Migration and Residence Patterns of Salmonids in Puget Sound, Washington

Thesis (Ph.D.)--University of Washington, 2016-08

Long-term fish community response to a reach-scale stream restoration

At a global scale, aquatic ecosystems are being altered by human activities at a greater rate than at any other time in history. In recent years, grassroots efforts have generated interest in the restoration of degraded or destroyed aquatic habitats, especially small wetlands and streams where such projects are feasible with local resources. We present ecological management lessons learned from 17 years of monitoring the fish community response to the channel relocation and reach-level restoration of Juday Creek, a 3rd-order tributary of the St. Joseph River in Indiana, USA. The project was designed to increase habitat complexity, reverse the effects of accumulated fine sediment (< 2 mm diameter), and mitigate for the impacts of a new golf course development. The 1997 restoration consisted of new channel construction within two reaches of a 1.2-km section of Juday Creek that also contained two control reaches. A primary social goal of the golf course development and stream restoration was to avoid harm to the non-native brown trout fishery, as symbolic of community concerns for the watershed. Our long-term monitoring effort revealed that, although fine sediment increased over time in the restored reaches, habitat conditions have promoted the resurgence of native fish species. Since restoration, the fish assemblage has shifted from non-native Salmonidae (brown trout, rainbow trout) to native Centrarchidae (rock bass, largemouth bass, smallmouth bass). In addition, native, nongame species have remained stable or have increased in population abundance (e.g., Johnny darter, mottled sculpin). The results of this study demonstrate the value of learning from a restoration project to adjust management decisions that enhance environmental quality.

A guideline to improve qualitative social science publishing in ecology and conservation journals

A rise in qualitative social science manuscripts published in ecology and conservation journals speaks to the growing awareness of the importance of the human dimension in maintaining and improving Earth’s ecosystems. Given the rise in the quantity of qualitative social science research published in ecology and conservation journals, it is worthwhile quantifying the extent to which this research is meeting established criteria for research design, conduct, and interpretation. Through a comprehensive review of this literature, we aimed to gather and assess data on the nature and extent of information presented on research design published qualitative research articles, which could be used to judge research quality. Our review was based on 146 studies from across nine ecology and conservation journals. We reviewed and summarized elements of quality that could be used by reviewers and readers to evaluate qualitative research (dependability, credibility, confirmability, and transferability); assessed the prevalence of these elements in research published in ecology and conservation journals; and explored the implications of sound qualitative research reporting for applying research findings. We found that dependability and credibility were reasonably well reported, albeit poorly evolved in relation to critical aspects of qualitative social science such as methodology and triangulation, including reflexivity. Confirmability was, on average, inadequately accounted for, particularly with respect to researchers’ ontology, epistemology, or philosophical perspective and their choice of methodology. Transferability was often poorly developed in terms of triangulation methods and the suitability of the sample for answering the research question/s. Based on these findings, we provide a guideline that may be used to evaluate qualitative research presented in ecology and conservation journals to help secure the role of qualitative research and its application to decision making.

Ancient clam gardens, traditional management portfolios, and the resilience of coupled human-ocean systems

Indigenous communities have actively managed their environments for millennia using a diversity of resource use and conservation strategies. Clam gardens, ancient rock-walled intertidal beach terraces, represent one example of an early mariculture technology that may have been used to improve food security and confer resilience to coupled human-ocean systems. We surveyed a coastal landscape for evidence of past resource use and management to gain insight into ancient resource stewardship practices on the central coast of British Columbia, Canada. We found that clam gardens are embedded within a diverse portfolio of resource use and management strategies and were likely one component of a larger, complex resource management system. We compared clam diversity, density, recruitment, and biomass in three clam gardens and three unmodified nonwalled beaches. Evidence suggests that butter clams (Saxidomus gigantea) had 1.96 times the biomass and 2.44 times the density in clam gardens relative to unmodified beaches. This was due to a reduction in beach slope and thus an increase in the optimal tidal range where clams grow and survive best. The most pronounced differences in butter clam density between nonwalled beaches and clam gardens were found at high tidal elevations at the top of the beach. Finally, clam recruits (0.5-2 mm in length) tended to be greater in clam gardens compared to nonwalled beaches and may be attributed to the addition of shell hash by ancient people, which remains on the landscape today. As part of a broader social-ecological system, clam garden sites were among several modifications made by humans that collectively may have conferred resilience to past communities by providing reliable and diverse access to food resources.

