Microbial Sciences Research Articles

Examination of public perceptions of microbes and microbiomes in the United States reveals insights for science communication.

Within a changing research and media landscape, misconceptions and misinformation about microorganisms and microbiomes can arise, necessitating improvements in science communication practices through insights in public perceptions of the microbial world. Yet, little is known about public perceptions of microorganisms and microbiomes, making it difficult to develop tailored messaging. Here we perform an inductive thematic analysis with interviews and surveys from thirty adults across the United States to identify key factors to enhance microbial science communication efforts. Together, our results underscore the importance of 1) recognizing the existing and desired future knowledge of an audience, 2) aligning with broader socio-scientific issues that resonate with people in relevant channels using social networks, 3) fostering collaboration between microbiologists, social scientists, and communicators to improve messaging, and 4) appealing to people's values and emotions to establish meaningful connections. This study concludes that non-microbial interests, such as an interest in health and wellness, may lead to acquisition of microbial knowledge and that people want scientists to share microbial messages preferably on platforms like social media. Additionally, we identified confusion about microbial terms and a desire to understand human-centric benefits of microorganisms and microbiomes. We suggest that microbiologists partner with science communicators to develop microbial messaging, capitalizing on connections to non-microbial interests and appealing to people's microbial worldview.

Perspectives on the future of ecology, evolution, and biodiversity from the Council on Microbial Sciences of the American Society for Microbiology.

The field of microbial ecology, evolution, and biodiversity (EEB) is at the leading edge of understanding how microbes shape our biosphere and influence the well-being of humankind and Earth. To that end, EEB is developing new transdisciplinary tools to analyze these ecologically critical, complex microbial communities. The American Society for Microbiology's Council on Microbial Sciences hosted a virtual retreat in 2023 to discuss the trajectory of EEB both within the Society and microbiology writ large. The retreat emphasized the interconnectedness of microbes and their outsized global influence on environmental and host health. The maximal potential impact of EEB will not be achieved without contributions from disparate fields that unite diverse technologies and data sets. In turn, this level of transdisciplinary efforts requires actively encouraging "broad" research, spanning inclusive global collaborations that incorporate both scientists and the public. Together, the American Society for Microbiology and EEB are poised to lead a paradigm shift that will result in a new era of collaboration, innovation, and societal relevance for microbiology.

Nature should be the model for microbial sciences.

Until recently, microbiologists have relied on cultures to understand the microbial world. As a result, model organisms have been the focus of research into understanding Bacteria and Archaea at a molecular level. Diversity surveys and metagenomic sequencing have revealed that these model species are often present in low abundance in the environment; instead, there are microbial taxa that are cosmopolitan in nature. Due to the numerical dominance of these microorganisms and the size of their habitats, these lineages comprise mind-boggling population sizes upward of 1028 cells on the planet. Many of these dominant groups have cultured representatives and have been shown to be involved in mediating key processes in nature. Given their importance and the increasing need to understand changes due to climate change, we propose that members of Nitrosophaerota (Nitrosopumilus maritimus), SAR11 (Pelagibacter ubique), Hadesarchaeia, Bathyarchaeia, and others become models in the future. Abundance should not be the only measure of a good model system; there are other organisms that are well suited to advance our understanding of ecology and evolution. For example, the most well-studied symbiotic bacteria, like Buchnera, Aliivibrio, and Rhizobium, should be models for understanding host-associations. Also, there are organisms that hold new insights into major transitions in the evolution of life on the planet like the Asgard Archaea (Heimdallarchaeia). Innovations in a variety of in situ techniques have enabled us to circumvent culturing when studying everything from genetics to physiology. Our deepest understanding of microbiology and its impact on the planet will come from studying these microbes in nature. Laboratory-based studies must be grounded in nature, not the other way around.

