Extreme Dysbiosis of the Microbiome in Critical Illness.

Critical illness is hypothesized to associate with loss of "health-promoting" commensal microbes and overgrowth of pathogenic bacteria (dysbiosis). This dysbiosis is believed to increase susceptibility to nosocomial infections, sepsis, and organ failure. A trial with prospective monitoring of the intensive care unit (ICU) patient microbiome using culture-independent techniques to confirm and characterize this dysbiosis is thus urgently needed. Characterizing ICU patient microbiome changes may provide first steps toward the development of diagnostic and therapeutic interventions using microbiome signatures. To characterize the ICU patient microbiome, we collected fecal, oral, and skin samples from 115 mixed ICU patients across four centers in the United States and Canada. Samples were collected at two time points: within 48 h of ICU admission, and at ICU discharge or on ICU day 10. Sample collection and processing were performed according to Earth Microbiome Project protocols. We applied SourceTracker to assess the source composition of ICU patient samples by using Qiita, including samples from the American Gut Project (AGP), mammalian corpse decomposition samples, childhood (Global Gut study), and house surfaces. Our results demonstrate that critical illness leads to significant and rapid dysbiosis. Many taxons significantly depleted from ICU patients versus AGP healthy controls are key "health-promoting" organisms, and overgrowth of known pathogens was frequent. Source compositions of ICU patient samples are largely uncharacteristic of the expected community type. Between time points and within a patient, the source composition changed dramatically. Our initial results show great promise for microbiome signatures as diagnostic markers and guides to therapeutic interventions in the ICU to repopulate the normal, "health-promoting" microbiome and thereby improve patient outcomes. IMPORTANCE Critical illness may be associated with the loss of normal, "health promoting" bacteria, allowing overgrowth of disease-promoting pathogenic bacteria (dysbiosis), which, in turn, makes patients susceptible to hospital-acquired infections, sepsis, and organ failure. This has significant world health implications, because sepsis is becoming a leading cause of death worldwide, and hospital-acquired infections contribute to significant illness and increased costs. Thus, a trial that monitors the ICU patient microbiome to confirm and characterize this hypothesis is urgently needed. Our study analyzed the microbiomes of 115 critically ill subjects and demonstrated rapid dysbiosis from unexpected environmental sources after ICU admission. These data may provide the first steps toward defining targeted therapies that correct potentially "illness-promoting" dysbiosis with probiotics or with targeted, multimicrobe synthetic "stool pills" that restore a healthy microbiome in the ICU setting to improve patient outcomes

The relationship between dietary quality and the local food environment differs according to level of educational attainment: A cross-sectional study.

There is evidence that food outlet access differs according to level of neighbourhood deprivation but little is known about how individual circumstances affect associations between food outlet access and diet. This study explored the relationship between dietary quality and a measure of overall food environment, representing the balance between healthy and unhealthy food outlet access in individualised activity spaces. Furthermore, this study is the first to assess effect modification of level of educational attainment on this relationship. A total of 839 mothers with young children from Hampshire, United Kingdom (UK) completed a cross-sectional survey including a 20-item food frequency questionnaire to measure diet and questions about demographic characteristics and frequently visited locations including home, children's centre, general practitioner, work, main food shop and physical activity location. Dietary information was used to calculate a standardised dietary quality score for each mother. Individualised activity spaces were produced by creating a 1000m buffer around frequently visited locations using ArcGIS. Cross-sectional observational food outlet data were overlaid onto activity spaces to derive an overall food environment score for each mother. These scores represented the balance between healthy and unhealthy food outlets using weightings to characterise the proportion of healthy or unhealthy foods sold in each outlet type. Food outlet access was dominated by the presence of unhealthy food outlets; only 1% of mothers were exposed to a healthy overall food environment in their daily activities. Level of educational attainment moderated the relationship between overall food environment and diet (mid vs low, p = 0.06; high vs low, p = 0.04). Adjusted stratified linear regression analyses showed poorer food environments were associated with better dietary quality among mothers with degrees (β = -0.02; 95%CI: -0.03, -0.001) and a tendency toward poorer dietary quality among mothers with low educational attainment, however this relationship was not statistically significant (β = 0.01; 95%CI: -0.01, 0.02). This study showed that unhealthy food outlets, like takeaways and convenience stores, dominated mothers' food outlet access, and provides some empirical evidence to support the concept that individual characteristics, particularly educational attainment, are protective against exposure to unhealthy food environments. Improvements to the imbalance of healthy and unhealthy food outlets through planning restrictions could be important to reduce dietary inequalities

