The effect of an educational animation on knowledge of testicular health and fertility of adolescents.

STUDY QUESTION: Does the provision of an educational animation, developed with young people, about testicular health and fertility impact the knowledge of these topics among adolescents? SUMMARY ANSWER: The development and provision of education on testicular health and fertility were welcomed by adolescents and associated with a significant increase in knowledge. WHAT IS KNOWN ALREADY: Young people may know less than they should about testicular health and male fertility topics. Lack of knowledge can have implications for health including late medical help-seeking for signs and symptoms of scrotal disorders, such as torsion, for which late presentation frequently results in testicular damage. STUDY DESIGN, SIZE, DURATION: A mixed methods experimental pre- and post-design was used with embedded qualitative data collection. High school students completed a pre-animation questionnaire, watched four animations on testicular health and fertility, and completed a post-animation questionnaire. Data were collected during Personal Social and Health Education lessons across a 2-week period. PARTICIPANTS/MATERIALS, SETTING, METHODS: Four animations on testicular health and fertility, informed by andrologists, academics, designers, boys, and young men, were developed. Eligible participants were boys and girls in the UK school years 8 and 9 (age 13-14 years). Participants completed a Time 1 (T1) survey (fertility knowledge, demographics) prior to watching the animations and a Time 2 (T2) survey (fertility knowledge, perceptions of the animations) immediately after the animations. Perceptions were rated on 10-point response scales (higher scores better). Participants additionally expressed in their own words positive and negative aspects of the animations. ANOVA was used to examine the effects of the animations using a 2 (time: T1, T2)×2 (gender: male, female) design on topic knowledge, perceived importance, usefulness, and style of the animations according to gender. Regression analysis examined the associations between gender, disability, class year, and knowledge at T2 while controlling for knowledge at T1. Qualitative data on perceptions of the animations were analyzed using inductive thematic analysis. MAIN RESULTS AND THE ROLE OF CHANCE: Results showed that the animations significantly increased testicular health and fertility-related knowledge from T1 (x̄=41.84 ± 24.72) to T2 (x̄=79.15, ±15.04). Boys had significantly higher levels of knowledge compared to girls at T1 (x̄=44.74, SD = 25.16 versus x̄=37.79 ± 23.49, respectively) and T2 (x̄=80.07, SD = 15.68 versus x̄=77.89 ± 14.30, respectively) but knowledge gain from T1 to T2 was not significantly different according to gender (P = 0.11) as shown by non-significant gender×time interaction. There were no significant gender differences in the perceived usefulness and importance of the animations or liking of the style of the animations, with both genders considering the animations as useful, important, and likable. Regression analysis showed only knowledge at T1 to be significantly associated with knowledge at T2. Qualitative data showed three main themes: accessibility of important and useful information; information engagement and help-seeking behaviour; and inclusivity of information. LIMITATIONS, REASONS FOR CAUTION: This was a pre- and post-study with a sample of young people from a selected educational institution without a control group. Only short-term effects of the animations were recorded. WIDER IMPLICATIONS OF THE FINDINGS: Adolescents are interested in and learn from the provision of engaging fertility-related information. Boys and men should be considered as being a relevant target population for fertility education, not just girls and women. STUDY FUNDING/COMPETING INTEREST(S): This research was carried out in partnership with the British Fertility Society, was financially supported by an Economic and Social Research Council Impact Acceleration Award (520792) and commercial sponsorship from iMediCare Ltd, Bayer AG, Merck Group, Cryos International given to the British Fertility Society, and a financial contribution from Orchid Cancer Appeal. The authors are fully responsible for the content of the animations and this manuscript, and the views and opinions described in the publication reflect solely those of the authors. J.B. reports a grant from Merck Serono Ltd outside the submitted work. C.H., G.G., A.D., E.B., U.G., M.L, B.W., and M.H. declare no conflict of interest. K.M. reports honoraria from Bayer and Merck. A.P. reports paid consultancy for Cryos International, Cytoswim Ltd, Exceed Health, and Merck Serono in the last 2 years, but all monies have been paid to the University of Sheffield. TRIAL REGISTRATION NUMBER: N/A.