Resilience of small-scale societies’ livelihoods: a framework for studying the transition from food gathering to food production

The origins of agriculture and the shift from hunting and gathering to committed agriculture is regarded as one of the major transitions in human history. Archeologists and anthropologists have invested significant efforts in explaining the origins of agriculture. A period of gathering intensification and experimentation and pursuing a mixed economic strategy seems the most plausible explanation for the transition to agriculture and provides an approach to study a process in which several nonlinear processes may have played a role. However, the mechanisms underlying the transition to full agriculture are not completely clear. This is partly due to the nature of the archeological record, which registers a practice only once it has become clearly established. Thus, points of transitions have limited visibility and the mechanisms involved in the process are difficult to untangle. The complexity of such transitions also implies that shifts can be distinctively different in particular environments and under varying historical and social conditions. In this paper we discuss some of the elements involved in the transition to food production within the framework of resilience theory. We propose a theoretical conceptual model in which the resilience of livelihood strategies lies at the intersection of three spheres: the environmental, economical, and social domains. Transitions occur when the rate of change, in one or more of these domains, is so elevated or its magnitude so large that the livelihood system is unable to bounce back to its original state. In this situation, the system moves to an alternative stable state, from one livelihood strategy to another.

The ecology and evolution of invasive Potamopyrgus antipodarum in Australia

The spread of invasive organisms is one of the greatest threats to ecosystems and biodiversity worldwide. Understanding the evolutionary and ecological factors responsible for the transport, introduction, establishment and spread of invasive species will assist the development of control strategies. The New Zealand mudsnail, Potamopyrgus antipodarum (Gray 1843) (Gastropoda: Hydrobiidae), is a global freshwater invader, with populations established in Europe, Asia, the Americas and Australia. While sexual and asexual P. antipodarum coexist in the native range, invasive populations reproduce by parthenogenesis, producing dense populations that compete for resources with native species. Potamopyrgus antipodarum is a natural model system for the study of evolutionary and ecological processes underlying invasion. This thesis assesses the invasion history, genetic diversity and ecology of P. antipodarum in Australia, with particular focus on: a) potential source populations, b) distribution and structure of populations, and c) species traits related to the establishment, persistence and spread of invasive P. antipodarum. Genetic analyses were carried out on specimens collected for this study from New Zealand and Australia, along with existing museum samples. In combination with published data, the analyses revealed low genetic diversity among and within invasive populations in south-eastern Australia, relative to New Zealand populations. Phylogenetic relationships inferred from mitochondrial sequences indicated that the Australian populations belong to clades dominated by parthenogenetic haplotypes that are known to be present in Europe and the US. These ‘invasive clades’ are likely to originate from the North Island of New Zealand, and suggest a role for selection in determining genetic composition of invasive populations. The genotypic diversity of Australian P. antipodarum was low, with few, closely related clones distributed across south-eastern Australia. The pattern of clone distribution was not consistent with any assessed geographical or abiotic factors; instead a few, widely-distributed clones were present in high frequencies at most sites. Differences in clone frequencies were found, which may indicate differential success of clonal lineages. A range of traits have been proposed as facilitators of invasion success, and within-species variation in these traits can promote differential success of genotypes. Using laboratory-based experiments, the performance of the three most common Australian clones was tested across a suite of invasion-relevant traits. Ecologically-relevant variation in traits was found among the clones. These differences may have determined the spatial distribution of clones, and may continue to do so into the future. This thesis found that the P. antipodarum invasion of Australia is the result of few introductions of a small number of globally-invasive genotypes that vary in ecologically-relevant traits. From a source of considerable genetic diversity in the native range, very few genotypes have become invasive. Those that are invasive appear to be very successful at continental scales. These findings highlight a capacity in asexual invaders to successfully invade, and potentially adapt to, a broad range of ecosystems. The P. antipodarum invasion system is amenable to research using combinations of field-based studies, molecular and laboratory approaches, and is likely to yield significant, broadly-applicable insights into invasion.

