Biology subjects

Kaushik, K. S.

Publications and source records attributed to Kaushik, K. S..

6 recordsLinked to original sources

bioRxiv2023

Optotracers to study biofilms in host-relevant systems and non-conventional treatments using Staphylococcus aureus wound biofilms as a case study

Optotracers have a wide-range of applications in the detection, visualization, and characterization of biofilms. More recently, optotracers have been used in antibiotic susceptibility assays for biofilms and for the detection of biomarkers in clinical biofilm infections. This is particularly important, given that the field is increasingly focused on the evaluation of novel anti-biofilm agents and the study of biofilms in host-relevant systems. Given this, the possibility of using optotracers for an expanded set of biofilm focus areas is important to explore. In this study, we examine the application of the optotracer EbbaBiolight 680 to study biofilms in a host-relevant system and for the evaluation of a non-conventional anti-biofilm remedy. Using Staphylococcus aureus wound biofilms as a case study, we leverage a previously built in vitro 4-D wound microenvironment platform and a plant-based wound remedy. We find that EbbaBiolight 680 can be used to visualize S. aureus biofilms, likely detecting both bacterial cells and bacterial EPS components. Further, the optotracer can be used to evaluate and quantify the effects of the plant-based wound remedy on S. aureus biomass formation. However, in the 4-D wound microenvironment, EbbaBiolight 680 detected host cellular and matrix elements, which confounded the detection of biofilms. Taken together, this study opens the possibility of using optotracers as screening tools for the identification of novel anti-biofilm treatments and underscores the need for modifications for their use in host-relevant systems.

microbiology↗

bioRxiv2022

Biofilms with a dash of color: A hands-on activity for school students to build a biofilm model, and use it to understand antibiotic tolerance in biofilms

It is increasingly recognized that microbes, such as bacteria, exist in communities or biofilms, both in the environment and human body. However, school biology curriculum continues to focus on the free-floating form of bacterial life, with minimal descriptions of biofilms. Consequently, there is a need to introduce biofilms to school students, to not only to develop a fundamental understanding of microbial life, but to also highlight the challenges posed by biofilm infections to antibiotic treatment. We have developed a hands-on activity in which students build a biofilm model, and use it to understand the role of the extracellular matrix in the antibiotic tolerance of biofilms. The activity uses simple, easy to obtain supplies, and can be conducted in an in-person or virtual format, with students participating from school or home. We conducted the activity in virtual mode for a group of 59 school students across India, and present feedback and learnings that could be used to execute and adapt this accessible and engaging science experience.

scientific communication and education↗

bioRxiv2022

Adding a new dimension: Multi-level structure and organization of mixed-species Pseudomonas aeruginosa and Staphylococcus aureus biofilms in a 4-D wound microenvironment

Biofilms in wounds typically consist of aggregates of bacteria, most often Pseudomonas aeruginosa and Staphylococcus aureus, in close association with each other and the host microenvironment. Given this, the interplay across host and microbial elements, including the biochemical and nutrient profile of the microenvironment, likely influences the structure and organization of wound biofilms. While clinical studies, in vivo and ex vivo model systems have provided insights into the distribution of P. aeruginosa and S. aureus in wounds, they are limited in their ability to provide a detailed characterization of biofilm structure and organization across the host-microbial interface. On the other hand, biomimetic in vitro systems, such as host cell surfaces and simulant media conditions, albeit reductionist, have been shown to support the co-existence of P. aeruginosa and S. aureus biofilms, with species-dependent localization patterns and interspecies interactions. Therefore, composite in vitro models that bring together key features of the wound microenvironment could provide unprecedented insights into the structure and organization of mixed-species biofilms. We have built a four-dimensional (4-D) wound microenvironment consisting of a 3-D host cell scaffold of co-cultured human epidermal keratinocytes and dermal fibroblasts, and an in vitro wound milieu (IVWM); the IVWM provides the fourth dimension that represents the biochemical and nutrient profile of the wound infection state. We leveraged this composite 4-D wound microenvironment to probe the structure of mixed-species P. aeruginosa and S. aureus biofilms across multiple levels of organization such as aggregate dimensions and biomass thickness, species co-localization and organization within the biomass, overall biomass composition and interspecies interactions. In doing so, the composite 4-D wound microenvironment platform provides multi-level insights into the structure of mixed-species biofilms, which we incorporate into the current understanding of P. aeruginosa and S. aureus organization in the wound bed.

microbiology↗

bioRxiv2021

Of Biofilms and Beehives: An Analogy-Based Instructional Tool to Introduce Biofilms to High-School and Undergraduate Students