Understanding adolescent girls' and young women's health-seeking for female genital cosmetic surgery: How can clinicians help their patients?

AIM: This study aimed to understand why adolescent girls and young women (AGYW) would seek consultation with a health professional about genital appearance concerns and/or request female genital cosmetic surgery (FGCS). The information derived from these participant interviews can inform clinical practice and help clinicians better navigate consultations with young women and girls requesting FGCS. METHODS: A qualitative exploratory study was conducted using in-depth, semi-structured interviews with AGYW (n = 11) in Victoria, Australia. Participants comprised 11 AGYW who sought consultation with a health professional when aged 13-19 years for genital appearance concerns and/or requests for FGCS. Key themes were identified using a thematic analysis approach. RESULTS: Of 11 participants, five had undergone FGCS between the ages of 13 and 23 years. Key reasons for seeking a consultation identified in the interviews included: ideas about what 'normal' genitals look like, experiences of sexual harassment and bullying, and concerns about genital appearance developing before sexual debut. CONCLUSIONS: It is important to understand why AGYW want to access these procedures, given the risks involved, and that FGCS is not recommended by paediatric specialist organisations. Understanding why AGYW seek consultation for FGCS can help inform clinical practice, and the views expressed by participants in this study can help clinicians who work in this area to better support their patients.

Ethical concerns in suicide research: thematic analysis of the views of human research ethics committees in Australia.

BACKGROUND: Suicide research aims to contribute to a better understanding of suicidal behaviour and its prevention. However, there are many ethical challenges in this research field, for example, regarding consent and potential risks to participants. While studies to-date have focused on the perspective of the researchers, this study aimed to investigate the views and experiences of members of Human Research Ethics Committees (HRECs) in dealing with suicide-related study applications. METHODS: This qualitative study entailed a thematic analysis using an inductive approach. We conducted semi-structured interviews with a purposive sample (N = 15) of HREC Chairs or their delegates from Australian research-intensive universities. The interview guide included questions regarding the ethical concerns and challenges in suicide-related research raised by HREC members, how they dealt with those challenges and what advice they could give to researchers. RESULTS: The analysis identified four main themes: (1) HREC members' experiences of reviewing suicide-related study applications, (2) HREC members' perceptions of suicide, suicide research, and study participants, (3) Complexity in HREC members' decision-making processes, and (4) HREC members' relationships with researchers. CONCLUSIONS: Reliance on ethical guidelines and dialogue with researchers are crucial in the assessment of suicide-related study applications. Both researchers and HREC members may benefit from guidance and resources on how to conduct ethically sound suicide-related studies. Developing working relationships will be likely to help HRECs to facilitate high quality, ethical suicide-related research and researchers to conduct such research.

Propionibacterium avidum: A Virulent Pathogen Causing Hip Periprosthetic Joint Infection.

Background: Propionibacteria are important members of the human skin microbiota, but are also opportunistic pathogens associated with periprosthetic joint infection (PJI). While the role of Propionibacterium acnes in PJI has been widely described, insight into the capacity of Propionibacterium avidum to cause PJI is limited. Methods: An unusual cluster of 4 hip PJIs caused by P. avidum in one orthopedic center in 2015 prompted us to retrospectively identify and analyze clinical data related to previous P. avidum PJI cases (1997-2015). We also characterized the hemolytic and biofilm-producing capacity of our 4 clinical P. avidum strains isolated in 2015, and investigated their phylogenetic relationships by whole-genome sequencing. Results: We retrospectively identified 13 P. avidum PJIs, with the majority being hip-related infections (n = 11). Preoperative synovial fluid cultures were P. avidum positive in 63.6% of cases. Six of 12 patients (50%) with available case histories were treated with an exchange of the prosthesis. In all but 1 of the 6 patients treated with debridement-retention of the prosthesis, treatment failed, thus requiring a 2-stage revision. The isolated P. avidum strains showed a more pronounced hemolytic activity, but a similar biofilm-forming ability when compared to P. acnes. Whole-genome sequencing identified 2 phylogenetic clusters highly related to P. avidum PJI strains isolated in Sweden. Conclusions: We describe the largest series of P. avidum PJI predominantly located in the hip. Phylogenetic similarity of our P. avidum strains to PJI strains isolated elsewhere suggests that these invasive lineages may be common.

