Abstracts
Jillian Banfield
Giant extrachromosomal elements and the three Domains of Life
Understanding of extrachromosomal elements (ECEs) of the three Domains of life has
grown extraordinarily over the past two decades, in part due to the development and
broad application of genome-resolved metagenomics. The genome sizes of these
ECEs are often obscured by assembly fragmentation, but this can be addressed to
some extent by genome curation and though long read sequencing. Classification of
ECEs now represented by genomes as viruses/phages, plasmids or “other” may be
difficult due to sequence divergence, but this can be somewhat circumvented via use of
in silico structure prediction methods. Bacteriophages (phages) with complete ~0.8
megabase pair (Mbp) genomes have now been described, as have enigmatic Mb-scale
linear genomes of some ECEs of archaea that we now suggest are giant archaeal
viruses. Given the existence of giant viruses of eukaryotes, there are now Mbp-scale
ECEs for all three Domains of life. Do these elements share a common ancestor or did
their huge sizes and vast gene inventories evolve independently? Our research now
suggests that virus-like Borg ECEs do not share a common ancestor with giant
eukaryotic viruses and that their many commonalities arose vis convergent evolution.
As the inventories of giant ECE sequences grow, it will be possible to explore, in detail,
the features and evolution of giant viruses and other ECEs.
Eugene Koonin
The world of viruses and its evolution through the lens of metagenomics and metatranscriptomics
Viruses and virus-like mobile genetic elements are ubiquitous parasites or symbionts of all cellular life forms and the most abundant biological entities on earth. The recent, unprecedented advances of comparative genomics, metagenomics and metatranscriptomics have led to the discovery of diverse novel groups of viruses and a rapid expansion of the chartered region of the virosphere. These discoveries provide for a vastly improved understanding of the evolutionary relationships within the virosphere. Arguably, we are approaching the point when the global architecture of the virus world can be outlined in its entirety, and the key evolutionary events in each of its domains can be reconstructed. I will present such an outline of the global organization of the virosphere and the corresponding megataxonomy, including 7 evolutionarily coherent virus realms, that has been recently approved by the International Committee on Taxonomy of Viruses, as well as additional candidate major taxa including new realms. The expansion of the prokaryotic virosphere that now includes many groups of viruses, particularly, those with RNA genomes, previously thought to be eukaryote-specific, will be emphasized. I will further discuss the position of viruses within the wider space of replicators and the recent dramatic expansion of the “alternative virosphere” that includes viroids and diverse viroid-like viruses that seem to have evolved on multiple, independent occasions.
Kasthuri Venkateswaran
Unlocking Extremophiles Hidden in NASA Spacecraft Assembly Environments
Is the rare microbiome real, and how can we uncover microorganisms that evade detection through metagenomics and metagenome-assembled genomes (MAGs)? Could single-cell genome assembly approaches hold the key to capturing these elusive microbes? What drives their resistance to cultivation, and can innovative strategies unlock their potential?
Extremophiles, often comprising less than 0.1% of the total microbial population, are notoriously difficult to detect in the NASA spacecraft assembly environments, where stringent decontamination and minimal nutrients suppress microbial activity. This reduced metabolic state results in the underrepresentation of these organisms in metagenomic sequencing data. Their resilience, particularly in spore form, complicates DNA extraction, further diminishing sequencing yields. Additionally, their genomes are often masked by more dominant species, limiting discovery.
The heavy reliance on existing reference databases exacerbates this issue. Without continuous updates reflecting newly identified extremophiles, many remain uncatalogued and thus undetected. Yet, understanding and cultivating these rare microbes are vital for industries like aerospace, pharmaceuticals, and medicine, where even small microbial populations can lead to significant consequences.
Over 15 years of microbiological surveillance at NASA cleanrooms and aboard the International Space Station (ISS) have led to the discovery of over 100 new species and the sequencing of 5,000 microbial isolates. This effort involved comprehensive physiological and phylogenomic analyses, revealing genetic markers and novel enzymes linked to nutrient-limited survival.
The quest to cultivate the rare microbiome has profound implications for astrobiology and life detection missions. Beyond deep sequencing and advanced DNA extraction, innovative cultivation methods remain crucial for uncovering the ecological roles of these extremophiles.