Measuring telomere length and telomere dynamics in evolutionary biology and ecology

Telomeres play a fundamental role in the protection of chromosomal DNA and in the regulation of cellular senescence. Recent work in human epidemiology and evolutionary ecology suggests adult telomere length (TL) may reflect past physiological stress and predict subsequent morbidity and mortality, independent of chronological age. Several different methods have been developed to measure TL, each offering its own technical challenges. The aim of this review is to provide an overview of the advantages and drawbacks of each method for researchers, with a particular focus on issues that are likely to face ecologists and evolutionary biologists collecting samples in the field or in organisms that may never have been studied in this context before. We discuss the key issues to consider and wherever possible try to provide current consensus view regarding best practice with regard to sample collection and storage, DNA extraction and storage, and the five main methods currently available to measure TL. Decisions regarding which tissues to sample, how to store them, how to extract DNA, and which TL measurement method to use cannot be prescribed, and are dependent on the biological question addressed and the constraints imposed by the study system. What is essential for future studies of telomere dynamics in evolution and ecology is that researchers publish full details of their methods and the quality control thresholds they employ

A SURVEY FOR ODONTOCETE CETACEANS OFF KAUA‘I AND NI‘IHAU, HAWAI‘I, DURING OCTOBER AND NOVEMBER 2005: EVIDENCE FOR POPULATION STRUCTURE AND SITE FIDELITY

Considerable uncertainty exists regarding population structure and population sizes of most species of odontocetes in the Hawaiian Islands. A small-boat based survey for odontocetes was undertaken off the islands of Kaua‘i and Ni‘ihau in October and November 2005 to photoidentify individuals and collect genetic samples for examining stock structure. Field effort on 24 days covered 2,194 km of trackline. Survey coverage was from shallow coastal waters out to over 3,000 m depth, though almost half (47%) was in waters less than 500 m in depth. There were 56 sightings of five species of odontocetes: spinner dolphins (30 sightings); bottlenose dolphins (14 sightings); short-finned pilot whales (6 sightings); rough-toothed dolphins (5 sightings); and pantropical spotted dolphins (1 sighting). One hundred and five biopsy samples were collected and 14,960 photographs were taken to document morphology and for individual photo-identification. Photographs of distinctive individuals of three species (bottlenose dolphins, 76 identifications; rough-toothed dolphins, 157 identifications; short-finned pilot whales, 68 identifications) were compared to catalogs of these species from a survey off Kaua‘i and Ni‘ihau in 2003, as well as from efforts off O‘ahu, Maui/Lana‘i and the island of Hawai‘i. Within- and between-year matches were found for all three species with individuals previously identified off Kaua‘i and Ni‘ihau, though no matches were found with individuals off any of the other islands. This suggests site fidelity to specific island areas, and population structure among island areas for all three species. Movements of photographically identified bottlenose dolphins were documented between deep water areas off the islands of Kaua‘i and Ni‘ihau, as well as between shallow (\u3c350 m) and deep (\u3e350 m) waters. A lack of sightings or reports of false killer whales off Kaua‘i or Ni‘ihau during our study, combined with documented movements among the other main Hawaiian Islands, suggest that there is no “resident” population of false killer whales that inhabits waters only off Kaua‘i or Ni‘iha