Harmonization of clinical practice guidelines for primary prevention and screening: actionable recommendations and resources for primary care.

BACKGROUND: Clinical practice guidelines (CPGs) synthesize high-quality information to support evidence-based clinical practice. In primary care, numerous CPGs must be integrated to address the needs of patients with multiple risks and conditions. The BETTER program aims to improve prevention and screening for cancer and chronic disease in primary care by synthesizing CPGs into integrated, actionable recommendations. We describe the process used to harmonize high-quality cancer and chronic disease prevention and screening (CCDPS) CPGs to update the BETTER program. METHODS: A review of CPG databases, repositories, and grey literature was conducted to identify international and Canadian (national and provincial) CPGs for CCDPS in adults 40-69 years of age across 19 topic areas: cancers, cardiovascular disease, chronic obstructive pulmonary disease, diabetes, hepatitis C, obesity, osteoporosis, depression, and associated risk factors (i.e., diet, physical activity, alcohol, cannabis, drug, tobacco, and vaping/e-cigarette use). CPGs published in English between 2016 and 2021, applicable to adults, and containing CCDPS recommendations were included. Guideline quality was assessed using the Appraisal of Guidelines for Research and Evaluation (AGREE) II tool and a three-step process involving patients, health policy, content experts, primary care providers, and researchers was used to identify and synthesize recommendations. RESULTS: We identified 51 international and Canadian CPGs and 22 guidelines developed by provincial organizations that provided relevant CCDPS recommendations. Clinical recommendations were extracted and reviewed for inclusion using the following criteria: 1) pertinence to primary prevention and screening, 2) relevance to adults ages 40-69, and 3) applicability to diverse primary care settings. Recommendations were synthesized and integrated into the BETTER toolkit alongside resources to support shared decision-making and care paths for the BETTER program. CONCLUSIONS: Comprehensive care requires the ability to address a person's overall health. An approach to identify high-quality clinical guidance to comprehensively address CCDPS is described. The process used to synthesize and harmonize implementable clinical recommendations may be useful to others wanting to integrate evidence across broad content areas to provide comprehensive care. The BETTER toolkit provides resources that clearly and succinctly present a breadth of clinical evidence that providers can use to assist with implementing CCDPS guidance in primary care.

Diagnosis and management of pyruvate kinase deficiency: international expert guidelines.

Pyruvate kinase (PK) deficiency is the most common cause of chronic congenital non-spherocytic haemolytic anaemia worldwide, with an estimated prevalence of one in 100 000 to one in 300 000 people. PK deficiency results in chronic haemolytic anaemia, with wide ranging and serious consequences affecting health, quality of life, and mortality. The goal of the International Guidelines for the Diagnosis and Management of Pyruvate Kinase Deficiency was to develop evidence-based guidelines for the clinical care of patients with PK deficiency. These clinical guidelines were developed by use of GRADE methodology and the AGREE II framework. Experts were invited after consideration of area of expertise, scholarly contributions in PK deficiency, and country of practice for global representation. The expert panel included 29 expert physicians (including adult and paediatric haematologists and other subspecialists), geneticists, laboratory specialists, nurses, a guidelines methodologist, patients with PK deficiency, and caregivers from ten countries. Five key topic areas were identified, the panel prioritised key questions, and a systematic literature search was done to generate evidence summaries that were used in the development of draft recommendations. The expert panel then met in person to finalise and vote on recommendations according to a structured consensus procedure. Agreement of greater than or equal to 67% among the expert panel was required for inclusion of a recommendation in the final guideline. The expert panel agreed on 31 total recommendations across five key topics: diagnosis and genetics, monitoring and management of chronic complications, standard management of anaemia, targeted and advanced therapies, and special populations. These new guidelines should facilitate best practices and evidence-based PK deficiency care into clinical practice.

Guidelines and quantitative standards for improved cetacean taxonomy using full mitochondrial genomes.

In many organisms, especially those of conservation concern, traditional lines of evidence for taxonomic delineation, such as morphological data, are often difficult to obtain. In these cases, genetic data are often the only source of information available for taxonomic studies. In particular, population surveys of mitochondrial genomes offer increased resolution and precision in support of taxonomic decisions relative to conventional use of the control region or other gene fragments of the mitochondrial genome. To improve quantitative guidelines for taxonomic decisions in cetaceans, we build on a previous effort targeting the control region and evaluate, for whole mitogenome sequences, a suite of divergence and diagnosability estimates for pairs of recognized cetacean populations, subspecies, and species. From this overview, we recommend new guidelines based on complete mitogenomes, combined with other types of evidence for isolation and divergence, which will improve resolution for taxonomic decisions, especially in the face of small sample sizes or low levels of genetic diversity. We further use simulated data to assist interpretations of divergence in the context of varying forms of historical demography, culture, and ecology.