Shaping of cutaneous function by encounters with commensals.

The skin is the largest organ in the human body and provides the first line of defence against environmental attack and pathogen invasion. It harbor multiple commensal microbial communities at different body sites, which play important roles in sensing the environment, protecting against colonization and infection of pathogens, and guiding the host immune system in response to foreign invasions. The skin microbiome is largely variable between individuals and body sites, with several core commensal members commonly shared among individuals at the healthy state. These microbial commensals are essential to skin health and can potentially lead to disease when their abundances and activities change due to alterations in the environment or in the host. While recent advances in sequencing technologies have enabled a large number of studies to characterize the taxonomic composition of the skin microbiome at various body sites and under different physiological conditions, we have limited understanding of the microbiome composition and dynamics at the strain level, which is highly important to many microbe-related diseases. Functional studies of the skin microbial communities and the interactions among community members and with the host are currently scant, warranting future investigations. In this review, we summarize the recent findings on the skin microbiome, highlighting the roles of the major commensals, including bacteria, fungi and bacteriophages, in modulating skin functions in health and disease. Functional studies of the skin microbiota at the metatranscriptomic and proteomic levels are also included to illustrate the interactions between the microbiota and the host skin.

Emendation of Propionibacterium acnes subsp. acnes (Deiko et al. 2015) and proposal of Propionibacterium acnes type II as Propionibacterium acnes subsp. defendens subsp. nov.

Recently, it has been proposed that strains of Propionibacterium acnes from the type III genetic division should be classified as P. acnessubsp. elongatum subsp. nov., with strains from the type I and II divisions collectively classified as P. acnessubsp. acnes subsp. nov. Under such a taxonomic re-appraisal, we believe that types I and II should also have their own separate rank of subspecies. In support of this, we describe a polyphasic taxonomic study based on the analysis of publicly available multilocus and whole-genome sequence datasets, alongside a systematic review of previously published phylogenetic, genomic, phenotypic and clinical data. Strains of types I and II form highly distinct clades on the basis of multilocus sequence analysis (MLSA) and whole-genome phylogenetic reconstructions. In silico or digital DNA-DNA similarity values also fall within the 70-80 % boundary recommended for bacterial subspecies. Furthermore, we see important differences in genome content, including the presence of an active CRISPR/Cas system in type II strains, but not type I, and evidence for increasing linkage equilibrium within the separate divisions. Key biochemical differences include positive test results for ß-haemolytic, neuraminidase and sorbitol fermentation activities with type I strains, but not type II. We now propose that type I strains should be classified as P. acnessubsp. acnes subsp. nov., and type II as P. acnessubsp. defendens subsp. nov. The type strain of P. acnessubsp. acnes subsp. nov. is NCTC 737T (=ATCC 6919T=JCM 6425T=DSM 1897T=CCUG 1794T), while the type strain of P. acnessubsp. defendens subsp. nov. is ATCC 11828 (=JCM 6473=CCUG 6369).

"We're checking them out": Indigenous and non-Indigenous research participants' accounts of deciding to be involved in research.

