Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition

Explorations of complex microbiomes using genomics greatly enhance our understanding about their diversity, biogeography, and function. The isolation of DNA from microbiome specimens is a key prerequisite for such examinations, but challenges remain in obtaining sufficient DNA quantities required for certain sequencing approaches, achieving accurate genomic inference of microbiome composition, and facilitating comparability of findings across specimen types and sequencing projects. These aspects are particularly relevant for the genomics-based global surveillance of infectious agents and antimicrobial resistance from different reservoirs. Here, we compare in a stepwise approach a total of eight commercially available DNA extraction kits and 16 procedures based on these for three specimen types (human feces, pig feces, and hospital sewage). We assess DNA extraction using spike-in controls and different types of beads for bead beating, facilitating cell lysis. We evaluate DNA concentration, purity, and stability and microbial community composition using 16S rRNA gene sequencing and for selected samples using shotgun metagenomic sequencing. Our results suggest that inferred community composition was dependent on inherent specimen properties as well as DNA extraction method. We further show that bead beating or enzymatic treatment can increase the extraction of DNA from Gram-positive bacteria. Final DNA quantities could be increased by isolating DNA from a larger volume of cell lysate than that in standard protocols. Based on this insight, we designed an improved DNA isolation procedure optimized for microbiome genomics that can be used for the three examined specimen types and potentially also for other biological specimens. A standard operating procedure is available from https://dx.doi.org/10.6084/m9.figshare.3475406. IMPORTANCE Sequencing-based analyses of microbiomes may lead to a breakthrough in our understanding of the microbial worlds associated with humans, animals, and the environment. Such insight could further the development of innovative ecosystem management approaches for the protection of our natural resources and the design of more effective and sustainable solutions to prevent and control infectious diseases. Genome sequence information is an organism (pathogen)-independent language that can be used across sectors, space, and time. Harmonized standards, protocols, and workflows for sample processing and analysis can facilitate the generation of such actionable information. In this study, we assessed several procedures for the isolation of DNA for next-generation sequencing. Our study highlights several important aspects to consider in the design and conduct of sequence-based analysis of microbiomes. We provide a standard operating procedure for the isolation of DNA from a range of biological specimens particularly relevant in clinical diagnostics and epidemiology

Extensive Internet Involvement—Addiction or Emerging Lifestyle?

In the discussions for the future DSM-5, the Substance-Related Disorders Work Group has been addressing “addiction-like” behavioral disorders such as “Internet addiction” to possibly be considered as potential additions for the diagnostic system. Most research aiming to specify and define the concept of Internet addiction (or: Excessive/Compulsive/Problematic Internet Use—PIU), takes its point of departure in conventional terminology for addiction, based in established DSM indicators. Still, it is obvious that the divide between characteristics of addiction and dimensions of new lifestyles built on technological progress is problematic and far from unambiguous. Some of these research areas are developing from the neurobiological doctrine of addiction as not being tied to specific substances. The concept of “behavioral addictions”, based on biological mechanisms such as the reward systems of the brain, has been launched. The problems connected to this development are in this study discussed and reflected with data from a Swedish survey on Internet use (n = 1,147). Most Swedes (85%) do use the Internet to some degree. The prevalence of excessive use parallels other similar countries. Respondents in our study spend (mean value) 9.8 hours per week online at home, only 5 percent spend more than 30 hours per week. There are both positive and negative social effects at hand. Many respondents have more social contacts due to the use of Internet, but there is a decline in face-to-face contacts. About 40% of the respondents indicate some experience of at least one problem related to Internet use, but only 1.8% marked the presence of all problems addressed. Most significant predictors for problem indicators, except for age, relate to “time” and time consuming activities such as gaming, other activities online or computer skills

Risk, pleasure and information – notes concerning the discursive space of prevention

In this paper the notions of risk, pleasure and information are discussed with reference both to their utilization within the prevention discourse and to their relation to a process of de-traditionalization. It is suggested that the current lack of options for moral discourse directed towards the individual's freedom of choice, restricts the vocabulary of prevention to deal only with the harm produced by alcohol consumption. Prevention discourses can-not address the motivational structure connected to the individual's pursuit for pleasure and self-fulfilling experiences. This constraint can be seen as a contributing factor to the centrality of risk in alcohol prevention discourses. Although risk-information is produced within the scientific community by a logic of its own, it is also related to the individuals expanding menu of choices that follows with subject-centered individualism with little or no room for moral discourse concerning the individual's construction of lifestyle and identity. When morality is no longer present, only risk can fill its traditional role, that of being a reason for renouncing. It is not by chance that the most important actors on the alcohol policy scene in traditional temperance societies now are professionals and bureaucrats and not voluntary temperance organizations and that the latter have increasingly adopted their arguments from the former. </jats:p