Evelien Adriaenssens
Viruses in the human gut microbiome: exploration in early life
Viruses are the most abundant biological entities on the planet. While a small minority of them have caused devastation around the globe, the vast majority of viruses have a beneficial effect on the ecosystem. In the human gut microbiome, the virome is mainly composed of bacteriophages, viruses infecting bacteria, with diet-associated viruses and potentially pathogenic viruses only making up a minor proportion of the total virome diversity.
Here, we are investigating the composition of the virome in pregnancy and early life from a cohort of mothers and infants from the East of England, focusing on transmission from mother to child as well as the prevalence of specific groups of viruses. We have found extensive sharing of viral operational taxonomic units between mothers and babies, including indirect evidence for co-infection.
We also took a closer look at the bacteriophages of the keystone microbiome member Bifidobacterium and found evidence of arms-race dynamics interactions between bifidobacteria and their infecting bacteriophages.
Deepa Agashe
Ecological drift in the flour beetle microbiome
Most eukaryotes harbor diverse and complex microbial communities. I will describe an interesting system – the red flour beetle – where the microbiome is beneficial for the host, but both the benefit and the microbial community structure vary dramatically. Across a 3-year period, the total load and composition of the bacterial community of laboratory stock populations fluctuated dramatically, cycling between a few dominant taxa and hundreds of rare taxa. Manipulative experiments suggest that this ecological drift is caused by changes in host population size and structure driven by laboratory maintenance protocols, as well as intrinsic differences in life stage-specific host-microbe interactions driven by host ecology. Unstable microbial communities can thus serve as great model systems to understand the evolution and ecology of diverse host-microbial interactions.
Karthik Anantharaman
Tracking Viral Ecology and Evolution in a Freshwater Lake Over Three Decades
Viruses including phage play a crucial role in human health, global ecosystem processes, and biogeochemistry. While uncultivated viral genomes are revolutionizing our understanding of viral diversity, ecology, and evolution, freshwater viruses remain significantly underexplored. As anthropogenic change begins to impact ecosystems globally, long-term ecological studies are emerging as powerful tools to investigate microbiome dynamics, evolution, and ecosystem change. However, such studies are rare in environmental microbiomes, and even less frequent on viral communities.
In this study, we recovered and studied 1.3 million viral genomes from 465 samples collected over a 20-year time-series of a model temperate freshwater lake, Lake Mendota, WI, USA. This comprehensive dataset provides unprecedented insights into viral ecological and evolutionary dynamics across time, seasons, and varying environmental conditions. First, this comprehensive investigation led to the identification of 578 auxiliary metabolic gene (AMG) families, encompassing over 150,000 AMGs. Strikingly, key AMGs associated with photosynthesis, methane oxidation, and hydrogen peroxide decomposition were found consistently in viruses across decades and seasons. This discovery establishes a foundation for understanding the long-term stability and functional significance of these viral AMGs. Second, our study addresses a critical gap in the current understanding of the evolutionary dynamics of viral populations over time in natural environments highlighting three key evolutionary processes: positive gene selection favoring fitness, reduced genomic heterogeneity over time, and the dominance of sub-populations carrying specific genes. These findings reveal new insights into the adaptive strategies of viruses in response to environmental pressures. Third, we illuminate the impact of environmental constraints, specifically inorganic carbon, ammonium, and magnesium, on viral abundances over time, and highlight roles of viruses in both “top-down” and “bottom-up” interactions in ecosystems. Overall, this pioneering long-term study underscores the profound implications of fine-scale, temporal observations of viruses in ecosystems that are critical to understanding the roles of viruses in nutrient, biogeochemical, and energy transformations within ecosystems.
Brett J Baker
The archaeal roots of eukaryotic life
There are several competing hypothetical scenarios for the origin of the eukaryotic cell. Hindering a greater understanding of these events is a lack of knowledge about the identity and nature of the archaeal host cell and its bacterial symbiont(s). Recently, we have obtained genomes belonging to archaea sharing a common ancestry with eukaryotes that have provided clues about this relationship. Phylogenetic analyses of these “Asgard” archaea have revealed they are diverse and consist of several uncultured candidate phyla, some of which are a sister group to eukaryotes (e.g. Heimdallarchaeota). These findings indicate that Asgard are direct descendants of the archaeal host that gave rise to eukaryotes. Genomic inference of the metabolisms of these archaea indicate they are capable of living in the presence of aerobic respiration pathways, suggesting that the archaeal host was capable of oxygen utilization prior to the acquisition of mitochondria. We have also recently characterized the lipid composition of these archaea and have identified ancestral mechanisms of symbiotic interactions. The identification and characterization of the closest archaea relative to eukaryotes is advancing our understanding of the biological events that led to the formation of the first eukaryotic cells.