BACKGROUND: It is important for researchers to understand the motivations and decision-making processes of participants who take part in their research. This enables robust informed consent and promotes research that meets the needs and expectations of the community. It is particularly vital when working with Indigenous communities, where there is a history of exploitative research practices. In this paper, we examine the accounts of Australian Indigenous and non-Indigenous research participants in terms of how and why they agree to take part in research. METHODS: A qualitative research approach was employed to undertake individual interviews with 36 research participants in Victoria, Australia. Eight participants identified as Indigenous and 28 were non-Indigenous. Thematic analysis was used to interpret the data. RESULTS: There were stark differences between Indigenous and non-Indigenous research participants in terms of why and how they decided to participate in research. For Indigenous participants, taking part in research was primarily to benefit their communities rather than for personal interests. Indigenous participants often started from a position of caution, and showed a considered and deliberate process of decision making. In weighing up their decision to participate, some Indigenous participants clearly articulated what was valued in conducting research with Indigenous communities, for example, honesty, reciprocity, and respect; these values were explicitly used to assist their decision whether or not to participate. This was in contrast to non-Indigenous participants who took researchers' claims on face value, and for whom deciding to participate in research was relatively straightforward. The motivations to participate of non-Indigenous participants were due to personal interests, a desire to help others, or trust in the medical practitioner who recruited them for the research project. CONCLUSION: Understanding research participants' motivations about taking part in research is important. This is particularly relevant for Indigenous communities where there is a reported history of research abuse leading to mistrust. This understanding can lead to research practice that is more respectful and responsive to the needs of Indigenous communities and abides by the values of Indigenous communities. Moreover it can lead to more ethical and respectful research practice for all.

Multiplex touchdown PCR for rapid typing of the opportunistic pathogen Propionibacterium acnes.

The opportunistic human pathogen Propionibacterium acnes is composed of a number of distinct phylogroups, designated types IA1, IA2, IB, IC, II, and III, which vary in their production of putative virulence factors, their inflammatory potential, and their biochemical, aggregative, and morphological characteristics. Although multilocus sequence typing (MLST) currently represents the gold standard for unambiguous phylogroup classification and individual strain identification, it is a labor-intensive and time-consuming technique. As a consequence, we developed a multiplex touchdown PCR assay that in a single reaction can confirm the species identity and phylogeny of an isolate based on its pattern of reaction with six primer sets that target the 16S rRNA gene (all isolates), ATPase (types IA1, IA2, and IC), sodA (types IA2 and IB), atpD (type II), and recA (type III) housekeeping genes, as well as a Fic family toxin gene (type IC). When applied to 312 P. acnes isolates previously characterized by MLST and representing types IA1 (n=145), IA2 (n=20), IB (n=65), IC (n=7), II (n=45), and III (n=30), the multiplex displayed 100% sensitivity and 100% specificity for detecting isolates within each targeted phylogroup. No cross-reactivity with isolates from other bacterial species was observed. This multiplex assay will provide researchers with a rapid, high-throughput, and technically undemanding typing method for epidemiological and phylogenetic investigations. It will facilitate studies investigating the association of lineages with various infections and clinical conditions, and it will serve as a prescreening tool to maximize the number of genetically diverse isolates selected for downstream higher-resolution sequence-based analyses.

Draft genome sequence of an antibiotic-resistant Propionibacterium acnes strain, PRP-38, from the novel type IC cluster.

Propionibacterium acnes, a non-spore-forming, anaerobic gram-positive bacterium, is most notably recognized for its association with acne vulgaris (I. Kurokawa et al., Exp. Dermatol. 18:821-832, 2009). We now present the draft genome sequence of an antibiotic-resistant P. acnes strain, PRP-38, isolated from an acne patient in the United Kingdom and belonging to the novel type IC cluster.

Complete genome sequences of three Propionibacterium acnes isolates from the type IA(2) cluster.

Propionibacterium acnes is an anaerobic Gram-positive bacterium that has been linked to a wide range of opportunistic human infections and conditions, most notably acne vulgaris (I. Kurokawa et al., Exp. Dermatol. 18:821-832, 2009). We now present the whole-genome sequences of three P. acnes strains from the type IA(2) cluster which were recovered from ophthalmic infections (A. McDowell et al., Microbiology 157:1990-2003, 2011).

A novel multilocus sequence typing scheme for the opportunistic pathogen Propionibacterium acnes and characterization of type I cell surface-associated antigens.