Education for empowerment

Syftet med den här undersökningen är att fördjupa förståelsen av hur undervisning i samhällskunskap kan bidra till att öka elevernas benägenhet att engagera sig i demokratiska processer. Syftet operationaliseras i två frågeställningar. Hur uppfattar elever sin demokratiska egenmakt och hur kan undervisningen utveckla elevernas upplevda demokratiska egenmakt?  En kartläggning genomförd i två gymnasieklasser i Stockholmsområdet visade att elevernas uppfattade egenmakt, med stöd i Amnås och Ekmans typer av passiva medborgare respektive Westheimer och Kahnes typer av aktiva medborgare, kan beskrivas i fyra upplevelsekategorier av växande egenmakt: ingen, liten, individuell och kommunitär egenmakt. De fyra upplevelsekategoriernas koppling till Amnås och Ekmans respektive Westheimer och Kahnes typer av medborgare gör vidare att de kan placeras och diskuteras i ett större ämnesdidaktiskt sammanhang. Undersökningens andra frågeställning besvaras med förslag på tre lärandeobjekt som möjliggör för elever att göra förflyttningar från upplevelsekategorier med ingen eller liten upplevd egenmakt till upplevelsekategorier med större upplevd egenmakt, nämligen det demokratiska systemet, opinionsbildning samt politiska rörelser

Om medikaliseringen av svensk missbrukarvård

Under de senaste 10 åren har propåerna om en radikal omorganisering av svensk missbrukarvård vuxit sig allt starkare. Den allmänna inriktningen hos dessa påtryckningar har utgjorts av en medikalisererande argumentation beträffande den vetenskapliga kunskapen om missbruk och behandling: I denna artikel granskas några av medikaliseringsdiskursens mest centrala argument.</jats:p

Education for empowerment

Syftet med den här undersökningen är att fördjupa förståelsen av hur undervisning i samhällskunskap kan bidra till att öka elevernas benägenhet att engagera sig i demokratiska processer. Syftet operationaliseras i två frågeställningar. Hur uppfattar elever sin demokratiska egenmakt och hur kan undervisningen utveckla elevernas upplevda demokratiska egenmakt?  En kartläggning genomförd i två gymnasieklasser i Stockholmsområdet visade att elevernas uppfattade egenmakt, med stöd i Amnås och Ekmans typer av passiva medborgare respektive Westheimer och Kahnes typer av aktiva medborgare, kan beskrivas i fyra upplevelsekategorier av växande egenmakt: ingen, liten, individuell och kommunitär egenmakt. De fyra upplevelsekategoriernas koppling till Amnås och Ekmans respektive Westheimer och Kahnes typer av medborgare gör vidare att de kan placeras och diskuteras i ett större ämnesdidaktiskt sammanhang. Undersökningens andra frågeställning besvaras med förslag på tre lärandeobjekt som möjliggör för elever att göra förflyttningar från upplevelsekategorier med ingen eller liten upplevd egenmakt till upplevelsekategorier med större upplevd egenmakt, nämligen det demokratiska systemet, opinionsbildning samt politiska rörelser

Artikel

Evidence-based practice (EBP) has been advocated since the beginning of the 1990s and is today, at least within the western hemisphere, an established doctrine in many professional fields. This holds true also for addiction treatment. Over time EBP has come to signify a more general orientation to a scientifically secured knowledgebase and by this partly obscuring the fact there exists different and to some extent contradictory opinions on how EBP should be implemented. The paper aims at an analysis of the newly published Swedish national guidelines for addiction treatment. The analysis addresses several dimensions of the guidelines: a) the quality of the guidelines in terms of their scientific underpinning. b) The usefulness of the guidelines, i.e. to what extent it is possible to use the guidelines in actual practice. c). How the guidelines were produced (time-aspects, involvement of experts and the role of the National Board of Health and welfare as the responsible organisation). d) To what extent the guidelines have been developed with reference to and a discussion of some of the major scientific controversies related to the EBP issue. </jats:p