Anshu Bhardwaj
Leveraging data driven approaches to understand and address complex diseases
AB-Data Science Lab is dedicated to unraveling the intricacies of complex phenotypes, with a keen focus on infectious and mitochondrial diseases. Our strategies encompass predicting potential drug targets in drug-resistant pathogens through network-based approaches, analyzing molecular function correlations between known drug-target pairs to identify new drug-target interactions for drug repurposing, employing structural alphabets to enhance genome annotation, and utilizing systems biology and machine learning to comprehend genotype-phenotype correlations. Over the years, we have developed numerous new algorithms and platforms that not only aid in discovering novel targets and inhibitors but also deepen our understanding of antimicrobial resistance and mitochondrial diseases. Our research has practical outcomes, including identifying new drug targets, designing innovative anti-infective agents based on structural insights and developing novel diagnostic methods. During the talk, we will discuss these methods and resources, highlighting their relevance in today's context. Additionally, we will discuss innovative educational approaches, such as video games, aimed at simplifying scientific concepts to raise awareness about some of the world's most urgent health challenges.
Narendra M Dixit
Linking interspecies interactions to microbial community structures
The design of stable multispecies communities relies on knowledge of underlying interspecies interactions. Here, we address two problems that challenge the establishment of precise links between such interactions and the resulting community structures. First, we consider high-order interactions, which involve 3 or more species, and devise an efficient algorithm that enables estimating the contributions from these interactions and predicting the resulting community structures. Second, we recognize that interactions between species are typically composed of positive and negative parts, the former from crossfeeding metabolites and the latter from competition for shared resources. We devise a strategy to disentangle these components, enabling, yet again, more accurate prediction of community structures. In both the scenarios above, we will draw connects with experimental data. We expect our algorithms to offer new, more robust handles to design communities and understand their behavior.
Veerendra Gadekar
Microbial Communities in Chennai Metro: Insights into the Urban Transit Microbiome
Urban public transport systems, particularly metro networks, act as focal points for microbial exchange. However, the urban microbiome in densely populated regions like India remains poorly characterized. These environments host diverse microbial communities, including both beneficial and potentially harmful species, with implications for public health. The COVID-19 pandemic further underscored the need to monitor microbial ecosystems, particularly antimicrobial resistance (AMR) genes, which may have escalated due to increased antibiotic use. In a first-of-its-kind study in India, we comprehensively characterized microbial communities and AMR gene prevalence in the Chennai Metro system. Surface swab samples from 12 stations were analyzed using whole-genome metagenomic sequencing. Comparative analysis with global urban microbiome datasets revealed distinct microbial profiles, including species unique to Chennai. Surface type significantly influenced microbial diversity, while AMR gene presence was minimal overall. These findings highlight unique microbial signatures in metro environments and emphasize the need for ongoing surveillance and targeted interventions to reduce potential exposure to harmful microbes in densely populated urban areas.
Yamini Jangir
Decoding microbial interactions in extreme environments
Microbial communities in extreme environments, such as terrestrial and marine subsurface, exhibit remarkable adaptability and metabolic diversity, enabling them to thrive under harsh conditions. These communities play pivotal roles in global biogeochemical cycles, driving carbon and nutrient turnover through intricate interspecies interactions and metabolic networks. Understanding these interactions is essential for uncovering the mechanisms that sustain life in these environments and their broader ecological and biotechnological implications.
This study focuses on decoding microbial interactions in anoxic marine sediments, using chitin degradation coupled to extracellular electron transfer as a model process. Employing methodologies, including electrochemical systems, 16S rRNA gene sequencing, FISH-BONCAT, and FIH-NanoSIMS, we reveal spatial and temporal dynamics of microbial community structure and function. Key findings include the identification of metabolic partnerships between chitin-degrading primary producers (Vallitalea sp2) and iron-reducing secondary consumers (Trichloromonas sp17), highlighting syntrophic cooperation as a critical driver of community stability.