The concept of biofilms and biofilm-based research is largely absent or minimally described in high school and undergraduate life science curriculum. While it is well-established that microbes, such as bacteria and fungi most often exist in multicellular biofilm communities, descriptions in standard biology textbooks continue to focus on the single-celled form of microbial life. We have developed an analogy-based instructional tool to introduce and explain biofilms to high school and undergraduate students. The module employs an analogy with beehives, given that biofilms and beehives are both superorganism states, to explain key biofilm features such as development and structure, chemical communication, division of labor and emergent properties. We delivered this analogy based learning tool to a cohort of 49 high school and undergraduate students, and based on participant feedback and learnings, present a formal evaluation of the instructional tool. Further, we outline prerequisites and learning approaches that can enable the delivery of this module in classroom and virtual learning settings, including suggestions for pre-lesson reading, student-centred interactive activities, and specific learning objectives. Taken together, this instructional analogy holds potential to serve as an educational tool to introduce biofilms in high school and undergraduate curricula in a relatable and comprehensible manner.

scientific communication and education↗

bioRxiv2021

Milieu matters: An in vitro wound milieu to recapitulate key features of, and probe new insights into, polymicrobial biofilms

Bacterial biofilms are a major cause of delayed wound healing. Consequently, the study of wound biofilms, particularly in host-relevant conditions, has gained importance. Most in vitro biofilm studies employ refined laboratory media to study biofilms, conditions that are not relevant to the infection state. To mimic the wound milieu, in vitro biofilm studies often incorporate serum or plasma in growth conditions, or employ clot or matrix-based biofilm models. While incorporating serum or plasma alone is a minimalistic approach, the more complex in vitro wound models are technically demanding, and poorly compatible with standard biofilm assays. Based on previous reports of clinical wound fluid composition, we have developed an in vitro wound milieu (IVWM) that includes, in addition to serum (to recapitulate wound fluid), matrix elements and biochemical factors. In comparison with Luria-Bertani broth and Fetal Bovine Serum (FBS), the IVWM was used to study planktonic growth and biofilm features, including interspecies interactions, of common wound pathogens, Staphylococcus aureus and Pseudomonas aeruginosa. We demonstrate that the IVWM recapitulates widely reported in vivo biofilm features such as metabolic activity, increased antibiotic tolerance, 3D structure, and interspecies interactions for single- and co-species biofilms. Further, the IVWM is simple to formulate, uses laboratory-grade components, and is compatible with standard biofilm assays. Given this, it holds potential as a tractable approach to study wound biofilms under host-relevant conditions.

microbiology↗

bioRxiv2020

Towards 'Ancientbiotics' for Biofilms: How can we bring traditional medicinal remedies out of treatise and into contemporary science?

IntroductionTraditional medicinal remedies hold vast potential as novel antimicrobial agents, particularly for recalcitrant infection states such as biofilms. To explore their potential, it is important to bring these remedies out of ancient treatise and into present-day scientific evaluation. For traditional medical practices, this development pipeline starts with probing treatise for potential remedies and testing them for anti-biofilm effects, or the treatise to test phase. AimThe aim of this work is to present a primer for developing ancientbiotics against biofilms, that focuses on the treatise to test phase of the pipeline. Based on our approach and results, we provide insights into the considerations and challenges relevant to evaluating traditional remedies as anti-biofilm agents. MethodologyWe identified and reconstituted plant-based medicinal formulations from historical treatises of Indian traditional medicine, and analyzed their efficacy using widely-employed microtiter based assays, that constitute the cornerstone of biofilm studies. Measuring biomass and metabolic activity, we evaluated effects on biofilm formation and eradication of pre-formed biofilms, of Pseudomonas aeruginosa and Staphylococcus aureus. ResultsBased on recipes and preparation practices across several texts, and with modifications to ensure compatibility with modern scientific practices, three plant-based traditional remedies were identified and formulated in sesame oil (Bryophyllum pinnatum, Cynodon dactylon, and Ocimum tenuiflorum). We observed differential effects on biomass and metabolic activity on the biofilm formation and eradication of P. aeruginosa and S. aureus; highlighting the value of the microtiter-based assays as an initial screening tool for traditional remedies. ConclusionThrough this study, we provide insights into considerations relevant to the treatise to test phase of the ancientbiotics pipeline, such as identifying ancient remedies, reconstituting them with present-day modifications, and using in vitro assay formats for evaluation. The learnings in this primer will be relevant to both contemporary scientists and practitioners of ancient medicine, and will serve as a starting point for future studies exploring anti-biofilm approaches at the interface of historical and modern medicine.

microbiology↗