We have developed a novel multilocus sequence typing (MLST) scheme and database (http://pubmlst.org/pacnes/) for Propionibacterium acnes based on the analysis of seven core housekeeping genes. The scheme, which was validated against previously described antibody, single locus and random amplification of polymorphic DNA typing methods, displayed excellent resolution and differentiated 123 isolates into 37 sequence types (STs). An overall clonal population structure was detected with six eBURST groups representing the major clades I, II and III, along with two singletons. Two highly successful and global clonal lineages, ST6 (type IA) and ST10 (type IB(1)), representing 64 % of this current MLST isolate collection were identified. The ST6 clone and closely related single locus variants, which comprise a large clonal complex CC6, dominated isolates from patients with acne, and were also significantly associated with ophthalmic infections. Our data therefore support an association between acne and P. acnes strains from the type IA cluster and highlight the role of a widely disseminated clonal genotype in this condition. Characterization of type I cell surface-associated antigens that are not detected in ST10 or strains of type II and III identified two dermatan-sulphate-binding proteins with putative phase/antigenic variation signatures. We propose that the expression of these proteins by type IA organisms contributes to their role in the pathophysiology of acne and helps explain the recurrent nature of the disease. The MLST scheme and database described in this study should provide a valuable platform for future epidemiological and evolutionary studies of P. acnes.

The GAL genetic switch: visualisation of the interacting proteins by split-EGFP bimolecular fluorescence complementation.

A split-EGFP bimolecular fluorescence complementation assay was used to visualise and locate three interacting pairs of proteins from the GAL genetic switch of the budding yeast, Saccharomyces cerevisiae. Both the Gal4p-Gal80p and Gal80p-Gal3p pairs were found to be located in the nucleus under inducing conditions. However, the Gal80p-Gal1p complex was located throughout the cell. These results support recent work establishing an initial interaction between Gal3p and Gal80p occurring in the nucleus. Labelling of all three protein pairs impaired the growth of the yeast strains and resulted in reduced galactokinase activity in cell extracts. The most likely cause of this impairment is decreased dissociation rates of the complexes, caused by the essentially irreversible reassembly of the EGFP fragments. This suggests that a fully functional GAL genetic switch requires dynamic interactions between the protein components. These results also highlight the need for caution in the interpretation of in vivo split-EGFP experiments.

Author Correction: The balance of metagenomic elements shapes the skin microbiome in acne and health.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

The subgingival microbiome associated with periodontitis in type 2 diabetes mellitus.

Type 2 diabetes mellitus (T2DM) is a systemic disease, predisposing patients to other inflammatory conditions including periodontitis. The subgingival microbiome, a key player in periodontitis pathogenesis, is not well characterized in T2DM population. To better understand whether the subgingival microbiome is different between T2DM and systemically healthy, nondiabetic (ND) subjects, we performed a longitudinal analysis of the subgingival microbiome in T2DM patients (n = 15) compared with ND subjects (n = 16). Using metagenomic shotgun sequencing, we investigated the microbiome in the healthy periodontal state, periodontitis state, and resolved state after treatment. We found that in the periodontitis state, the shift in the subgingival microbiome from the healthy state was less prominent in T2DM compared with ND subjects, yet the clinical signs of disease were similar for both. Furthermore, we revealed highly correlated presence of pathogenic species in relative abundance not only in the periodontitis state, but also in the healthy state in T2DM, suggesting an elevated risk of progression to periodontitis in this cohort. We further investigated the functional potentials of the subgingival microbiome and identified a set of microbial marker genes associated with the clinical states. These genes were significantly enriched in 21 pathways, some of which are associated with periodontitis and some potentially link T2DM and periodontitis. This study identified the longitudinal changes of the subgingival microbiome associated with periodontitis in T2DM and suggests that T2DM patients are more susceptible to shifts in the subgingival microbiome toward dysbiosis, potentially due to impaired host metabolic and immune regulation.

Porphyrin Production and Regulation in Cutaneous Propionibacteria.

