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Two major outstanding questions in microbiome research ask what microbes are present in a community and how they interact with each other and their hosts. Recent, rapid improvements in nucleic acid (DNA and RNA) sequencing allow us to study the composition and function of microbiomes in unprecedented detail, leading to a step change in our understanding of host–microbe interactions. This chapter gives a broad overview of the basic toolkit available to modern microbiologists and microbial ecologists, exploring their application to key questions about microbiome structure and function. We cover tools based on nucleic acid sequencing (e.g. amplicon sequencing, metagenomics, metatranscriptomics) as well as approaches targeting larger molecules such as metabolomics and proteomics. We discuss the use of microbial culture as a means of measuring functional capacity of individual microbes, or building artificial communities to understand emergent properties of consortia. We emphasise the advantages of combining multiple techniques alongside robust experimental design to garner powerful quantitative estimates of microbiome structure, and how this relates to host–microbe interactions.
Item 9 of the Patient Health Questionnaire-9 (PHQ-9) queries about thoughts of death and self-harm, but not suicidality. Although it is sometimes used to assess suicide risk, most positive responses are not associated with suicidality. The PHQ-8, which omits Item 9, is thus increasingly used in research. We assessed equivalency of total score correlations and the diagnostic accuracy to detect major depression of the PHQ-8 and PHQ-9.
We conducted an individual patient data meta-analysis. We fit bivariate random-effects models to assess diagnostic accuracy.
16 742 participants (2097 major depression cases) from 54 studies were included. The correlation between PHQ-8 and PHQ-9 scores was 0.996 (95% confidence interval 0.996 to 0.996). The standard cutoff score of 10 for the PHQ-9 maximized sensitivity + specificity for the PHQ-8 among studies that used a semi-structured diagnostic interview reference standard (N = 27). At cutoff 10, the PHQ-8 was less sensitive by 0.02 (−0.06 to 0.00) and more specific by 0.01 (0.00 to 0.01) among those studies (N = 27), with similar results for studies that used other types of interviews (N = 27). For all 54 primary studies combined, across all cutoffs, the PHQ-8 was less sensitive than the PHQ-9 by 0.00 to 0.05 (0.03 at cutoff 10), and specificity was within 0.01 for all cutoffs (0.00 to 0.01).
PHQ-8 and PHQ-9 total scores were similar. Sensitivity may be minimally reduced with the PHQ-8, but specificity is similar.
Cambodia supports populations of three Critically Endangered vulture species that are believed to have become isolated from the rest of the species’ global range. Until recently Cambodia’s vulture populations had remained stable. However a recent spike in the number of reports of the use of poisons in hunting practices suggests the need to re-evaluate the conservation situation in Cambodia. Population trend analysis showed that since 2010 populations of the White-rumped Vulture Gyps bengalensis and Red-headed Vulture Sarcogyps calvus have declined, while the Slender-billed Vulture Gyps tenuirostris may also have started to decline since 2013. These trends are supported by evidence of reduced nesting success. A survey of veterinary drug availability revealed that diclofenac, the non-steroid anti-inflammatory drug responsible for vulture declines in South Asia was not available for sale in any of the 74 pharmacies surveyed. However, a poisoned Slender-billed Vulture tested positive for carbofuran in toxicology tests. This provides the first evidence of a vulture mortality resulting from carbofuran in Cambodia. The findings suggest the urgent need to tackle use of carbamate pesticides in hunting. Proposed conservation actions are: a) prevention of poisoning through national bans on harmful carbamate pesticides and diclofenac and education campaigns to reduce demand and use; b) training of personnel in priority protected areas in detection and response to poisoning incidents; c) maintenance of a safe and reliable food source through vulture restaurants to ensure short-term survival, and d) protection and restoration of large areas of deciduous dipterocarp forests to enable long-term species recovery.