"Type D" killer whale genomes reveal long-term small population size and low genetic diversity.

Genome sequences can reveal the extent of inbreeding in small populations. Here, we present the first genomic characterization of type D killer whales, a distinctive eco/morphotype with a circumpolar, subantarctic distribution. Effective population size is the lowest estimated from any killer whale genome and indicates a severe population bottleneck. Consequently, type D genomes show among the highest level of inbreeding reported for any mammalian species (FROH ≥ 0.65). Detected recombination cross-over events of different haplotypes are up to an order of magnitude rarer than in other killer whale genomes studied to date. Comparison of genomic data from a museum specimen of a type D killer whale that stranded in New Zealand in 1955, with 3 modern genomes from the Cape Horn area, reveals high covariance and identity-by-state of alleles, suggesting these genomic characteristics and demographic history are shared among geographically dispersed social groups within this morphotype. Limitations to the insights gained in this study stem from the nonindependence of the 3 closely related modern genomes, the recent coalescence time of most variation within the genomes, and the nonequilibrium population history which violates the assumptions of many model-based methods. Long-range linkage disequilibrium and extensive runs of homozygosity found in type D genomes provide the potential basis for both the distinctive morphology, and the coupling of genetic barriers to gene flow with other killer whale populations.

Investigating demographic differences in patients' decisions to consent to COVID-19 research.

OBJECTIVE: COVID-19 disease severely impacted pregnant persons, resulting in a significant increase in poor maternal health outcomes, with a disproportionate impact on minority populations and individuals with low socioeconomic status. We sought to determine demographic differences between birthing parents with SARS-CoV-2 infections who consented to research study participation versus those who declined. By analyzing demographic differences, we are able to ensure the generalizability of study outcomes and to aid in future prospective research design, with the ultimate goal of recognizing and ameliorating research disparities. METHODS: We conducted a secondary analysis to investigate demographic differences in patients who consented to versus declined study participation, in an effort to confirm the external validity of the study results and ensure minority populations most affected by SARS-CoV-2 infection were accurately represented. An IRB waiver was obtained to conduct retrospective chart review for demographic data collection of all patients approached for the COVID-19 Analysis on Perinatal Specimens Related to ExpoSure (CARES) research study. Pregnant patients with SARS-CoV-2 infection were identified at a single hospital center and approached either in person or via phone, with a translator if primary language listed as non-English. Demographic variables including race, ethnicity, primary language, and insurance type were obtained from the electronic medical record and analyzed via Chi-square to determine significant differences between individuals who consented to participation and those who declined participation. RESULTS: One hundred and fifty-eight pregnant patients with SARS-CoV-2 infection were approached for CARES study participation. Eighty-nine patients consented to study participation, while 69 declined study participation. A retrospective chart review was conducted on all 158 patients. Patients who identified as Black race or non-White race were more likely to decline participation (23.2%, p = .031, 68.1%, p = .026), compared to patients who identified as White (31.9%) (Table 1). Patients with public insurance were also more likely to decline study participation (72.5%, p = .049) compared to those with private insurance (27.5%). There was no significant difference between primary language spoken or ethnicity in patients who participated or declined. There was no difference in study participation between patients who identified as Asian race or Other race, compared to patients who identified as White race. CONCLUSIONS: We found significant differences in race and insurance type between pregnant patients with SARS-CoV-2 infection who consented versus declined research study participation. Our study showed that patients who identify as Black race or have public insurance are less likely to consent to research study participation. However, when demographics of consented patients are compared to county, state, and national demographics of female patients age 18-49 with confirmed SARS-CoV-2 infection obtained from a dataset collected by the Center for Disease Control and Prevention (CDC), there was no significant difference between race representation of patients who consented to study participation. This suggests that though the external validity of the CARES study is confirmed, more efforts need to be made to address racial and socioeconomic disparities in research participation.

Effectiveness of a "Suppression Bundle" to improve HIV virologic suppression in an outpatient infectious disease clinic: a pilot implementation study.