Porphyrins are intermediate metabolites in the biosynthesis of vital molecules, including heme, cobalamin, and chlorophyll. Bacterial porphyrins are known to be proinflammatory, with high levels linked to inflammatory skin diseases. Propionibacterium species are dominant skin commensals and play essential roles in defending against pathogens and in triggering an inflammatory response. To better understand how the inflammatory potential of the skin microbiome may vary depending on its propionibacterial composition, we compared the production levels of porphyrins among Propionibacterium acnes, Propionibacterium granulosum, Propionibacterium avidum, and Propionibacterium humerusii strains. We found that porphyrin production varied among these species, with P. acnes type I strains producing significantly larger amounts of porphyrins than P. acnes type II and III strains and other Propionibacterium species. P. acnes strains that are highly associated with the common skin condition acne vulgaris responded to vitamin B12 supplementation with significantly higher porphyrin production. In contrast, vitamin B12 supplementation had no effect on the porphyrin production of health-associated P. acnes strains and other propionibacteria. We observed low-level porphyrin production in most Propionibacterium strains harboring the deoR repressor gene, with the exception of P. acnes strains belonging to type I clades IB-3 and IC. Our findings shed light on the proinflammatory potential of distinct phylogenetic lineages of P. acnes as well as other resident skin propionibacteria. We demonstrate that the overall species and strain composition is important in determining the metabolic output of the skin microbiome in health and disease.IMPORTANCE Porphyrins are a group of metabolites essential to the biosynthesis of heme, cobalamin, and chlorophyll in living organisms. Bacterial porphyrins can be proinflammatory, with high levels linked to human inflammatory diseases, including the common skin condition acne vulgaris. Propionibacteria are among the most abundant skin bacteria. Variations in propionibacteria composition on the skin may lead to different porphyrin levels and inflammatory potentials. This study characterized porphyrin production in all lineages of Propionibacterium acnes, the most dominant skin Propionibacterium, and other resident skin propionibacteria, including P. granulosum, P. avidum, and P. humerusii We revealed that P. acnes type I strains produced significantly more porphyrins than did type II and III strains and other Propionibacterium species. The findings from this study shed light on the proinflammatory potential of the skin microbiome and can be used to guide the development of effective acne treatments by modulating the skin microbiome and its metabolic activities.

Understanding barriers, enablers, and long-term adherence to a health behavior intervention in people with multiple sclerosis.

Background: The optimal management strategy for multiple sclerosis (MS), and many other chronic diseases, likely involves health behavior modification. Multimodal behavioral interventions may be most effective, but little is known about long-term adherence in people with MS.Methods: This qualitative study assessed barriers and enablers to long-term adherence by people with MS who self-selected for a 5-day health behavior intervention 3-5 years prior. Thirteen women and five men participated in semi-structured phone interviews, which were transcribed and thematically analyzed.Results: The experience was described as useful for information gathering, decision making, and practical strategies regarding health behaviors. The majority still followed supplementation and dietary recommendations most of the time, although consuming non-recommended food while eating out was common. Support at home, ability and enjoyment in food preparation, and ability to resist unhealthy foods were both barriers and enablers. Adherence to "time-consuming" exercise and meditation recommendations were less common and episodic. Many reported competing interests on time from work and family; and barriers including injuries and symptoms, weather, financial or geographical barriers, and lack of person-centred support and motivation. Increased fitness and mobility, weight loss, and a sense of accomplishment and control were advantages and motivators. Practical and attitudinal strategies employed included planning, tailoring activities to ability and preference, and self-monitoring.Conclusion: While most people attempted to engage with all components of the intervention initially, only some still engaged with all components, and none to the recommended levels. These data can inform future quantitative studies and health behavior interventions.Implications for rehabilitationA multimodal group lifestyle intervention may be useful to assist people with multiple sclerosis in information gathering, decision making, attitudinal changes, and practical strategies regarding health behaviors; as well as providing a sense of hope for the future and control over wellbeing.While participants are unlikely to engage with all components of a multimodal intervention to the recommended level, they are likely to make improvements to one or more health behaviors.Experiential learning, including going through recipes and ingredient lists, and practicing meditation and physical exercises, is helpful to instigate behavior change.The initiation and maintenance of behavior change was assisted by support from family, friends, and health practitioners; and practical strategies employed by participants, including planning, self-monitoring, and tailoring activities to ability and preference.

