Lab Manual

Welcome

Greetings and a warm welcome to the LEAPH Lab at Virginia Tech (VT)! We are thrilled to have you onboard as a part of our team. Together, we aim to push the boundaries of scientific knowledge and cultivate new skills. The primary purpose of this lab manual is to establish a shared foundation for everyone working in our group. Our hope is that your time spent in the lab will be both productive and enjoyable. To get it started, please refer to our onboarding checklist.

Vision

At the core of our mission is the aspiration to advance a mechanistic and predictive understanding of microbial biodiversity, ecosystem functioning, and environment-microbe interactions. We strive to apply this knowledge towards practical solutions that can foster improvements in environmental sustainability, food safety, and public health.

Mission

Research mission: Our research focuses on investigating the ecology and evolution of microbiomes, foodborne pathogens, and antimicrobial resistance within both natural and food-associated environments. To achieve this, we use a diverse array of methodologies, including field sampling, (meta)genomics, data analytics, machine learning, and laboratory experiments. Our ultimate goal is to characterize microorganisms in real-world settings and to develop ecologically-informed tools that can optimize the beneficial effects of microbes while minimizing their negative impact on environmental and human health.

Professional development mission: Our group’s research is inherently interdisciplinary, encompassing a broad range of fields such as microbiology, environmental science and engineering, ecology and evolution, and public health. By conducting both fundamental and applied research, we aim to train a new generation of scientists, engineers, and innovators who will be equipped with the skills and knowledge needed to address complex environmental and public health challenges. Ultimately, our research is focused on developing innovative and impactful solutions that will safeguard and enhance both environmental and public health.

Culture

Our primary goal is to cultivate a research group culture that places a premium on curiosity and innovation, while also fostering collaboration, diversity, and honest feedback. We strive to create an inclusive and empathetic environment that fosters mutual trust and respect among all members. Within our group, we firmly believe in the power of cooperation and reject competition. Just as mutualistic bacteria work together for the collective benefit of the community, we seek to support each other and promote mutual growth and development.

Responsibilities and Expectations

Principal Investigator

As the Principal Investigator of our group, my foremost responsibility is to enable and encourage the professional and scientific development of our members. Additionally, I am dedicated to ensuring that we stay true to our research and professional development mission and work towards fulfilling our long-term vision.

Mentoring: My primary responsibility is to work closely with each group member to develop and implement a personalized research and education plan that meets several objectives. Firstly, the plan must align with the specific deliverables of the project that the group member is working on. Additionally, it should provide each group member with the necessary training and resources to acquire the expertise required to achieve their research goals and advance towards their desired career objectives. I am committed to helping each group member navigate the challenges that may arise while working in an academic research environment and providing them with the knowledge and skills needed to excel in their chosen profession. Importantly, I view mentoring as a collaborative process that relies on open communication, mutual trust, and a willingness to invest time and energy from both parties. My ultimate goal is to support the success of each group member, even after they have left our research group.

Funding: My role as a mentor includes ensuring that all group members have access to the necessary resources to successfully execute their research projects. In this capacity, I am responsible for securing financial support for undergraduate, graduate, and post-graduate research projects, with the type and level of financial support being contingent on the specific research stage. Adequate funding is essential to cover expenses related to laboratory instrumentation and software, field work, experiments, computational work, publishing research, and supporting professional development activities such as conference and workshop travel. I am committed to ensuring that all group members receive full financial support in these areas. Furthermore, while I am responsible for identifying and pursuing funding opportunities, I also expect each group member to independently track funding opportunities and seek out their own sources of funding (e.g., the Graduate Research Development Program [GRDP] ). This approach benefits everyone involved by providing valuable learning experiences and enhancing CVs. I am happy to provide guidance on identifying appropriate funding opportunities and mentoring group members through the application process.

Safe, diverse, and inclusive environment: Creating an environment where every group member feels equally valued and respected is crucial to our success. As the leader of this group, I will do my best to foster such an environment by leading by example and ensuring that every group member is supported according to their unique needs and circumstances. It is also important to note that any form of discriminatory or abusive behavior will not be tolerated within the group. If any group member feels that they have been discriminated against based on protected criteria such as race, religious beliefs, gender/gender identity, sexual orientation, ethnicity, or nationality, they should feel safe to speak with me. Appropriate actions will be taken in accordance with VT’s policies.

Disagreements and conflicts are a natural part of any team environment. Ideally, conflicts should be resolved through open communication between group members as early as possible. If necessary, I will step in to facilitate a fair and impartial resolution to the best of my abilities. Let’s remember that we are a team, and we must work together to achieve our goals.