Nme Gene Family Evolutionary History Reveals Pre-Metazoan Origins and High Conservation between Humans and the Sea Anemone, Nematostella vectensis

Background: The Nme gene family is involved in multiple physiological and pathological processes such as cellular differentiation, development, metastatic dissemination, and cilia functions. Despite the known importance of Nme genes and their use as clinical markers of tumor aggressiveness, the associated cellular mechanisms remain poorly understood. Over the last 20 years, several non-vertebrate model species have been used to investigate Nme functions. However, the evolutionary history of the family remains poorly understood outside the vertebrate lineage. The aim of the study was thus to elucidate the evolutionary history of the Nme gene family in Metazoans. Methodology/Principal Findings: Using a total of 21 eukaryote species including 14 metazoans, the evolutionary history of Nme genes was reconstructed in the metazoan lineage. We demonstrated that the complexity of the Nme gene family, initially thought to be restricted to chordates, was also shared by the metazoan ancestor. We also provide evidence suggesting that the complexity of the family is mainly a eukaryotic innovation, with the exception of Nme8 that is likely to be a choanoflagellate/metazoan innovation. Highly conserved gene structure, genomic linkage, and protein domains were identified among metazoans, some features being also conserved in eukaryotes. When considering the entire Nme family, the starlet sea anemone is the studied metazoan species exhibiting the most conserved gene and protein sequence features with humans. In addition, we were able to show that most of the proteins known to interact with human NME proteins were also found in starlet sea anemone. Conclusion/Significance: Together, our observations further support the association of Nme genes with key cellular functions that have been conserved throughout metazoan evolution. Future investigations of evolutionarily conserved Nme gene functions using the starlet sea anemone could shed new light on a wide variety of key developmental and cellular processes.

Influence of Food Distribution and Human Disturbance on the Reproductive Success of Herring Gulls

A three year study of Herring Gull (Larus argentatus) reproductive success on four i~lands in Maine indicate.d that production of young was controlled by different factors operating on the eggs and chicks. Hatching success was inversely related to the disturbance of co.Ionics by pic~i~kers, which apparently caused the adults to leave their eggs exposed 10 sufficient solar rad1a11on to addle the eggs. The survival of chicks was lower on islands distant ~rom sources of edible r~~use (ou.ter. islands) than o.n. islands close to sources of waste (inner islands), regardless of visits by picnickers. The nutrition and growth rates of chicks on inner and outer islands were similar. The attendance of parents on the territories was found to be less o~ an out~r islan~ than on an inner island. It is concluded that differences in parental behavior associated with greater foraging effort were responsible for a higher loss of chicks to predation on the outer islands.

Quantification of the human postural control system to perturbations

Human standing posture is inherently unstable. The postural control system (PCS), which maintains standing posture, is composed of the sensory, musculoskeletal, and central nervous systems. Together these systems integrate sensory afferents and generate appropriate motor efferents to adjust posture. The PCS maintains the body center of mass (COM) with respect to the base of support while constantly resisting destabilizing forces from internal and external perturbations. To assess the human PCS, postural sway during quiet standing or in response to external perturbation have frequently been examined descriptively. Minimal work has been done to understand and quantify the robustness of the PCS to perturbations. Further, there have been some previous attempts to assess the dynamical systems aspects of the PCS or time evolutionary properties of postural sway. However those techniques can only provide summary information about the PCS characteristics; they cannot provide specific information about or recreate the actual sway behavior. This dissertation consists of two parts: part I, the development of two novel methods to assess the human PCS and, part II, the application of these methods. In study 1, a systematic method for analyzing the human PCS during perturbed stance was developed. A mild impulsive perturbation that subjects can easily experience in their daily lives was used. A measure of robustness of the PCS, 1/MaxSens that was based on the inverse of the sensitivity of the system, was introduced. 1/MaxSens successfully quantified the reduced robustness to external perturbations due to age-related degradation of the PCS. In study 2, a stochastic model was used to better understand the human PCS in terms of dynamical systems aspect. This methodology also has the advantage over previous methods in that the sway behavior is captured in a model that can be used to recreate the random oscillatory properties of the PCS. The invariant density which describes the long-term stationary behavior of the center of pressure (COP) was computed from a Markov chain model that was applied to postural sway data during quiet stance. In order to validate the Invariant Density Analysis (IDA), we applied the technique to COP data from different age groups. We found that older adults swayed farther from the centroid and in more stochastic and random manner than young adults. In part II, the tools developed in part I were applied to both occupational and clinical situations. In study 3, 1/MaxSens and IDA were applied to a population of firefighters to investigate the effects of air bottle configuration (weight and size) and vision on the postural stability of firefighters. We found that both air bottle weight and loss of vision, but not size of air bottle, significantly decreased balance performance and increased fall risk. In study 4, IDA was applied to data collected on 444 community-dwelling elderly adults from the MOBILIZE Boston Study. Four out of five IDA parameters were able to successfully differentiate recurrent fallers from non-fallers, while only five out of 30 more common descriptive and stochastic COP measures could distinguish the two groups. Fall history and the IDA parameter of entropy were found to be significant risk factors for falls. This research proposed a new measure for the PCS robustness (1/MaxSens) and a new technique for quantifying the dynamical systems aspect of the PCS (IDA). These new PCS analysis techniques provide easy and effective ways to assess the PCS in occupational and clinical environments.

