Shift in the paradigm towards next-generation microbiology

In this work, the position of contemporary microbiology is considered from the perspective of scientific success, and a list of historical points and lessons learned from the fields of medical microbiology, microbial ecology and systems biology is presented. In addition, patterns in the development of top-down research topics that emerged over time as well as overlapping ideas and personnel, which are the first signs of trans-domain research activities in the fields of metagenomics, metaproteomics, metatranscriptomics and metabolomics, are explored through analysis of the publication networks of 28 654 papers using the computer programme Pajek. The current state of affairs is defined, and the need for meta-analyses to leverage publication biases in the field of microbiology is put forward as a very important emerging field of microbiology, especially since microbiology is progressively dealing with multi-scale systems. Consequently, the need for cross-fertilisation with other fields/disciplines instead of ‘more microbiology’ is needed to advance the field of microbiology as such. The reader is directed to consider how novel technologies, the introduction of big data approaches and artificial intelligence have transformed microbiology into a multi-scale field and initiated a shift away from its history of mostly manual work and towards a largely technology-, data- and statistics-driven discipline that is often coupled with automation and modelling.