All Lab Members

Academic research provides a unique opportunity to cultivate expertise in a specific area while also developing a broad range of technical, experimental, computational, and soft skills. The expected outcome of a graduate/post-doctoral research experience is the creation of novel and impactful knowledge that benefits society while also training professionals who can work independently. To empower you to meet your personal goals, I have outlined some responsibilities and expectations below.

Plan: To maximize your productivity and reach your research goals, you should be proactive in planning and managing your work, including experimental design, timeline, and expected outcomes. While I am here to support you, it is crucial that you take ownership of your work and manage your time effectively. You should establish weekly priorities and set achievable deadlines to ensure that you meet your objectives. During our regular one-on-one meetings, we will collaborate to establish clear, agreed-upon deadlines for each phase of your work.

Organize: You are responsible for maintaining detailed records of your research, including notes, progress updates, code, and experimental results. As a requirement, all physical copies of laboratory/experiment notes must remain in the laboratory upon your departure, while all data and code must be securely maintained on VT’s Advanced Research Computing (ARC) systems and lab GitHub, respectively. It is recommended to backup work-related materials from your personal computer on a weekly basis, either on an external hard drive or cloud-based platform such as Google Drive. For further details, refer to the Logistics section.

Read: You are expected to take an active effort to keep up with literature in your field to (1) avoid repeating research that has already been done, (2) build on the work of others, and (3) generate new ideas. It is also helpful to read papers outside your own immediate focus area to identify ideas and methods that can be applied to your own research.

Think and ask: It is expected that you engage in deep thinking about your research and ask critical questions such as why, how, and what for. This includes reflecting on the importance of your research, understanding the workings of different methods and tools, and interpreting the meaning behind your results. By asking these questions, you can gain a deeper understanding of your research and contribute to its overall impact.

Publish: Our research is largely taxpayer funded, and and it is our responsibility to disseminate our findings to the scientific community and the general public. To achieve this, we publish peer-reviewed papers in reputable journals. The publishing expectations will differ depending on your career stage, and the requirements for graduate and post-doctoral researchers are listed separately. Keep in mind that quality outweighs quantity. Therefore, publishing fewer papers is acceptable provided they reflect higher scholarly impact. We encourage you to utilize the writing resources and training opportunities offered by VT to hone your scientific paper writing skills.

Working hours: You are free to arrange your own work schedule as long as you are meeting productivity and expectation standards. Ideally, I anticipate that you will be present in the lab/office during regular work hours (9:00 am - 5:00 pm) to facilitate interactions with your peers. My focus is on evaluating the progress that has been accomplished, rather than the specific time frame in which it was accomplished. The anticipated time commitment is elaborated on separately for graduate and post-doctoral researchers below.

Be courteous: Please ensure that you allocate enough time in your schedule for cleaning up after your experiments, analyses, or instrument use. In the event of instrumentation failure, please inform me immediately so that we can develop a plan to fix it and leave a note on the instrumentation indicating that it is not to be used. If a mistake is made, our objective is not to assign blame, but to ensure that we assess and address the consequences of the mistake appropriately and learn from it to prevent similar errors in the future. It is difficult to do this if mistakes are concealed, so if you are unsure, please do not hesitate to ask.

Graduate Students

Graduate researchers are expected to take full responsibility for their academic and research experience at VT. This entails making sure that they take the required courses and exams, such as qualifying exams, preliminary exams, and proposal/thesis defense, in a timely manner, as well as demonstrating dedication, professionalism, engagement, and upholding high ethical standards while fulfilling various aspects of their degree requirements. Note that the expectations outlined below applies to salaried graduate researchers. Graduate researchers paid by hours, volunteering, and/or working for course credits should discuss their expectations with me.

Time commitment: Graduate students are expected to devote 40 hours per week to activities related to their graduate degree, including coursework, research, and teaching assistantship. At the beginning of your program, it is typical to take more courses (usually three, but no more than four) to develop your skills and knowledge. Thus, you must effectively manage your time to balance coursework and research. As you progress, you will take fewer courses (possibly only one or none) and devote more attention to research, allowing you to complete a thesis or dissertation, publish your work, graduate, and advance your career.

Coursework: The requirements for courses may vary depending on your major and the stage of your graduate program, such as if you are an M.S. student, a direct Ph.D. student, or a Ph.D. student with an M.S. degree. For CEE students, to obtain this information, please review the latest CEE Graduate Student Handbook and EWR Degree Requirements. For GBCB students, please visit the program website. For more specific information, you can contact the program coordinator for your degree program, who would be the best point of contact for this matter. Once you have an idea of course requirements, we can work together to plan out the courses (1) you will need to take as part of the degree program and (2) ideal to take to help develop skills/expertise for your research projects.