Despite effectiveness and accessibility of combined anti-retroviral therapy (cART), only 85% of people living with HIV (PLHIV) in the United States are virologically suppressed. Improving suppression is complex. Our objective was to consider unique factors in PLHIV with non-suppressed viral loads in clinic and improve the percentage of suppressed patients by implementing a "Suppression Bundle" consisting of three to five bundled interventions with the goal of improved suppression. Prior to the study, there were 567 HIV-positive patients receiving care in clinic. Of those, 89 had a measurable viral load (>40 copies/mL). In this pilot pre-post implementation, we focused on the 89 non-suppressed patients to (1) determine feasibility of implementing bundles and (2) increase the number of patients with suppressed viral loads pre- to post-intervention. Of non-suppressed patients, 65 were active in care immediately pre-intervention and participated in the pilot. At the completion of the 9-month intervention, 46 had viral loads <40 copies/mL, demonstrating substantial improvement with 70.1% of the previously non-suppressed patients achieving suppression. By considering unique patient factors, an individualized Suppression Bundle is acceptable, feasible, and may increase virally suppressed patients in an outpatient clinic. Next steps include determining whether suppression bundles can be implemented in differing practices.

Implementation of Effective Smoking Cessation Strategies for People Living with HIV: A Pilot Implementation Study.

Introduction: Use of tobacco products carries significant long-term health risks, and rates of smoking in persons living with HIV are as high as two to three times that of the general population. This study aimed to increase assessment of readiness to quit smoking and provide cessation counseling to patients receiving HIV care through an infectious disease clinic. Methods: This study was a pilot implementation in a single-center teaching hospital. In total, 603 active patients with HIV were followed in clinic at the time of the study start; of these, 79 were active tobacco smokers (13%) and eligible for the intervention. Providers were educated on recommendations for tobacco smoking cessation counseling, intervention strategies, and options for treatment. Patients who smoked tobacco were assessed for readiness to quit. Cessation counseling and tobacco cessation mediations or nicotine replacement were provided at the discretion of the patient and physician based on visit discussions. Primary outcome measures were increase in assessment of readiness to quit and in providing cessation counseling. Secondary measures included tabulation of the number of patients provided with a tobacco smoking cessation treatment and those with a successful quit episode. Results: There was a moderate increase in patients assessed for readiness to quit and who received tobacco smoking cessation counseling and treatment medications during the pilot. In total, 11 patients (8.7%) reported quitting smoking for at least two weeks. Conclusions: Additional work on streamlined mechanisms to identify tobacco use and provide efficient and effective tobacco smoking cessation counseling are needed in this high-risk population.

The critically endangered vaquita is not doomed to extinction by inbreeding depression.

In cases of severe wildlife population decline, a key question is whether recovery efforts will be impeded by genetic factors, such as inbreeding depression. Decades of excess mortality from gillnet fishing have driven Mexico's vaquita porpoise (Phocoena sinus) to ~10 remaining individuals. We analyzed whole-genome sequences from 20 vaquitas and integrated genomic and demographic information into stochastic, individual-based simulations to quantify the species' recovery potential. Our analysis suggests that the vaquita's historical rarity has resulted in a low burden of segregating deleterious variation, reducing the risk of inbreeding depression. Similarly, genome-informed simulations suggest that the vaquita can recover if bycatch mortality is immediately halted. This study provides hope for vaquitas and other naturally rare endangered species and highlights the utility of genomics in predicting extinction risk.

Runs of homozygosity in killer whale genomes provide a global record of demographic histories.

Runs of homozygosity (ROH) occur when offspring inherit haplotypes that are identical by descent from each parent. Length distributions of ROH are informative about population history; specifically, the probability of inbreeding mediated by mating system and/or population demography. Here, we investigated whether variation in killer whale (Orcinus orca) demographic history is reflected in genome-wide heterozygosity and ROH length distributions, using a global data set of 26 genomes representative of geographic and ecotypic variation in this species, and two F1 admixed individuals with Pacific-Atlantic parentage. We first reconstructed demographic history for each population as changes in effective population size through time using the pairwise sequential Markovian coalescent (PSMC) method. We found a subset of populations declined in effective population size during the Late Pleistocene, while others had more stable demography. Genomes inferred to have undergone ancestral declines in effective population size, were autozygous at hundreds of short ROH (<1 Mb), reflecting high background relatedness due to coalescence of haplotypes deep within the pedigree. In contrast, longer and therefore younger ROH (>1.5 Mb) were found in low latitude populations, and populations of known conservation concern. These include a Scottish killer whale, for which 37.8% of the autosomes were comprised of ROH >1.5 Mb in length. The fate of this population, in which only two adult males have been sighted in the past five years, and zero fecundity over the last two decades, may be inextricably linked to its demographic history and consequential inbreeding depression.