Conservation value, biodiversity value and methods of assessment in regenerating and human disturbed tropical forest

Although the value of primary forests for biodiversity conservation is well known, the potential biodiversity and conservation value of regenerating forests remains controversial. Many factors likely contribute to this, including: 1. the variable ages of regenerating forests being studied (often dominated by relatively young regenerating forests); 2. the potential for confounding on-going human disturbance (such as logging and hunting); 3. the relatively low number of multi-taxa studies; 4. the lack of studies that directly compare different historic disturbances within the same location; 5. contrasting patterns from different survey methodologies and the paucity of knowledge on the impacts across different vertical levels of rainforest biodiversity (often due to a lack of suitable methodologies available to assess them). We also know relatively little as to how biodiversity is affected by major current impacts, such as unmarked rainforest roads, which contribute to this degradation of habitat and fragmentation. This thesis explores the potential biodiversity value of regenerating rainforests under the best of scenarios and seeks to understand more about the impact of current human disturbance to biodiversity; data comes from case studies from the Manu and Sumaco Biosphere Reserves in the Western Amazon. Specifically, I compare overall biodiversity and conservation value of a best case regenerating rainforest site with a selection of well-studied primary forest sites and with predicted species lists for the region; including a focus on species of key conservation concern. I then investigate the biodiversity of the same study site in reference to different types of historic anthropogenic disturbance. Following this I investigate the impacts to biodiversity from an unmarked rainforest road. In order to understand more about the differential effects of habitat disturbance on arboreal diversity I directly assess how patterns of butterfly biodiversity vary between three vertical strata. Although assessments within the canopy have been made for birds, invertebrates and bats, very few studies have successfully targeted arboreal mammals. I therefore investigate the potential of camera traps for inventorying arboreal mammal species in comparison with traditional methodologies. Finally, in order to investigate the possibility that different survey methodologies might identify different biodiversity patterns in habitat disturbance assessments, I investigate whether two different but commonly used survey methodologies used to assess amphibians, indicate the same or different responses of amphibian biodiversity to historic habitat change by people. The regenerating rainforest study site contained high levels of species richness; both in terms of alpha diversity found in nearby primary forest areas (87% ±3.5) and in terms of predicted primary forest diversity from the region (83% ±6.7). This included 89% (39 out of 44) of the species of high conservation concern predicted for the Manu region. Faunal species richness in once completely cleared regenerating forest was on average 13% (±9.8) lower than historically selectively logged forest. The presence of the small unmarked road significantly altered levels of faunal biodiversity for three taxa, up to and potentially beyond 350m into the forest interior. Most notably, the impact on biodiversity extended to at least 32% of the whole reserve area. The assessment of butterflies across strata showed that different vertical zones within the same rainforest responded differently in areas with different historic human disturbance. A comparison between forest regenerating after selective logging and forest regenerating after complete clearance, showed that there was a 17% greater reduction in canopy species richness in the historically cleared forest compared with the terrestrial community. Comparing arboreal camera traps with traditional ground-based techniques suggests that camera traps are an effective tool for inventorying secretive arboreal rainforest mammal communities and detect a higher number of cryptic species. Finally, the two survey methodologies used to assess amphibian communities identified contrasting biodiversity patterns in a human modified rainforest; one indicated biodiversity differences between forests with different human disturbance histories, whereas the other suggested no differences between forest disturbance types. Overall, in this thesis I find that the conservation and biodiversity value of regenerating and human disturbed tropical forest can potentially contribute to rainforest biodiversity conservation, particularly in the best of circumstances. I also highlight the importance of utilising appropriate study methodologies that to investigate these three-dimensional habitats, and contribute to the development of methodologies to do so. However, care should be taken when using different survey methodologies, which can provide contrasting biodiversity patterns in response to human disturbance.