Degree-specific deadlines: Besides the coursework, graduate programs have other requirements that must be met. These include passing qualifying exams, preliminary exams, and the final exam (dissertation defense). It’s crucial to identify these key exams and their expected timelines in your degree program. While the timeline for the dissertation defense can be flexible, the timelines for the other exams are usually predetermined. Be sure to identify these timelines early in your degree and incorporate them into your coursework planning.

Publications: Prior to graduation, Ph.D. students are expected to have at least 3 first-author journal papers published or submitted for publication, as well as having co-authored 2-3 additional papers in collaboration with other group members or external collaborators. On the other hand, thesis-track M.S. students are expected to have either published or submitted at least one paper as a first author or have made a significant contribution to at least one paper that is currently under submission.

Mentorship and training: It is expected of graduate researchers to play an active role in mentoring and training junior researchers. These responsibilities may include, but are not limited to: (1) providing guidance on experimental and computational methods utilized in research projects, (2) collaborating on ideas for experiments and data analysis, (3) offering constructive feedback on manuscripts, presentations, and posters, and (4) providing guidance on navigating the academic research experience. The mentoring process can be extremely rewarding for both the mentor and mentee in terms of professional development.

Postdocs

Postdoctoral researchers in the group may be interested in pursuing an academic career path, such as a faculty position. Therefore, the expectations outlined below are designed to facilitate a smooth and successful transition to an independent academic career. However, this may not be the case for all postdocs, and I am open to discussing a set of expectations and training plan that aligns better with your career goals.

Time commitment: Postdoctoral researchers are expected to work 40 hours per week in research-related activities (including mentoring).

Publications: Post-doctoral researchers are expected to lead on more than 1 paper per year as first author and co-author 1-2 papers per year through collaborative work with other group members.

Mentorship and training: As a postdoctoral researcher in the group, it is expected that you engage in mentoring and training of junior researchers. This involves activities such as (1) providing training on experimental and computational methods used in research projects, (2) collaborating on ideas for experiments and data analysis, (3) offering feedback on manuscripts, presentations, posters, etc., and (4) guiding junior researchers through the academic research experience.

Proposal writing: Securing research funding is a vital component of academic research labs. As the PI, I am responsible for providing postdoctoral researchers with the necessary training in proposal writing to enable them to launch their independent academic careers successfully. To accomplish this, I will encourage postdoctoral researchers to participate in the development of research proposals that I am working on and support their applications for funding opportunities to the best of my ability.

Undergraduate Students

We welcome undergraduate students to work in our group while fulfilling their degree requirements. As an undergraduate researcher, you are expected to (1) commit a minimum of 12 hours per week to research-related activities and ideally commit to working for at least one semester, (2) maintain a positive, solution-oriented, and curious attitude, (3) handle all lab equipment with care and maintain a well-organized and up-to-date lab notebook, (4) if your work is computational, document your code well on GitHub, (5) actively participate in laboratory group activities, and (6) represent the lab with pride, integrity, and respect for others. Moreover, you are expected to include your mentors and me on all communications related to lab research and to be mindful of what information you share about our work with people outside our group. If you are unsure about what can be shared and with whom, please consult with your mentor or me.

Meetings, Reporting, and Communications

Meetings

1:1 meetings: Weekly 1:1 meetings provide a chance to have detailed conversations about research objectives/progress and career advancement goals. Each member of the group is expected to attend these meetings.

It is expected that group members upload an agenda for their weekly 1:1 meeting to the “1-1 Meetings” folder in the group’s Google Drive at least one day in advance. Please be aware that the meeting agenda will be accessible to the entire group. If you have any items that you wish to discuss privately, please send a separate email to me or communicate via direct message on the group workspace on Slack.

The standard structure for the meeting agenda should consist of (1) discussion items, (2) accomplishments from the previous week, (3) plans for the upcoming week, and (4) notes taken during the meeting. It is encouraged to include as much detail as possible to reflect and summarize your weekly activities. A meeting agenda template can be accessed here.

Group meetings: The weekly group meetings provide a valuable opportunity for the entire group to come together and engage in discussions on a particular topic. Therefore, it is crucial for all group members to attend these meetings and avoid missing them. In the event that you are unable to attend any of the group meetings, please inform me in advance. These meetings usually involve a variety of activities such as journal clubs, research updates, invited presentations, and training sessions.