Unraveling emergent network indeterminacy in complex ecosystems: A random matrix approach

Indeterminacy of ecological networks-the unpredictability of ecosystem responses to persistent perturbations-is an emergent property of indirect effects a species has on another through interaction chains. Thus, numerous indirect pathways in large, complex ecological communities could make forecasting the long-term outcomes of environmental changes challenging. However, a comprehensive understanding of ecological structures causing indeterminacy has not yet been reached. Here, using random matrix theory (RMT), we provide mathematical criteria determining whether network indeterminacy emerges across various ecological communities. Our analytical and simulation results show that indeterminacy intricately depends on the characteristics of species interaction. Specifically, contrary to conventional wisdom, network indeterminacy is unlikely to emerge in large competitive and mutualistic communities, while it is a common feature in top-down regulated food webs. Furthermore, we found that predictable and unpredictable perturbations can coexist in the same community and that indeterminate responses to environmental changes arise more frequently in networks where predator-prey relationships predominate than competitive and mutualistic ones. These findings highlight the importance of elucidating direct species relationships and analyzing them with an RMT perspective on two fronts: It aids in 1) determining whether the network's responses to environmental changes are ultimately indeterminate and 2) identifying the types of perturbations causing less predictable outcomes in a complex ecosystem. In addition, our framework should apply to the inverse problem of network identification, i.e., determining whether observed responses to sustained perturbations can reconstruct their proximate causalities, potentially impacting other fields such as microbial and medical sciences.

Perspectives on the future of host-microbe biology from the Council on Microbial Sciences of the American Society for Microbiology.

Host-microbe biology (HMB) stands on the cusp of redefinition, challenging conventional paradigms to instead embrace a more holistic understanding of the microbial sciences. The American Society for Microbiology (ASM) Council on Microbial Sciences hosted a virtual retreat in 2023 to identify the future of the HMB field and innovations needed to advance the microbial sciences. The retreat presentations and discussions collectively emphasized the interconnectedness of microbes and their profound influence on humans, animals, and environmental health, as well as the need to broaden perspectives to fully embrace the complexity of these interactions. To advance HMB research, microbial scientists would benefit from enhancing interdisciplinary and transdisciplinary research to utilize expertise in diverse fields, integrate different disciplines, and promote equity and accessibility within HMB. Data integration will be pivotal in shaping the future of HMB research by bringing together varied scientific perspectives, new and innovative techniques, and 'omics approaches. ASM can empower under-resourced groups with the goal of ensuring that the benefits of cutting-edge research reach every corner of the scientific community. Thus, ASM will be poised to steer HMB toward a future that champions inclusivity, innovation, and accessible scientific progress.

Exabiome: Advancing Microbial Science through Exascale Computing

Exabiome: Advancing Microbial Science through Exascale Computing

First person – Alexander Whitehead

ABSTRACT First Person is a series of interviews with the first authors of a selection of papers published in Journal of Cell Science, helping researchers promote themselves alongside their papers. Alexander Whitehead is first author on ‘ AP-1 signaling modulates cardiac fibroblast stress responses’, published in JCS. Alexander conducted the research described in this article while an NSF GRFP Graduate Fellow in Adam Engler's lab at Sanford Consortium for Regenerative Medicine, La Jolla, USA. He is now a Hartwell Postdoctoral Fellow in the lab of Bruce Klein at Microbial Sciences Building, Madison, USA. His research interests include regenerative medicine, stem cell modeling, immunity and fibrosis.

Biotech and its Role in Agriculture: A Review

Throughout the course of recent many years, mechanical turns of events and modernization have developed concomitantly. For model, propels in biotechnology have been utilized as an apparatus to increment food creation. Progresses in hereditary designing have made conceivable the control of harvests to increment yield, ensuring food supplies for the rising total populace. In any case, transgenic crops have not been generally welcomed by all citizenry, and there is still vulnerability about their social advantages and the potential ramifications to human wellbeing. Biotechnology is the quickly developing portion in natural sciences. It has enhanced applications in practical farming. The survey manages microorganisms in biotechnology and their expanded applications in agribusiness as biofertilizers, bio-pesticides, bio-herbicides, bioinsecticides, contagious based bioinsecticides and viral based bioinsecticides. Further, exact portrayals have been made on Microbial science Environment Biotechnology and Reasonable agribusiness in the later piece of the audit. At last, a short feature has been given on the job of Microbial Biotechnology on Natural Wellbeing.

