Showing papers by "Daniel McDonald published in 2015"

Context and the human microbiome

Abstract: Human microbiome reference datasets provide epidemiological context for researchers, enabling them to uncover new insights into their own data through meta-analyses. In addition, large and comprehensive reference sets offer a means to develop or test hypotheses and can pave the way for addressing practical study design considerations such as sample size decisions. We discuss the importance of reference sets in human microbiome research, limitations of existing resources, technical challenges to employing reference sets, examples of their usage, and contributions of the American Gut Project to the development of a comprehensive reference set. Through engaging the general public, the American Gut Project aims to address many of the issues present in existing reference resources, characterizing health and disease, lifestyle, and dietary choices of the participants while extending its efforts globally through international collaborations.

Towards large-cohort comparative studies to define the factors influencing the gut microbial community structure of ASD patients.

Abstract: Differences in the gut microbiota have been reported between individuals with autism spectrum disorders (ASD) and neurotypical controls, although direct evidence that changes in the microbiome contribute to causing ASD has been scarce to date. Here we summarize some considerations of experimental design that can help untangle causality in this complex system. In particular, large cross-sectional studies that can factor out important variables such as diet, prospective longitudinal studies that remove some of the influence of interpersonal variation in the microbiome (which is generally high, especially in children), and studies transferring microbial communities into germ-free mice may be especially useful. Controlling for the effects of technical variables, which have complicated efforts to combine existing studies, is critical when biological effect sizes are small. Large citizen-science studies with thousands of participants such as the American Gut Project have been effective at uncovering subtle microbiome effects in self-collected samples and with self-reported diet and behavior data, and may provide a useful complement to other types of traditionally funded and conducted studies in the case of ASD, especially in the hypothesis generation phase.

Ribosomal RNA, the lens into life

Abstract: Our world is, to a first approximation, a microbial world—even our own lives are evolutionarily and molecularly linked to that which we cannot see. This “invisible” world contains nearly unfathomable molecular and genetic diversity. Throughout the 20th century, a metaphor of “war against disease” prevailed: Microbes were hunted under the guise of health and agriculture, the goal being the eradication of “pathogens” at a global scale. Microbes were considered at best a nuisance and at worst a threat: a target for technological solutions. Humanity invested heavily, with the broad support of the scientific community, in the advancement of weapons for the war against microbes. We sought out novel antibiotics and antimicrobials as our enemy mounted resistance.