Semiannual Progress Report

At the end of every semester, group members are required to write a progress report which highlights their accomplishments, challenges, and learnings over the past semester, as well as their plans for the upcoming one. This report is an opportunity for you to provide feedback, and I encourage you to be honest so that I can support you better. To help you create your report, a semiannual progress report template is provided here.

Communications

Within LEAPH: For communication within the research group, we utilize a combination of email and Slack. Day-to-day communication should be conducted on Slack, while email should be used for formal communications (such as institutional communications) or communication with collaborators. Our group currently utilizes a free version of Slack that automatically deletes messages, including associated files/attachments, that are older than 90 days. Therefore, it is recommended to minimize the transfer of files/documents on Slack as much as possible and instead send them via email. We also use Google Group (leaph-g@vt.edu) to send one mail message that reaches all group members.

Outside LEAPH: Our lab places great importance on maintaining high standards for interactions outside the group as they reflect on our lab as a whole. Broadly speaking, lab-related interactions with non-lab members should be discussed and reviewed with me. Submitting conference abstracts, papers or scientific fellowships (i.e., those requiring a proposal), or the acceptance of speaking invitations, requires my approval and a review of the materials (e.g., abstract, slides, practice talk). For “Complicated” e-mails (e.g., dealing with data sharing, price negotiations, initiating collaborations, etc.), please discuss strategy with me first and cc me on all communications.

Logistics

Lab Safety and Training

Lab safety training: Before beginning any laboratory-based research, it is mandatory for all group members to complete the required trainings and comply with the health and safety guidelines outlined in the respective training. Our priority is always safety. Please carefully read the LEAPH Lab-Specific Biosafety Manual and SOPs available here. At the start of your tenure in the research group, we will utilize the Environmental Health and Safety website to identify all the trainings you are obligated to complete before commencing work in the laboratory.

Instrumentation: Before using any instrumentation, group members must receive training from a senior member or from me. All expensive instruments (over $10,000) will have a user log sheet, and both group members and external collaborators must record their use in the log. For these instruments, a group member will be designated as the instrumentation manager and will review the user log on a monthly basis and schedule service appointments. If an instrument breaks, please inform me and the designated group member so that we can develop a plan to fix it. In the meantime, please leave a post-it note with a “do not use” message on the instrument.

Data, Code, and Computing

Data: All of your data should be either stored on the VT’s ARC clusters or cloud (e.g., OneDrive, Google Drive). Your personal computer should never be used as the primary storage location. Additionally, you may choose to back up work-related materials from your personal computer onto an external hard drive on a weekly basis.

Code: It is expected that you regularly commit and push your code to our lab GitHub repositories. By “regularly,” we mean on a daily basis. Generally, the lab’s GitHub repositories should remain private until a paper is published. Additionally, we expect that your code will be written in Python.

Computing: If you require high-performance computing, please use ARC. We have created a tutorial to help you with the basic usage of ARC. Before submitting large jobs, it is important to ensure that your code has been thoroughly tested and that there is sufficient disk space available to save your results. It would be a waste of computing resources to run a job only to discover that your results were not saved due to a bug.

Absence and Time-off

Absences from work: If you anticipate being absent from the office or lab for more than two days (excluding weekends or public holidays), please inform me ahead of time. If you intend to work remotely for an extended period or will be taking a holiday longer than two days, please discuss the timing with me before confirming your plans.

Time-off: You are not expected to work during Virginia Tech’s official paid holidays, which can be found at here. On public holidays, there will be no regularly scheduled meetings. It is important for everyone to take time off to unwind and recharge. To facilitate this, each team member can take an additional 10 vacation days every year. Occasionally, some members may prefer to take a longer vacation and opt not to take a paid official holiday. They may choose to combine this with their travel plans or take a day off on a different holiday for religious reasons. If this is the case, please notify me in advance. If you need to take medical or family leave, please discuss this with me, and we will work out a plan on a case-by-case basis.

Publication and Authorship

Publications: We have outlined specific expectations for the number of papers per group member in the Responsibilities and Expectations section. Our aim is to ensure that our research is openly accessible, and we will strive to publish all manuscripts as open access. However, in some cases, the article processing charges (APCs) for open access publication may be prohibitively expensive. In such cases, we expect all publications to be deposited on the appropriate pre-print server (such as bioRxiv, engRxiv, medRxiv, etc.) prior to submission to a peer-reviewed journal. These pre-prints should be updated throughout the revision process.