The effect of soil degradation on human, animal and plant health

The effect of soil degradation on human, animal and plant health Soil degradation is the biological, physical, chemical, and biological decline of soil quality or health. This phenomenon is problematic because it reduces the capacity of soils to support plant and animal life. Additionally, it reduces the ability of soils to regulate essential ecosystem services such as water regulation and nutrient cycling. Soil degradation has become a global issue and has come about largely due to land conversion from forests and grasslands to intensive agricultural practices. Land conversion depletes soil organic matter values, releasing large amounts of carbon dioxide into the atmosphere, contributing to global climate change and reducing soil fertility and soil health. Dr. Christine Sprunger, soil scientist and ecologist at W.K. Kellogg Biological Station (KBS) and the Department of Plant, Soil, and Microbial Sciences at Michigan State University, discusses the danger of soil degradation on human and animal life, and what we can do to mitigate it.

“Micro World – Exploring the Microbial Kingdom”: design and testing of a microbial VR science product

ABSTRACT We designed a microbial science popularization product based on virtual reality technology, “Micro World – Exploring the Microbial Kingdom,” and conducted usability tests. Participants used head-mounted VR glasses to experience virtual scenarios teaching microbiological knowledge. The product’s user experience was evaluated through a User Experience Questionnaire (UEQ), and the results showed that our product provided both usefulness and enjoyment. In addition, the quality of participants’ relevant knowledge acquisition was measured using the Student Education of Educational Quality (SEEQ). The SEEQ results show that “Micro World” is an effective tool for popularizing microbiology science and can actively promote students’ independent learning and improve learning quality.

The International Society for Biological and Environmental Repositories Presents Abstracts from Its Annual Meeting

The International Society for Biological and Environmental Repositories Presents Abstracts from Its Annual Meeting

Approaches for introducing large DNA molecules into bacterial cells.

Engineering of the bacterial genome plays a key role in systems biology and synthetic biology. Genetic engineering of the bacterial genome involves the design and synthesis of large DNA molecules. However, functional studies of the designed and synthesized large DNA molecules are lagging. Methods for the transformation of large DNA molecules of bacterial chromosome size into bacterial cells through a single operation have not yet been established. Two major methods can be used for transferring large DNA molecules of bacterial chromosome size into bacterial cells: transformation mediated by liposomes or by microinjection. In both methods, cell wall (peptidoglycan layer)-deficient cells (l-form, protoplast, or spheroplast) should be used as the bacterial host cells. We succeeded in transferring a heterologous bacterial genome into an enlarged bacterial protoplast using a micromanipulator. This method for transferring large DNA molecules into bacterial cells through a single operation will contribute to both fundamental and applied research in microbial genome science.

Plant and microbial sciences as key drivers in the development of metabolomics research

This year marks the 25th anniversary of the coinage of the term metabolome [S. G. Oliver et al., Trends Biotech. 16, 373–378 (1998)]. As the field rapidly advances, it is important to take stock of the progress which has been made to best inform the disciplines future. While a medical-centric perspective on metabolomics has recently been published [M. Giera et al., Cell Metab. 34, 21–34 (2022)], this largely ignores the pioneering contributions made by the plant and microbial science communities. In this perspective, we provide a contemporary overview of all fields in which metabolomics is employed with particular emphasis on both methodological and application breakthroughs made in plant and microbial sciences that have shaped this evolving research discipline from the very early days of its establishment. This will not cover all types of metabolomics assays currently employed but will focus mainly on those utilizing mass spectrometry–based measurements since they are currently by far the most prominent. Having established the historical context of metabolomics, we will address the key challenges currently facing metabolomics and offer potential approaches by which these can be faced. Most salient among these is the fact that the vast majority of mass features are as yet not annotated with high confidence; what we may refer to as definitive identification. We discuss the potential of both standard compound libraries and artificial intelligence technologies to address this challenge and the use of natural variance–based approaches such as genome-wide association studies in attempt to assign specific functions to the myriad of structurally similar and complex specialized metabolites. We conclude by stating our contention that as these challenges are epic and that they will need far greater cooperative efforts from biologists, chemists, and computer scientists with an interest in all kingdoms of life than have been made to date. Ultimately, a better linkage of metabolome and genome data will likely also be needed particularly considering the Earth BioGenome Project.