From the human rights-based approach to an ecological approach on how to achieve successful inclusion in international disability education

The barriers that people with disabilities face around the world are not only inherent to the limitations resulting from the disability itself, but, more importantly, these barriers rest with the societal technologies of exclusion. Using a mixed methodology approach, I conduct a quest to revealing several societal factors that limit full participation of people with disabilities in their communities, which will contribute to understanding and developing a more comprehensive framework for full inclusion of people with disabilities into the society. First, I conduct a multiple regression analysis to seek whether there is a statistical relationship between the national level of development, the level of democratization, and the level of education within a country’s population on one hand, and expressed concern for and preparedness to improve the quality of life for people of disabilities on another hand. The results from the quantitative methodology reveal that people without disabilities are more prepared to take care of people with disabilities when the level of development of the country is higher, when the people have more freedom of expression and hold the government accountable for its actions, and when the level of corruption is under control. However, a greater concern for the well-being of people with disabilities is correlated with a high level of country development, a decreased value of political stability and absence of violence, a decreased level of government effectiveness, and a greater level of law enforcement. None of the dependent variables are significantly correlated with the level of education from a given country. Then, I delve into an interpretive analysis to understand multiple factors that contribute to the construction of attitudes and practices towards people with disabilities. In doing this, I build upon the four main principles outlined by the United Nations as strongly recommended to be embedded in all international programmes: (1) identification of claims of human rights and the corresponding obligations of governments, hence, I assess and analyze disability rights in education, looking at United Nation, United States, and European Union Perspectives Educational Rights Provisions for People with Disabilities (Ch. 3); (2) estimated capacity of individuals to claim their rights and of governments to fulfill their obligations, hence, I look at the people with disabilities as rights-holders and duty-bearers and discuss the importance of investing in special capital in the context of global development (Ch. 4); (3) programmes monitor and evaluate the outcomes and the processes under the auspices of human rights standards, hence, I look at the importance of evaluating the UN World Programme of Action Concerning People with Disabilities from multiple perspectives, as an example of why and how to monitor and evaluate educational human rights outcomes and processes (Ch. 5); and (4) programming should reflect the recommendations of international human rights bodies and mechanisms, hence, I focus on programming that fosters development of the capacity of people with disabilities, that is, planning for an ecology of disabilities and ecoducation for people with disabilities (Ch. 6). Results from both methodologies converge to a certain point, and they further complement each other. One common result for the two methodologies employed is that disability is an evolving concept when viewed in a broader context, which integrates the four spaces that the ecological framework incorporates. Another common result is that factors such as economic, social, legal, political, and natural resources and contexts contribute to the health, education and employment opportunities, and to the overall well-being of people with disabilities. The ecological framework sees all these factors from a meta-systemic perspective, where bi-directional interactions are expected and desired, and also from a human rights point of view, where the inherent value of people is upheld at its highest standard.

Applied evolution: An integrated approach to studying life history traits in response to drug selection

The use of chemical control measures to reduce the impact of parasite and pest species has frequently resulted in the development of resistance. Thus, resistance management has become a key concern in human and veterinary medicine, and in agricultural production. Although it is known that factors such as gene flow between susceptible and resistant populations, drug type, application methods, and costs of resistance can affect the rate of resistance evolution, less is known about the impacts of density-dependent eco-evolutionary processes that could be altered by drug-induced mortality. The overall aim of this thesis was to take an experimental evolution approach to assess how life history traits respond to drug selection, using a free-living dioecious worm (Caenorhabditis remanei) as a model. In Chapter 2, I defined the relationship between C. remanei survival and Ivermectin dose over a range of concentrations, in order to control the intensity of selection used in the selection experiment described in Chapter 4. The dose-response data were also used to appraise curve-fitting methods, using Akaike Information Criterion (AIC) model selection to compare a series of nonlinear models. The type of model fitted to the dose response data had a significant effect on the estimates of LD50 and LD99, suggesting that failure to fit an appropriate model could give misleading estimates of resistance status. In addition, simulated data were used to establish that a potential cost of resistance could be predicted by comparing survival at the upper asymptote of dose-response curves for resistant and susceptible populations, even when differences were as low as 4%. This approach to dose-response modeling ensures that the maximum amount of useful information relating to resistance is gathered in one study. In Chapter 3, I asked how simulations could be used to inform important design choices used in selection experiments. Specifically, I focused on the effects of both within- and between-line variation on estimated power, when detecting small, medium and large effect sizes. Using mixed-effect models on simulated data, I demonstrated that commonly used designs with realistic levels of variation could be underpowered for substantial effect sizes. Thus, use of simulation-based power analysis provides an effective way to avoid under or overpowering a study designs incorporating variation due to random effects. In Chapter 4, I 3 investigated how Ivermectin dosage and changes in population density affect the rate of resistance evolution. I exposed replicate lines of C. remanei to two doses of Ivermectin (high and low) to assess relative survival of lines selected in drug-treated environments compared to untreated controls over 10 generations. Additionally, I maintained lines where mortality was imposed randomly to control for differences in density between drug treatments and to distinguish between the evolutionary consequences of drug treatment versus ecological processes affected by changes in density-dependent feedback. Intriguingly, both drug-selected and random-mortality lines showed an increase in survivorship when challenged with Ivermectin; the magnitude of this increase varied with the intensity of selection and life-history stage. The results suggest that interactions between density-dependent processes and life history may mediate evolved changes in susceptibility to control measures, which could result in misleading conclusions about the evolution of heritable resistance following drug treatment. In Chapter 5, I investigated whether the apparent changes in drug susceptibility found in Chapter 4 were related to evolved changes in life-history of C. remanei populations after selection in drug-treated and random-mortality environments. Rapid passage of lines in the drug-free environment had no effect on the measured life-history traits. In the drug-free environment, adult size and fecundity of drug-selected lines increased compared to the controls but drug selection did not affect lifespan. In the treated environment, drug-selected lines showed increased lifespan and fecundity relative to controls. Adult size of randomly culled lines responded in a similar way to drug-selected lines in the drug-free environment, but no change in fecundity or lifespan was observed in either environment. The results suggest that life histories of nematodes can respond to selection as a result of the application of control measures. Failure to take these responses into account when applying control measures could result in adverse outcomes, such as larger and more fecund parasites, as well as over-estimation of the development of genetically controlled resistance. In conclusion, my thesis shows that there may be a complex relationship between drug selection, density-dependent regulatory processes and life history of populations challenged with control measures. This relationship could have implications for how resistance is monitored and managed if life histories of parasitic species show such eco-evolutionary responses to drug application.