Authorship: Our policy is that group members who contribute ideas, work, and time to research that leads to a manuscript should be credited as co-authors on that manuscript. Collaborative efforts typically lead to higher productivity and better scientific outcomes than independent work. We also value the importance of ownership in research. The order of authorship will generally follow the convention that the lead researcher on the paper will be the first author. In some cases, joint first authorship may be appropriate, and this should be discussed with me early in the process. If you ever feel like you are in competition with a lab member or collaborator, please let me know so that we can address the issue. Disagreements over authorship and author order can sometimes arise among collaborators, and we will work through these issues as needed.

Conference and Workshop Attendance

Conferences: Attending conferences is a crucial part of disseminating research, gaining recognition in the field, and networking, all of which are critical for professional growth. In our group, we typically attend conferences within specific domains, such as Applied and Environmental Microbiology (ASM) Microbe, Association of Environmental Engineering and Science Professors (AEESP) Research & Education Conference, and International Association for Food Protection (IAFP) Annual Meetings. Gordon Research Conferences (GRC), Cold Spring Harbor Laboratory (CSHL) Scientific Meetings, and American Geophysical Union (AGU) also offer conferences/meetings/workshops that are relevant to our research. If you are interested in attending a particular conference, it is your responsibility to stay on top of abstract submission and early registration deadlines. Before preparing the abstract, please discuss the conference of interest with me. You are also expected to share the first draft of the abstract with me at least 3-5 business days before the deadline. This will allow me to review and edit the abstract and obtain feedback from other internal or external co-authors with sufficient time.

As a general policy, I will cover the expenses associated with attending one conference per year per group member, including travel, registration, accommodation, and incidentals, provided that your abstract has been accepted for a poster or oral presentation. If the conference offers travel awards, please make sure to apply for them. Additionally, the VT Graduate School has a Travel Fund Program that provides funding for conferences and workshops. Graduate students in our group who wish to attend a conference are expected to apply for this travel support.

Workshops: If you are interested in attending a workshop that can enhance your research skills or professional growth, please inform me well in advance. We can assess whether attending the workshop aligns with your career stage and identify the most appropriate time to attend, if necessary. Many workshops offer financial assistance to participants, but these opportunities usually have early application deadlines. Therefore, it is crucial to plan ahead.

Scientific Conduct

Our lab is committed to conducting research that is rigorous, ethical, replicable, and validated to the best of our abilities. While our hypotheses guide our study design, our conclusions are ultimately driven by the data we collect. It is our responsibility to adhere to Virginia Tech’s policy on research integrity, and we all have different roles to play in ensuring the integrity of our experiments, data, code, analysis, and insights. As a member of our lab, you are responsible for the integrity of your work. If you are uncertain about an important point, it is your responsibility to investigate further or seek assistance. Our group members will support you in reviewing your results, helping you develop analyses and validations to ensure the accuracy of our research.

One area where we can improve as a lab is in maintaining the quality of our code. To avoid accumulating bugs, we encourage the use of frameworks that many lab members regularly utilize. Collaborating on existing code is only possible if we regularly push our code to Github, document it, and assist others in using it. Additionally, we implement peer code review to ensure that our code is error-free. We strive to make our research as reproducible as possible. After publication, we release our code, data, and often the code that generates our main figures. It is essential to transition from quick and dirty methods to well-documented, high-quality code for long-term reproducibility.

Mental Health Support

Performing research can be a thrilling experience, but it can also be challenging and stressful at times. If you or any of your colleagues are facing any obstacles or require any additional support, please do not hesitate to reach out to me or other members of the lab. We will work together to find solutions to address these concerns. Alternatively, you may explore various mental health resources available through VT to seek the necessary assistance.

Offboarding

Group members leaving the research group should complete a checklist below.

• Return office and laboratory keys
• Return laboratory notebooks
• Document location of your samples, reagents, data, code etc. in a word document along with photos when appropriate and email me the document with “[Laboratory Inventory – YOUR NAME] subject line
• If you have data that are stored in your personal computer, external hard drive, or cloud, please make a copy in the lab hard drive.
• If you need to maintain access to Slack workspace and shared Google Drive folder, please contact me.
• We encourage you to keep in touch with us even after you leave! We are always interested in hearing about your achievements, regardless of how big or small they may be. If you need any assistance or support, please don’t hesitate to reach out to us. We are always happy to help in any way we can!

Acknowledgements

This lab manual was inspired by several others, and borrows heavily from them (e.g., Pinto Lab, Lowe-Power Lab, and Korem Lab). It’s also a work in progress. If you have any suggestions or concerns regarding what should be added or clarified, feel free to discuss them with me.