Challenges and Perspective in Integrated Multi-Omics in Gut Microbiota Studies

The advent of omic technology has made it possible to identify viable but unculturable micro-organisms in the gut. Therefore, application of multi-omic technologies in gut microbiome studies has become invaluable for unveiling a comprehensive interaction between these commensals in health and disease. Meanwhile, despite the successful identification of many microbial and host–microbial cometabolites that have been reported so far, it remains difficult to clearly identify the origin and function of some proteins and metabolites that are detected in gut samples. However, the application of single omic techniques for studying the gut microbiome comes with its own challenges which may be overcome if a number of different omics techniques are combined. In this review, we discuss our current knowledge about multi-omic techniques, their challenges and future perspective in this field of gut microbiome studies.

Omic-style statistical clustering reveals old and new patterns in the Gulf of Maine ecosystem

The burgeoning of omic technology has spawned a new subfield of statistics aimed at interpreting the complex information contained in omic data. Some of these statistical methods can be applied to any data set with taxonomic counts, and they have the potential to provide additional insights over traditional approaches. We test this potential by reanalyzing a well-studied zooplankton data set — the Gulf of Maine continuous plankton recorder series — using a modified Dirichlet-multinomial mixture (DMM) model. The data set has ∼50 years of approximately monthly samples along a transect from Boston, USA, to Yarmouth, Canada. The results from the DMM analysis were largely consistent with previous analyses but also provided new insights. Notably, the Calanus-dominated communities that returned following a reduction in the 1990s showed a loss of background diversity, suggesting a shift in sources and possibly higher vulnerability of these communities. The DMM analysis also revealed a breakdown of seasonal ecological succession in the 1990s. These changes could be a precursor to similar changes in other Calanus-dominated systems. The approach demonstrates a path toward linking traditional analyses with recent omic-style analyses.

Recent Advances and Perspective of Studies on Phlegm Syndrome in Chinese Medicine

This review paper summarized the current situation of studies on the essence of phlegm syndrome and relation between phlegm syndrome, diseases, and therapeutics based on published English articles. In studies on the essence of phlegm syndrome, omic technologies were used to explore the molecular basis of phlegm syndrome; in studies on relation between phlegm syndrome and diseases, discovery of markers of phlegm syndrome in diseases becomes a hotspot; the distribution of phlegm syndromes in some common chronic diseases was found; in the therapy of phlegm syndrome, two therapeutic models, treatment with CM formula and treatment with a combination of CM formula and Western medicine, were used most frequently. It is certainly that using one omic technology is not able to deal with the complexity of phlegm syndrome and that the use of a combination of multiple omic methods will be a trend in future studies. Meanwhile, for rapidly increasing clinical research quality of phlegm syndrome, a series of agreed criteria, such as syndrome diagnostic criteria and efficacy criteria clinical studies of phlegm syndrome, needed to be established urgently, and there was an urgent need of standardizing syndrome names in English.

Metabolomic Profiling in Perinatal Asphyxia: A Promising New Field

Metabolomics, the latest “omic” technology, is defined as the comprehensive study of all low molecular weight biochemicals, “metabolites” present in an organism. As a systems biology approach, metabolomics has huge potential to progress our understanding of perinatal asphyxia and neonatal hypoxic-ischaemic encephalopathy, by uniquely detecting rapid biochemical pathway alterations in response to the hypoxic environment. The study of metabolomic biomarkers in the immediate neonatal period is not a trivial task and requires a number of specific considerations, unique to this disease and population. Recruiting a clearly defined cohort requires standardised multicentre recruitment with broad inclusion criteria and the participation of a range of multidisciplinary staff. Minimally invasive biospecimen collection is a priority for biomarker discovery. Umbilical cord blood presents an ideal medium as large volumes can be easily extracted and stored and the sample is not confounded by postnatal disease progression. Pristine biobanking and phenotyping are essential to ensure the validity of metabolomic findings. This paper provides an overview of the current state of the art in the field of metabolomics in perinatal asphyxia and neonatal hypoxic-ischaemic encephalopathy. We detail the considerations required to ensure high quality sampling and analysis, to support scientific progression in this important field.