A holistic approach to assessing soil health

A holistic approach to assessing soil health In this Q&A, Dr Christine Sprunger, Assistant Professor of Soil Health in the Department of Plant, Soil, and Microbial Sciences assesses the chemical, physical, and biological processes of performing soil health assessments. With her research focusing on the intersection of agriculture and the environment, Dr. Sprunger notes how soil health has gained heightened attention from both farmers and scientists because of its association with agronomic performance and environmental sustainability, evaluating soil respiration, active carbon, soil protein, beneficial free-living nematodes. Dr. Sprunger, in this interview, analyses the importance of soil health research, finding the link between soil health and ecosystem services, how climate change influences soil health, and the future of soil health research in a factsheet for farmers interested in soil assessment.

Let's Have Some Clarity on Academic Parity

1Institute of Liver Studies, Department of Inflammation Biology, School of Immunology and Microbial Sciences, Faculty of Life Sciences and Medicine, King's College London, UK; 2Division of Gastroenterology and Hepatology, Department of Medicine, University of Toronto, Ontario, Canada. Correspondence: Florence Wong, MD. E-mail: [email protected].

To assemble or not to assemble: metagenomic profiling of microbially mediated biogeochemical pathways in complex communities.

High-throughput profiling of microbial functional traits involved in various biogeochemical cycling pathways using shotgun metagenomic sequencing has been routinely applied in microbial ecology and environmental science. Multiple bioinformatics data processing approaches are available, including assembly-based (single-sample assembly and multi-sample assembly) and read-based (merged reads and raw data). However, it remains not clear how these different approaches may differ in data analyses and affect result interpretation. In this study, using two typical shotgun metagenome datasets recovered from geographically distant coastal sediments, the performance of different data processing approaches was comparatively investigated from both technical and biological/ecological perspectives. Microbially mediated biogeochemical cycling pathways, including nitrogen cycling, sulfur cycling and B12 biosynthesis, were analyzed. As a result, multi-sample assembly provided the most amount of usable information for targeted functional traits, at a high cost of computational resources and running time. Single-sample assembly and read-based analysis were comparable in obtaining usable information, but the former was much more time- and resource-consuming. Critically, different approaches introduced much stronger variations in microbial profiles than biological differences. However, community-level differences between the two sampling sites could be consistently observed despite the approaches being used. In choosing an appropriate approach, researchers shall balance the trade-offs between multiple factors, including the scientific question, the amount of usable information, computational resources and time cost. This study is expected to provide valuable technical insights and guidelines for the various approaches used for metagenomic data analysis.

Unexplored Challenges of Minoritized Microbiologists in Academia.

The scientific community is making significant efforts to be inclusive and to promote diversity and equity. The microbial sciences are not the exception, and organizations, such as the American Society for Microbiology (ASM), are implementing strategic plans to advance these initiatives. However, one unexplored topic is whether the recruitment of minoritized microbiologists should use tailored programs for the success of trainees and faculty. Some challenges and opportunities are presented for consideration while developing recruitment, retention, and advancement programs in the microbial sciences.

Gaining control of bacterial cellulose colonization by polyhydroxyalkanoate-producing microorganisms to develop bioplasticized ultrathin films

Synergistic methodological strategies based on the fields of microbial biotechnology and materials science open up an enormous range of possibilities for the sustainable production of advanced materials with predictable properties. This study shows how naturally produced polyhydroxyalkanoate (PHA) particles are introduced into bacterial cellulose (BC) driven by their bacterial producers. Thanks to an extensive knowledge of the internal structure of BC, it was possible to control the colonization process, i.e. loading and localization of PHA. A subsequent acid treatment favored the PHA-BC bonding at the position reached by the bacteria. These biodegradable films showed improved mechanical and barrier properties even with respect to reference plastic films 8 times thicker, reaching a Young's modulus 4.25 times higher and an oxygen permeability 3 times lower than those of polyethylene terephthalate (PET) films. Owing to the versatility of the method, a wide variety of materials can be developed for very diverse fields of application.

