Draft genome sequence of Micrococcus luteus strain O'Kane implicates metabolic versatility and the potential to degrade polyhydroxybutyrates

Hanafy, Radwa A.; Couger, Matthew Brian; Baker, Kristina; Murphy, Chelsea L.; O'Kane, Shannon D.; Budd, Connie; French, Donald P.; Hoff, Wouter D.; Youssef, Noha H.

doi:10.1016/j.gdata.2016.08.006

Cited by 6 publications

(5 citation statements)

References 27 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The selection of these organisms followed practical considerations and with the intended later application of studying potential microbiome-mediated substance toxification in mind. Both species are biologically relevant (Chiller et al 2001 ; Wang et al 2019 ), have an established potential for xenobiotic metabolism (Egea et al 2017 ; Hanafy et al 2016 ; Sowada et al 2014 ; Viggor et al 2020 ) and have been isolated repeatedly from healthy volunteers at different sites (Khayyira et al 2020 ; Sowada et al 2014 ; Steglinska et al 2019 ; Wang et al 2019 ). Amongst the skin’s Micrococcaceae M. luteus is the predominant species (Chiller et al 2001 ).…”

Section: Introductionmentioning

confidence: 99%

Microbially competent 3D skin: a test system that reveals insight into host–microbe interactions and their potential toxicological impact

et al. 2020

View full text Add to dashboard Cite

The skin`s microbiome is predominantly commensalic, harbouring a metabolic potential far exceeding that of its host. While there is clear evidence that bacteria-dependent metabolism of pollutants modulates the toxicity for the host there is still a lack of models for investigating causality of microbiome-associated pathophysiology or toxicity. We now report on a biologically characterised microbial–skin tissue co-culture that allows studying microbe–host interactions for extended periods of time in situ. The system is based on a commercially available 3D skin model. In a proof-of-concept, this model was colonised with single and mixed cultures of two selected skin commensals. Two different methods were used to quantify the bacteria on the surface of the skin models. While Micrococcus luteus established a stable microbial–skin tissue co-culture, Pseudomonas oleovorans maintained slow continuous growth over the 8-day cultivation period. A detailed skin transcriptome analysis showed bacterial colonisation leading to up to 3318 significant changes. Additionally, FACS, ELISA and Western blot analyses were carried out to analyse secretion of cytokines and growth factors. Changes found in colonised skin varied depending on the bacterial species used and comprised immunomodulatory functions, such as secretion of IL-1α/β, Il-6, antimicrobial peptides and increased gene transcription of IL-10 and TLR2. The colonisation also influenced the secretion of growth factors such as VFGFA and FGF2. Notably, many of these changes have already previously been associated with the presence of skin commensals. Concomitantly, the model gained first insights on the microbiome’s influence on skin xenobiotic metabolism (i.e., CYP1A1, CYP1B1 and CYP2D6) and olfactory receptor expression. The system provides urgently needed experimental access for assessing the toxicological impact of microbiome-associated xenobiotic metabolism in situ.

show abstract

Section: Introductionmentioning

confidence: 99%

Microbially competent 3D skin: a test system that reveals insight into host–microbe interactions and their potential toxicological impact

et al. 2020

View full text Add to dashboard Cite

show abstract

“…Given this, Yang et al had further speculated that its primary adaptation is to mammalian skin, and that its occasional presence elsewhere might possibly arise from contamination by skin akes; and the transposable elements could have played a part in the contraction of the M. luteus genome [3]. Now genome sequences of more than 70 M. luteus strains have been published and/or are available at the NCBI GenBank database [34][35][36][37][38][39], providing rich resources for the study of the genetic diversity, evolutionary history, and the potential ecological differentiation of the species.…”

Section: Introductionmentioning

confidence: 99%

Comparative Genomics Reveals Broad Genetic Diversity, Extensive Recombination and Nascent Ecological Adaptation in Micrococcus luteus