Cervical-Vaginal Microbiome and Associated Cytokine Profiles in a Prospective Study of HPV 16 Acquisition, Persistence, and Clearance.

Persistent human papillomavirus (HPV) infections is necessary for the development of cervical cancers. Consequently, understanding the biologic mechanisms resulting in clearance is key in cancer prevention. Similar to other mucosal sites, it is expected that the local microbiome plays a significant role in shaping the immune response responsible for HPV clearance. Using cervical wash repository samples from a prospective study of HPV in women, this study investigates the microbiome and its associated inflammatory milieu during HPV 16 pre-acquisition, persistence and clearance states. For comparison, samples from women with no history of HPV ever during the study period were selected. We showed that 9 of 13 inflammatory cytokines were found to be significantly increased in the immediate post-clearance visit compared to the pre-acquisition or infection visits. Gardnerella vaginalis was associated with higher levels of inflammatory cytokines. Women with no history of HPV infection had similar cytokine profiles as those with HPV 16 post-clearance. This in vivo study documented an immune response shortly after HPV 16 clearance. G. vaginalis appeared to be involved in shaping this immune response. The appearance of G. vaginalis may have resulted from a shift from anti-microbial to anti-viral immune response with loss of bacterial control. The similar high levels of cytokines seen in women with no history of HPV suggest that a certain level of inflammatory surveillance is required to maintain an HPV negative state. This data may inform therapies such as probiotics or pro-inflammatory agents for treatment of persistent HPV.

MG-MLST: Characterizing the Microbiome at the Strain Level in Metagenomic Data.

The microbiome plays an important role in human physiology. The composition of the human microbiome has been described at the phylum, class, genus, and species levels, however, it is largely unknown at the strain level. The importance of strain-level differences in microbial communities has been increasingly recognized in understanding disease associations. Current methods for identifying strain populations often require deep metagenomic sequencing and a comprehensive set of reference genomes. In this study, we developed a method, metagenomic multi-locus sequence typing (MG-MLST), to determine strain-level composition in a microbial community by combining high-throughput sequencing with multi-locus sequence typing (MLST). We used a commensal bacterium, Propionibacterium acnes, as an example to test the ability of MG-MLST in identifying the strain composition. Using simulated communities, MG-MLST accurately predicted the strain populations in all samples. We further validated the method using MLST gene amplicon libraries and metagenomic shotgun sequencing data of clinical skin samples. MG-MLST yielded consistent results of the strain composition to those obtained from nearly full-length 16S rRNA clone libraries and metagenomic shotgun sequencing analysis. When comparing strain-level differences between acne and healthy skin microbiomes, we demonstrated that strains of RT2/6 were highly associated with healthy skin, consistent with previous findings. In summary, MG-MLST provides a quantitative analysis of the strain populations in the microbiome with diversity and richness. It can be applied to microbiome studies to reveal strain-level differences between groups, which are critical in many microorganism-related diseases.

Propionibacterium acnes and Acne Vulgaris: New Insights from the Integration of Population Genetic, Multi-Omic, Biochemical and Host-Microbe Studies.

The anaerobic bacterium Propionibacterium acnes is believed to play an important role in the pathophysiology of the common skin disease acne vulgaris. Over the last 10 years our understanding of the taxonomic and intraspecies diversity of this bacterium has increased tremendously, and with it the realisation that particular strains are associated with skin health while others appear related to disease. This extensive review will cover our current knowledge regarding the association of P. acnes phylogroups, clonal complexes and sequence types with acne vulgaris based on multilocus sequence typing of isolates, and direct ribotyping of the P. acnes strain population in skin microbiome samples based on 16S rDNA metagenomic data. We will also consider how multi-omic and biochemical studies have facilitated our understanding of P. acnes pathogenicity and interactions with the host, thus providing insights into why certain lineages appear to have a heightened capacity to contribute to acne vulgaris development, while others are positively associated with skin health. We conclude with a discussion of new therapeutic strategies that are currently under investigation for acne vulgaris, including vaccination, and consider the potential of these treatments to also perturb beneficial lineages of P. acnes on the skin.