Effective data filtering is prerequisite for robust microbial association network construction.

Microorganisms do not exist as individual population in the environment. Rather, they form complex assemblages that perform essential ecosystem functions and maintain ecosystem stability. Besides the diversity and composition of microbial communities, deciphering their potential interactions in the form of association networks has attracted many microbiologists and ecologists. Much effort has been made toward the methodological development for constructing microbial association networks. However, microbial profiles suffer dramatically from zero values, which hamper accurate association network construction. In this study, we investigated the effects of zero-value issues associated with microbial association network construction. Using the TARA Oceans microbial profile as an example, different zero-value-treatment approaches were comparatively investigated using different correlation methods. The results suggested dramatic variations of correlation coefficient values for differently treated microbial profiles. Most specifically, correlation coefficients among less frequent microbial taxa were more affected, whichever method was used. Negative correlation coefficients were more problematic and sensitive to network construction, as many of them were inferred from low-overlapped microbial taxa. Consequently, microbial association networks were greatly differed. Among various approaches, we recommend sequential calculation of correlation coefficients for microbial taxa pairs by excluding paired zero values. Filling missing values with pseudo-values is not recommended. As microbial association network analyses have become a widely used technique in the field of microbial ecology and environmental science, we urge cautions be made to critically consider the zero-value issues in microbial data.

Recent Findings in the Gut-Liver Axis and Associated Disease Therapy

Several presentations at the recent International Liver Congress™ (ILC), held in London, UK, from 22nd–26th of June 2022, addressed the role of the gut microbiome in chronic liver disease. Debbie L. Shawcross from the Department of Inflammation Biology, School of Immunology and Microbial Sciences, Institute of Liver Studies, King’s College London, UK, outlined the role of the gut-liver axis in the pathogenesis of cirrhosis, and how existing and novel therapies manipulate gut microbes. Emina Halilbasic from the Medical University of Vienna, Austria, and Benjamin H. Mullish from the Division of Digestive Diseases, Imperial College London, UK. Focused on the use of gut-based therapies in cholestatic liver disease. They explained the current understanding of the interplay between bile acids, microbiota, and the mucosal immune system, and the ways in which this may be manipulated for therapeutic gain. The role of gut barrier impairment in alcohol-related liver disease (ArLD) was presented by Shilpa Chokshi from the Roger Williams Institute of Hepatology, Foundation for Liver Research, London, UK, and School of Immunology and Microbial Sciences, Faculty of Life Sciences and Medicine, King’s College London, UK. Charlotte Skinner from the Department of Metabolism, Digestion, and Reproduction, Division of Digestive Diseases, Imperial College London, UK, described the role of gut proteases in this process, while Jasmohan S. Bajaj from the Virginia Commonwealth University, Richmond, USA, and Central Virginia Veterans Healthcare System, Richmond, USA, illustrated new therapies that target the gut-liver axis in this condition. Yue Shen from Zhongshan Hospital, Fudan University, Shanghai, China, and the Department of Gastroenterology and Hepatology, Shanghai Institute of Liver Diseases, China, described a combined microbiome-metabolome study to characterise the gut microbiome in hepatitis B virus infection-associated liver diseases (HBV-CLD), and how specific microbes might impact peripheral immunity. Finally, Bajaj outlined why the gut is a major target for hepatic encephalopathy (HE) treatment and described cutting edge research into therapies that show promise in this arena, such as soluble solid dispersion rifaximin, faecal microbiota transplantation (FMT), and rationally defined bacterial consortia. Overall, these presentations highlight an expanding knowledge of the gut-liver axis and promise an exciting future in liver treatment.