Our understanding of microbiomes, or the collection of microorganisms and their genes in a given environment, has been revolutionized by technological and computational advances. However, many undergraduate students do not get hands-on experiences with processing, analyzing, or interpreting these types of datasets. Recent global events have increased the need for effective educational activities that can be performed virtually and remotely. Here, we present a module that introduces STEM undergraduates to the bioinformatic and statistical analyses of bacterial communities using a combination of free, web-based data processing software. These lessons allow students to engage with the studies of microbiomes; gain valuable experiences processing large, high-throughput datasets; and practice their science communication skills. The lessons presented here walk students through two web-based platforms. The first (DNA Subway) is an easy-to-use wrapper of the popular QIIME (pronounced “chime”) pipeline, which performs quality control analysis of the raw sequence data and outputs a community matrix file with assigned bacterial taxonomies. The second, ranacapa, is an R Shiny App that allows students to compare microbial communities, perform statistical analyses and visualize community data. Students may communicate their findings with a written final report or oral presentation. While the lessons presented here use a sample dataset based on the gut-microbiome of the bean beetle (Callosobruchus maculatus), the materials are easily modified to use original next-generation amplicon sequence data from any host or environment. Additionally, options for alternative datasets are also provided facilitating flexibility within the curriculum.

Previous theoretical work has suggested that females should prefer to mate with older males, as older males should have higher fitness than the average fitness of the cohort into which they were born. However, studies in humans and model organisms have shown that as males age, they accumulate deleterious mutations in their germ-line at an ever-increasing rate, thereby reducing the quality of genes passed on to the next generation. Thus, older males may produce relatively poor-quality offspring. To better understand how male age influences female mate preference and offspring quality, we used a genetic algorithm model to study the effect of age-related increases in male genetic load on female mate preference. When we incorporate age-related increases in mutation load in males into our model, we find that females evolve a preference for younger males. Females in this model could determine a male's age, but not his inherited genotype nor his mutation load. Nevertheless, females evolved age-preferences that led them to mate with males that had low mutation loads, but showed no preference for males with respect to their somatic quality. These results suggest that germ-line quality, rather than somatic quality, should be the focus of female preference in good genes models.

Curricular reform efforts depend on our ability to determine how courses are taught and how instructional practices affect student outcomes. In this study, we developed a 30-question survey on inquiry-based learning and assessment in undergraduate laboratory courses that was administered to 878 students in 54 courses (41 introductory level and 13 upper level) from 20 institutions (four community colleges, 11 liberal arts colleges, and five universities, of which four were minority-serving institutions). On the basis of an exploratory factor analysis, we defined five constructs: metacognition, feedback and assessment, scientific synthesis, science process skills, and instructor-directed teaching. Using our refined survey of 24 items, we compared student and faculty perceptions of instructional practices both across courses and across instructors. In general, faculty and student perceptions were not significantly related. Although mean perceptions were often similar, faculty perceptions were more variable than those of students, suggesting that faculty may have more nuanced views than students. In addition, student perceptions of some instructional practices were influenced by their previous experience in laboratory courses and their self-efficacy. As student outcomes, such as learning gains, are ultimately most important, future research should examine the degree to which faculty and student perceptions of instructional practices predict student outcomes in different contexts.

Course-based undergraduate research experiences (CUREs) are an effective means of transforming the learning and teaching of science by involving students in the scientific process. The potential importance of the microbiome in shaping both environmental health and disease makes investigations of microbiomes an excellent teaching tool for undergraduate microbiology. Here, we present a CURE based on the microbiome of the bean beetle (Callosobruchus maculatus), a model system for undergraduate laboratory education. Despite the extensive research literature on bean beetles, little is known about their microbiome, making them an ideal system for a discovery-based CURE. In the CURE, students acquire microbiological technical skills by characterizing both culturable and unculturable members of the beetle gut-microbial community. Students plate beetle gut homogenates on different media, describe the colonies that are formed to estimate taxonomic diversity, extract DNA from colonies of interest, PCR amplify the16S rRNA gene for Sanger sequencing, and use the NCBI-nBLAST database to taxonomically classify sequences. Additionally, students extract total DNA from beetle gut homogenates for high-throughput paired-end sequencing and perform bioinformatic and statistical analyses of bacterial communities using a combination of open-access data processing software. Each activity allows students to engage with studies of microbiomes in a real-world context, to apply concepts and laboratory techniques to investigate either student or faculty-driven research questions, and to gain valuable experiences working with large high-throughput datasets. The CURE is designed such that it can be implemented over either 6-weeks (half semester) or 12-weeks (full semester), allowing for flexibility within the curriculum. Furthermore, student-generated data from the CURE (including bacterial colony phenotypic data, full-length 16S rRNA gene sequences from cultured isolates, and bacterial community sequences from gut homogenates) has been compiled in a continuously curated open-access database on the Bean Beetle Microbiome Project website, facilitating the generation of broader research questions across laboratory classrooms.