Population structure in a continuously distributed coastal marine species, the harbor porpoise, based on microhaplotypes derived from poor-quality samples.

Harbor porpoise in the North Pacific are found in coastal waters from southern California to Japan, but population structure is poorly known outside of a few local areas. We used multiplexed amplicon sequencing of 292 loci and genotyped clusters of single nucleotide polymoirphisms as microhaplotypes (N = 271 samples) in addition to mitochondrial (mtDNA) sequence data (N = 413 samples) to examine the genetic structure from samples collected along the Pacific coast and inland waterways from California to southern British Columbia. We confirmed an overall pattern of strong isolation-by-distance, suggesting that individual dispersal is restricted. We also found evidence of regions where genetic differences are larger than expected based on geographical distance alone, implying current or historical barriers to gene flow. In particular, the southernmost population in California is genetically distinct (FST  = 0.02 [microhaplotypes]; 0.31 [mtDNA]), with both reduced genetic variability and high frequency of an otherwise rare mtDNA haplotype. At the northern end of our study range, we found significant genetic differentiation of samples from the Strait of Georgia, previously identified as a potential biogeographical boundary or secondary contact zone between harbor porpoise populations. Association of microhaplotypes with remotely sensed environmental variables indicated potential local adaptation, especially at the southern end of the species' range. These results inform conservation and management for this nearshore species, illustrate the value of genomic methods for detecting patterns of genetic structure within a continuously distributed marine species, and highlight the power of microhaplotype genotyping for detecting genetic structure in harbor porpoises despite reliance on poor-quality samples.

Mitochondrial genomics reveals the evolutionary history of the porpoises (Phocoenidae) across the speciation continuum.

Historical variation in food resources is expected to be a major driver of cetacean evolution, especially for the smallest species like porpoises. Despite major conservation issues among porpoise species (e.g., vaquita and finless), their evolutionary history remains understudied. Here, we reconstructed their evolutionary history across the speciation continuum. Phylogenetic analyses of 63 mitochondrial genomes suggest that porpoises radiated during the deep environmental changes of the Pliocene. However, all intra-specific subdivisions were shaped during the Quaternary glaciations. We observed analogous evolutionary patterns in both hemispheres associated with convergent evolution to coastal versus oceanic environments. This suggests that similar mechanisms are driving species diversification in northern (harbor and Dall's) and southern species (spectacled and Burmeister's). In contrast to previous studies, spectacled and Burmeister's porpoises shared a more recent common ancestor than with the vaquita that diverged from southern species during the Pliocene. The low genetic diversity observed in the vaquita carried signatures of a very low population size since the last 5,000 years. Cryptic lineages within Dall's, spectacled and Pacific harbor porpoises suggest a richer evolutionary history than previously suspected. These results provide a new perspective on the mechanisms driving diversification in porpoises and an evolutionary framework for their conservation.

Second International Guidelines for the Diagnosis and Management of Hereditary Hemorrhagic Telangiectasia.

DESCRIPTION: Hereditary hemorrhagic telangiectasia (HHT) is an autosomal dominant disease with an estimated prevalence of 1 in 5000 that is characterized by the presence of vascular malformations (VMs). These result in chronic bleeding, acute hemorrhage, and complications from shunting through VMs. The goal of the Second International HHT Guidelines process was to develop evidence-based consensus guidelines for the management and prevention of HHT-related symptoms and complications. METHODS: The guidelines were developed using the AGREE II (Appraisal of Guidelines for Research and Evaluation II) framework and GRADE (Grading of Recommendations Assessment, Development and Evaluation) methodology. The guidelines expert panel included expert physicians (clinical and genetic) in HHT from 15 countries, guidelines methodologists, health care workers, health care administrators, patient advocacy representatives, and persons with HHT. During the preconference process, the expert panel generated clinically relevant questions in 6 priority topic areas. A systematic literature search was done in June 2019, and articles meeting a priori criteria were included to generate evidence tables, which were used as the basis for recommendation development. The expert panel subsequently convened during a guidelines conference to conduct a structured consensus process, during which recommendations reaching at least 80% consensus were discussed and approved. RECOMMENDATIONS: The expert panel generated and approved 6 new recommendations for each of the following 6 priority topic areas: epistaxis, gastrointestinal bleeding, anemia and iron deficiency, liver VMs, pediatric care, and pregnancy and delivery (36 total). The recommendations highlight new evidence in existing topics from the first International HHT Guidelines and provide guidance in 3 new areas: anemia, pediatrics, and pregnancy and delivery. These recommendations should facilitate implementation of key components of HHT care into clinical practice.