Sun

Rong

et al. 2020

Preprint

View full text Add to dashboard Cite

Background: Micrococcus luteus is a group of actinobacteria that is widely used in biotechnology and is being thought as an emerging nosocomial pathogen. With one of the smallest genomes of free-living actinobacteria, it is found in a wide range of environments, but intraspecies genetic diversity and adaptation strategies to various environments remain unclear. Here, comparative genomics, phylogenomics, and genome-wide association studies (GWAS) were used to investigate the genomic diversity, evolutionary history, and the potential ecological differentiation of the species.Results: High-quality genomes of 66 M. luteus strains were downloaded from the NCBI GenBank database and core and pangenome analysis revealed a considerable intraspecies heterogeneity. Phylogenomic analysis, gene content comparison, and average nucleotide identity calculation consistently indicated that the species has diverged into three well-differentiated clades. Population structure analysis revealed four admixed ancestral subpopulations, with three of them corresponding to the three clades, respectively, and the fourth corresponding to an unknown ancestor or the fourth, yet unsampled, clade. Reconstruction of gene gain/loss events along the evolutionary history revealed both early events that contributed to the inter-clade divergence and recent events leading to the intra-clade diversity. We also found convincing evidence that recombination has played a key role of the evolutionary process of the species, with upto two-thirds of the core genes have been affected by recombination. Furthermore, distribution of mammal-associated strains (including pathogens) on the phylogenetic tree strongly suggested that the last common ancestor had a free-living lifestyle, and a few recently diverged lineages have developed a mammal-associated lifestyle separately. Consistently, genome-wide association studies revealed that mammal-associated strains from different lineages shared genes functionally relevant to the host-associated lifestyle, indicating a recent ecological adaption to the new host-associated habitats.Conclusions: These results revealed high intraspecies genomic diversity of M. luteus and highlighted that gene gain/loss events and extensive recombination events played key roles in the genome evolution. Our study also indicated that, as a free-living species, some lineages have recently developed or are developing a mammal-associated lifestyle. This study provides insights into the mechanisms that drive the genome evolution and adaption to various environments of a bacterial species.

show abstract

“…12,16,20,21,26,40,49 In one contamination, we also identified M. luteus, which belongs to the phylum Actinobacteria and is an obligate aerobe associated with soil, plants, and the human skin microbiome. 17 The characteristics of the contaminants do not directly allow reconstruction of the contamination routes, but they suggest that contamination occurred either via surfaces contaminated by contact with human skin (for example, hands) or unclean air or through the introduction of contaminated feed or bedding. We did not identify any anaerobes among contaminants, and no growth was ever detected under anaerobic conditions only, consistent with the assumption that contaminants presumably exist in viable form for extended periods with access to air, as might be expected for surface contaminations.…”

Section: Discussionmentioning

confidence: 99%

Evaluation of Peroxides and Chlorine Oxides as Disinfectants for Chemical Sterilization of Gnotobiotic Rodent Isolators

Moody

Miyamoto

Ang

et al. 2019

j am assoc lab anim sci

View full text Add to dashboard Cite

Gnotobiotic animal research has expanded markedly over the past decade. Although germ-free animals were first described more than 100 y ago, little evidence-based guidance is available on best operational procedures. A key aspect of gnotobiotic technology is the sterilization of animal enclosures, most commonly flexible vinyl film isolators. The objective of this study was to determine the most effective methods for chemical sterilization of gnotobiotic isolators and associated equipment. As test microbes, we used bacteria from 4 different accidental isolator contaminations that occurred in a gnotobiotic core facility. Identification by 16S ribotyping revealed facultative anaerobic firmicutes, including several Paenibacillus and Bacillus species, and obligate aerobic actinobacteria, namely Micrococcus luteus, among the contaminants. We selected 6 products commonly used for disinfecting hospital rooms, kitchens, and veterinary facilities to represent chlorine-oxideand peroxide-based disinfectants and tested the hypothesis that these 2 classes are equally effective. However, evaluation of bactericidal and sporicidal activity in liquid cultures revealed that chlorine oxide-based disinfectants were more effective than peroxide-based disinfectants. In both groups, various products effectively sterilized gnotobiotic isolators by fogging in field tests, although bactericidal concentrations were markedly higher than those in suspension cultures, and effectiveness was contact-time-dependent. In addition, in both groups, some disinfectants were excessively corrosive to ferrous metals and acrylic. These results demonstrate that no single disinfectant has all desirable properties and that the different characteristics of disinfectants must be balanced during their selection. However, chlorine oxide-based disinfectants were generally more effective and less corrosive than peroxide-based products.

show abstract

Draft genome sequence of Micrococcus luteus strain O'Kane implicates metabolic versatility and the potential to degrade polyhydroxybutyrates

Cited by 6 publications

References 27 publications

Microbially competent 3D skin: a test system that reveals insight into host–microbe interactions and their potential toxicological impact

Microbially competent 3D skin: a test system that reveals insight into host–microbe interactions and their potential toxicological impact

Comparative Genomics Reveals Broad Genetic Diversity, Extensive Recombination and Nascent Ecological Adaptation in Micrococcus luteus

Evaluation of Peroxides and Chlorine Oxides as Disinfectants for Chemical Sterilization of Gnotobiotic Rodent Isolators

Contact Info

Product

Resources

About