Over the past decade, repeated calls have been made to incorporate more active teaching and learning in undergraduate biology courses. The emphasis on inquiry-based teaching is especially important in laboratory courses, as these are the courses in which students are applying the process of science. To determine the current state of research on inquiry-based teaching in undergraduate biology laboratory courses, we reviewed the recent published literature on inquiry-based exercises. The majority of studies in our data set were in the subdisciplines of biochemistry, cell biology, developmental biology, genetics, and molecular biology. In addition, most exercises were guided inquiry, rather than open ended or research based. Almost 75% of the studies included assessment data, with two-thirds of these studies including multiple types of assessment data. However, few exercises were assessed in multiple courses or at multiple institutions. Furthermore, assessments were rarely based on published instruments. Although the results of the studies in our data set show a positive effect of inquiry-based teaching in biology laboratory courses on student learning gains, research that uses the same instrument across a range of courses and institutions is needed to determine whether these results can be generalized.

Although we agree with Theobold and Freeman (2014) that linear models are the most appropriate way in which to analyze assessment data, we show the importance of testing for interactions between covariates and factors.

Faculty development workshops are frequently used to bring about change in faculty teaching. Yet, the characteristics of successful faculty professional development in the context of laboratory teaching are unclear. In this Perspective, we describe our approach to intensive hands-on faculty development workshops for fostering change in laboratory teaching and present evidence for the effectiveness of the approach. The outcomes from our workshops and feedback from past participants support the following recommendations: 1) faculty should attend workshops in teams from their institutions, 2) workshops should allow participants to develop curricula that can be implemented with relatively little additional work after the workshop, 3) workshops should allow faculty time to “work” on tangible products and should involve hands-on activities, 4) workshops should be of sufficient duration to allow for faculty to develop expertise and tangible products but short enough that faculty do not “burn out,” and 5) a structure for ongoing and systematic follow-up with participants is essential.

Past studies on the differential effects of active learning based on students’ prior preparation and knowledge have been mixed. The purpose of the present study was to ask whether students with different levels of prior preparation responded differently to laboratory courses in which a guided-inquiry module was implemented. In the first study, we assessed student scientific reasoning skills, and in the second we assessed student experimental design skills. In each course in which the studies were conducted, student gains were analyzed by pretest quartiles, a measure of their prior preparation. Overall, student scientific reasoning skills and experimental design skills did not improve pretest to posttest. However, when divided into quartiles based on pretest score within each course, students in the lowest quartile experienced significant gains in both studies. Despite the significant gains observed among students in the lowest quartile, significant posttest differences between lowest and highest quartiles were observed in both scientific reasoning skills and experimental design skills. Nonetheless, these findings suggest that courses with guided-inquiry laboratory activities can foster the development of basic scientific reasoning and experimental design skills for students who are least prepared across a range of course levels and institution types.

Numerous national reports have called for reforming laboratory courses so that all students experience the research process. In response, many course-based research experiences (CREs) have been developed and implemented. Research on the impact of these CREs suggests that student benefits can be similar to those of traditional apprentice-model research experiences. However, most assessments of CREs have been in individual courses at individual institutions or across institutions using the same CRE model. Furthermore, which structures and components of CREs result in the greatest student gains is unknown. We explored the impact of different CRE models in different contexts on student self-reported gains in understanding, skills, and professional development using the Classroom Undergraduate Research Experience (CURE) survey. Our analysis included 49 courses developed and taught at seven diverse institutions. Overall, students reported greater gains for all benefits when compared with the reported national means for the Survey of Undergraduate Research Experiences (SURE). Two aspects of these CREs were associated with greater student gains: 1) CREs that were the focus of the entire course or that more fully integrated modules within a traditional laboratory and 2) CREs that had a higher degree of student input and results that were unknown to both students and faculty.

Course-based undergraduate research experiences (CUREs) rapidly have become more common in biology laboratory courses. The effort to implement CUREs has stimulated attempts to differentiate CUREs from other types of laboratory teaching. The Laboratory Course Assessment Survey (LCAS) was developed to measure students' perceptions of how frequently they participate in activities related to iteration, discovery, broader relevance, and collaboration in their laboratory courses. The LCAS has been proposed as an instrument that can be used to define whether a laboratory course fits the criteria for a CURE or not. However, the threshold LCAS scores needed to define a course as a CURE are unclear. As a result, we examined variation in published LCAS scores among different laboratory course types. In addition, we examined the distribution of LCAS scores for students enrolled in our research-for-credit course. Overall, we found substantial variation in scores among CUREs and broad overlap among course types in scores related to all three scales measured by the LCAS. Furthermore, the mean LCAS scores for all course types fell within the main part of the distribution of scores for our mentored research students. These results suggest that the LCAS cannot be used to easily quantify whether a course is a CURE or not. We propose that the biology education community needs to move beyond trying to quantitatively identify whether a course is a CURE. Instead, we should use tools like the LCAS to investigate what students are actually doing in their laboratory courses and how those activities impact student outcomes.