Nobiletin affects circadian rhythms and oncogenic characteristics in a cell-dependent manner.

The natural product nobiletin is a small molecule, widely studied with regard to its therapeutic effects, including in cancer cell lines and tumors. Recently, nobiletin has also been shown to affect circadian rhythms via their enhancement, resulting in protection against metabolic syndrome. We hypothesized that nobiletin's anti-oncogenic effects, such as prevention of cell migration and formation of anchorage independent colonies, are correspondingly accompanied by modulation of circadian rhythms. Concurrently, we wished to determine whether the circadian and anti-oncogenic effects of nobiletin differed across cancer cell lines. In this study, we assessed nobiletin's circadian and therapeutic characteristics to ascertain whether these effects depend on cell line, which here also varied in terms of baseline circadian rhythmicity. Three cell culture models where nobiletin's effects on cell proliferation and migration have been studied previously were evaluated: U2OS (bone osteosarcoma), which possesses robust circadian rhythms; MCF7 (breast adenocarcinoma), which has weak circadian rhythms; and MDA-MB-231 (breast adenocarcinoma), which is arrhythmic. We found that circadian, migration, and proliferative effects following nobiletin treatment were subtle in the U2OS and MCF7 cells. On the other hand, changes were clear in MDA-MB-231s, where nobiletin rescued rhythmicity and substantially reduced oncogenic features, specifically two-dimensional cell motility and anchorage-independent growth. Based on these results and those previously described, we posit that the effects of nobiletin are indeed cell-type dependent, and that a positive correlation may exist between nobiletin's circadian and therapeutic effects.

Oncogenic and Circadian Effects of Small Molecules Directly and Indirectly Targeting the Core Circadian Clock.

Circadian rhythms are essential for controlling the cell cycle, cellular proliferation, and apoptosis, and hence are tightly linked to cell fate. Several recent studies have used small molecules to affect circadian oscillations; however, their concomitant cellular effects were not assessed, and they have not been compared under similar experimental conditions. In this work, we use five molecules, grouped into direct versus indirect effectors of the circadian clock, to modulate periods in a human osteosarcoma cell line (U2OS) and determine their influences on cellular behaviors, including motility and colony formation. Luciferase reporters, whose expression was driven via Bmal1- or Per2-promoters, were used to facilitate the visualization and quantitative analysis of circadian oscillations. We show that all molecules increase or decrease the circadian periods of Bmal1 and Per2 in a dose-dependent manner, but period length does not correlate with the extent of cell migration or proliferation. Nonetheless, molecules that affected circadian oscillations to a greater degree resulted in substantial influence on cellular behaviors (ie, motility and colony formation), which may also be attributable to noncircadian targets. Furthermore, we find that the ability and extent to which the molecules are able to affect oscillations is independent of whether they are direct or indirect modulators. Because of the numerous connections and feedback between the circadian clock and other pathways, it is important to consider the effects of both in assessing these and other compounds.

Chemical modulation of circadian rhythms and assessment of cellular behavior via indirubin and derivatives.

Circadian rhythms are critical regulators of many physiological and behavioral functions. The use and abilities of small molecules to affect oscillations have recently received significant attention. These manipulations can be reversible and tunable, and have been used to study various biological mechanisms and molecular properties. Here, we outline procedures for assessment of cellular circadian changes following treatment with small molecules, using luminescent reporters. We describe reporter generation, luminometry experiments, and data analysis. Protocols for studies of accompanying effects on cells, including motility, viability, and anchorage-independent proliferation assays are also presented. As examples, we use indirubin-3'-oxime and two derivatives, 5-iodo-indirubin-3'-oxime and 5-sulfonic acid-indirubin-3'-oxime. In this case study, we analyze effects of these compounds on Bmal1 and Per2 (positive and negative core circadian elements) oscillations and provide step-by-step protocols for data analysis, including removal of trends from raw data, period estimations, and statistical analysis. The reader is provided with detailed protocols, and guidance regarding selection of and alternative approaches.

Correction to: The International/Canadian Hereditary Angioedema Guideline.

[This corrects the article DOI: 10.1186/s13223-019-0376-8.].