Vitamin D status in a Brazilian cohort of adolescents and young adults with perinatally acquired human immunodeficiency virus infection

The purpose was to determine the prevalence and related factors of vitamin D (VitD) insufficiency in adolescents and young adults with perinatally acquired human immunodeficiency virus. A cohort of 65 patients (17.6 ± 2 years) at the Federal University of Rio de Janeiro, Brazil, were examined for pubertal development, nutrition, serum parathormone and serum 25-hydroxyvitamin D [s25(OH)D]. s25(OH)D levels < 30 ng/mL (< 75 nmol/L) were defined as VitD insufficiency. CD4+ T-cell counts and viral load, history of worst clinical status, immunologic status as nadir, current immunologic status, and antiretroviral (ART) regimen were also evaluated as risk factors for VitD insufficiency. Mean s25(OH)D was 37.7 ± 13.9 ng/mL and 29.2% had VitD insufficiency. There was no difference between VitD status and gender, age, nutritional status, clinical and immunological classification, and type of ART. Only VitD consumption showed tendency of association with s25(OH)D (p = 0.064). Individuals analysed in summer/autumn season had a higher s25(OH)D compared to the ones analysed in winter/spring (42.6 ± 14.9 vs. 34.0 ± 11.9, p = 0.011). Although, the frequency of VitD insufficiency did not differ statistically between the groups (summer/autumn 17.9% vs. winter/spring 37.8%, p = 0.102), we suggest to monitor s25(OH)D in seropositive adolescents and young adults, especially during winter/spring months, even in sunny regions.

The microbiological signature of human cutaneous leishmaniasis lesions exhibits restricted bacterial diversity compared to healthy skin

Localised cutaneous leishmaniasis (LCL) is the most common form of cutaneous leishmaniasis characterised by single or multiple painless chronic ulcers, which commonly presents with secondary bacterial infection. Previous culture- based studies have found staphylococci, streptococci, and opportunistic pathogenic bacteria in LCL lesions, but there have been no comparisons to normal skin. In addition, this approach has strong bias for determining bacterial composition. The present study tested the hypothesis that bacterial communities in LCL lesions differ from those found on healthy skin (HS). Using a high throughput amplicon sequencing approach, which allows for better populational evaluation due to greater depth coverage and the Quantitative Insights Into Microbial Ecology pipeline, we compared the microbiological signature of LCL lesions with that of contralateral HS from the same individuals. Streptococcus , Staphylococcus , Fusobacterium and other strict or facultative anaerobic bacteria composed the LCL microbiome. Aerobic and facultative anaerobic bacteria found in HS, including environmental bacteria, were significantly decreased in LCL lesions (p < 0.01). This paper presents the first comprehensive microbiome identification from LCL lesions with next generation sequence methodology and shows a marked reduction of bacterial diversity in the lesions.