was enriched for distinct gene-sets that are potentially involved in site tropism. Finally, we conducted gene expression studies of select isolates showing variable growth phenotypes in skin-like medium. In vitro expression revealed extensive intra- and inter-species gene expression variation, substantially expanding the functional diversification within each species. Our study provides an important resource for future ecological and translational studies to examine the role of shared and strain-specific staphylococcal genes within the skin environment., Competing Interests: DECLARATION OF INTERESTS The authors declare no competing interests.