The International/Canadian Hereditary Angioedema Guideline.

This is an update to the 2014 Canadian Hereditary Angioedema Guideline with an expanded scope to include the management of hereditary angioedema (HAE) patients worldwide. It is a collaboration of Canadian and international HAE experts and patient groups led by the Canadian Hereditary Angioedema Network. The objective of this guideline is to provide evidence-based recommendations, using the GRADE system, for the management of patients with HAE. This includes the treatment of attacks, short-term prophylaxis, long-term prophylaxis, and recommendations for self-administration, individualized therapy, quality of life, and comprehensive care. New to the 2019 version of this guideline are sections covering the diagnosis and recommended therapies for acute treatment in HAE patients with normal C1-INH, as well as sections on pregnant and paediatric patients, patient associations and an HAE registry. Hereditary angioedema results in random and often unpredictable attacks of painful swelling typically affecting the extremities, bowel mucosa, genitals, face and upper airway. Attacks are associated with significant functional impairment, decreased health-related quality of life, and mortality in the case of laryngeal attacks. Caring for patients with HAE can be challenging due to the complexity of this disease. The care of patients with HAE in Canada, as in many countries, continues to be neither optimal nor uniform. It lags behind some other countries where there are more organized models for HAE management, and greater availability of additional licensed therapeutic options. It is anticipated that providing this guideline to caregivers, policy makers, patients, and advocates will not only optimize the management of HAE, but also promote the importance of individualized care. The primary target users of this guideline are healthcare providers who are managing patients with HAE. Other healthcare providers who may use this guideline are emergency and intensive care physicians, primary care physicians, gastroenterologists, dentists, otolaryngologists, paediatricians, and gynaecologists who will encounter patients with HAE and need to be aware of this condition. Hospital administrators, insurers and policy makers may also find this guideline helpful.

Killer whale genomes reveal a complex history of recurrent admixture and vicariance.

Reconstruction of the demographic and evolutionary history of populations assuming a consensus tree-like relationship can mask more complex scenarios, which are prevalent in nature. An emerging genomic toolset, which has been most comprehensively harnessed in the reconstruction of human evolutionary history, enables molecular ecologists to elucidate complex population histories. Killer whales have limited extrinsic barriers to dispersal and have radiated globally, and are therefore a good candidate model for the application of such tools. Here, we analyse a global data set of killer whale genomes in a rare attempt to elucidate global population structure in a nonhuman species. We identify a pattern of genetic homogenisation at lower latitudes and the greatest differentiation at high latitudes, even between currently sympatric lineages. The processes underlying the major axis of structure include high drift at the edge of species' range, likely associated with founder effects and allelic surfing during postglacial range expansion. Divergence between Antarctic and non-Antarctic lineages is further driven by ancestry segments with up to four-fold older coalescence time than the genome-wide average; relicts of a previous vicariance during an earlier glacial cycle. Our study further underpins that episodic gene flow is ubiquitous in natural populations, and can occur across great distances and after substantial periods of isolation between populations. Thus, understanding the evolutionary history of a species requires comprehensive geographic sampling and genome-wide data to sample the variation in ancestry within individuals.

Host-derived population genomics data provides insights into bacterial and diatom composition of the killer whale skin.

Recent exploration into the interactions and relationship between hosts and their microbiota has revealed a connection between many aspects of the host's biology, health and associated micro-organisms. Whereas amplicon sequencing has traditionally been used to characterize the microbiome, the increasing number of published population genomics data sets offers an underexploited opportunity to study microbial profiles from the host shotgun sequencing data. Here, we use sequence data originally generated from killer whale Orcinus orca skin biopsies for population genomics, to characterize the skin microbiome and investigate how host social and geographical factors influence the microbial community composition. Having identified 845 microbial taxa from 2.4 million reads that did not map to the killer whale reference genome, we found that both ecotypic and geographical factors influence community composition of killer whale skin microbiomes. Furthermore, we uncovered key taxa that drive the microbiome community composition and showed that they are embedded in unique networks, one of which is tentatively linked to diatom presence and poor skin condition. Community composition differed between Antarctic killer whales with and without diatom coverage, suggesting that the previously reported episodic migrations of Antarctic killer whales to warmer waters associated with skin turnover may control the effects of potentially pathogenic bacteria such as Tenacibaculum dicentrarchi. Our work demonstrates the feasibility of microbiome studies from host shotgun sequencing data and highlights the importance of metagenomics in understanding the relationship between host and microbial ecology.