Microbiomes for All

Abstract

Microbiome research projects are often interdisciplinary, involving fields such as microbiology, genetics, ecology, evolution, bioinformatics, and statistics. These research projects can be an excellent fit for undergraduate courses ranging from introductory biology labs to upper-level capstone courses. Microbiome research projects can attract the interest of students majoring in health and medical sciences, environmental sciences, and agriculture, and there are meaningful ties to real-world issues relating to human health, climate change, and environmental sustainability and resilience in pristine, fragile ecosystems to bustling urban centers. In this review, we will discuss the potential of microbiome research integrated into classes using a number of different modalities. Our experience scaling-up and implementing microbiome projects at a range of institutions across the US has provided us with insight and strategies for what works well and how to diminish common hurdles that are encountered when implementing undergraduate microbiome research projects. We will discuss how course-based microbiome research can be leveraged to help faculty make advances in their own research and professional development and the resources that are available to support faculty interested in integrating microbiome research into their courses.

Communicating the utility of the microbiome and bioinformatics to small flock poultry producers

“…The idea of cross training between the disciplines of computer science and other fields such as food science may offer a partial solution to some of this by creating interactions between the 2 groups during classroom discussions ( Feye et al, 2020c ). This is also consistent with Muth and Caplan's (2020) observation that microbiome projects support development of critical thinking, problem solving, and collaboration skills which, in turn is more reflective of the changing requirements of the workforce. This holds true for food safety issues in the poultry food industries as well ( Dittmar et al, 2006 ; Ricke, 2015a ; Thompson et al, 2017 ).…”

“…Increased efforts to develop educational materials and laboratory exercises for microbiome training at both the high school and college undergraduate level may change the level of familiarity with microbiome/bioinformatics in the next generation. Muth and Caplan (2020) summarized the efforts in different universities to develop microbiome research projects for undergraduates. Based on their surveys of biology faculty, they concluded that for some aspects such as quantitative and data processing, the lack of basic computing background in students, insufficient bioinformatic lesson plans, coupled with the rapidly changing bioinformatic program content were challenges along with limited faculty expertise and time.…”

“…This holds true for food safety issues in the poultry food industries as well ( Dittmar et al, 2006 ; Ricke, 2015a ; Thompson et al, 2017 ). As Muth and Caplan (2020) suggest, the teaching elements involved in undergraduate microbiome research projects offer insights into topics of concern to the public sector such as climate change, food security, and human health.…”

Combating Antimicrobial Resistance Through Student-Driven Research and Environmental Surveillance

“…PARE provides an opportunity for scaffolding of different modules in different courses. In addition, it is complementary to other nationally-disseminated semester-long CUREs such as Tiny Earth/Small World Initiative ( Barral et al, 2014 , 2016 ; Hurley et al, 2020 ), SEA PHAGES ( Hatfull et al, 2006 ; Jordan et al, 2014 ), and Authentic Research Experience in Microbiology ( Muth and McEntee, 2014 ; Muth and Caplan, 2020 ). All are focused on some aspect of environmental microbiology, so together they provide ready-to-use options for scaffolding.…”

It is time to authenticate the Microbiome Sciences with accredited educational programs and departments

“…The answer is no. It does not simply fit into any one of those boxes, but rather it is the nexus of those and several other fields, thereby making it a unique synthesis-an intricate composite of field, wet lab, theoretical, and computational work aimed at decoding microbial interactions with hosts and with each other [11,12]. Similarly, microbiome researchers often experience a limbo in expertise, relating to the Shakespearean phrase, "a jack of all trades, a master of none."…”