Our results demonstrate how microbes adapt to environmental constraints, such as limited oxygen and nutrient availability, by leveraging division of labor and extracellular electron transfer to sustain metabolic activity. These insights provide a framework for understanding microbial ecology in extreme environments and offer strategies for leveraging these systems in bioelectrochemical applications, such as renewable energy production and bioremediation. By decoding these microbial interactions, we advance our knowledge of life in Earth's most extreme ecosystems and contribute to exploring their resilience and potential role in addressing global environmental challenges.
Fumito MARUYAMA
Unveiling the Hidden Dynamics of Non-Tuberculous Mycobacteria in Built Environments
Exploring microbial life in built environments is increasingly important for understanding human health. This presentation highlights genetic and ecological approaches to studying the transmission pathways of non-tuberculous Mycobacterium (NTM) species, particularly in residential settings. Non-tuberculous mycobacteria, common in water sources and households, can cause infections, mainly in elderly women and immunocompromised individuals. Understanding their environmental reservoirs and transmission pathways is crucial since they do not spread human-to-human.
Our research uses advanced genomic techniques to analyze bioaerosol samples from urban and rural settings. High-volume air samplers and long-read sequencing technologies identify microbial communities. We also examine the impact of environmental factors such as CO2 levels, temperature, and particulate matter on indoor microbial dynamics.
We have sequenced bioaerosol samples from urban and rural areas, showing significant differences in microbial community composition and diurnal variations in bioaerosol concentrations, which affect infection risks. Parameters like CO2 levels and temperature significantly influence indoor microbial counts. Real-time monitoring indicates the need to consider viable particulate matter when assessing ventilation's effects on microbial dynamics. Genome-wide association studies (GWAS) have identified specific genomic regions in NTM that differ in recombination frequency and type, contributing to understanding their evolutionary dynamics. Surveys of drinking water treatment plants in Hiroshima reveal various NTM species, with water treatment processes, including chlorine levels, affecting microbial community structures.
Our analysis of NTM in built environments highlights the need for precise and holistic methods to assess bioaerosol impacts on public health. We aim to standardize sampling and analytical procedures, improving risk assessments and informing public health interventions.
We plan to expand sampling efforts, enhance questionnaire methodologies, and conduct GIS analyses with more patient data. International and interdisciplinary collaboration will be crucial for advancing microbial genomics and ecology.
Keywords: Non-tuberculous Mycobacteria, Bioaerosol, Microbial Genomics, Indoor Air Quality, Environmental Microbiology
Georgios Miliotis
New horizons in One Health and the curious case of Kalamiella piersonii
Recent advances in space technology are rapidly paving the way for a sustained human presence beyond Earth. These developments necessitate a critical reassessment of health paradigms, given the potential impacts of microbial pathogens in non-terrestrial habitats. Within the New Horizons in One Health framework, the traditional concept of human–animal–environment interactions could be expanded to the edge of the anthroposphere, encompassing outer space. A prime example of this extended paradigm is Kalamiella piersonii.
Originally identified aboard the International Space Station, K. piersonii is the first bacterial genus to be initially identified and described beyond Earth, illustrating the adaptive potential of previously unknown microbial species in spaceflight conditions that may exhibit pathogenic traits. By charting K. piersonii’s genomic journey from terrestrial settings to orbit and back, this study discusses its distinct space-adaptive genomic features in comparison to Earth-based lineages, as well as its associations with invasive infections, antimicrobial resistance, and hypervirulence factors, including the putatively novel blaKALP1 beta-lactamase and the hypervirulence associated aerobactin loci. Mobile genetic elements underlying these genotypes and phenotypes are examined alongside broader genomic epidemiological patterns. Within the context of medical astro-microbiology, these findings highlight the unique microbiome challenges introduced by spaceflight and the potential public health risks posed by microbial transfer across planetary boundaries.
Ultimately, K. piersonii underscores the necessity of a multidisciplinary One Health approach that transcends the Kármán line, emphasizing proactive strategies to safeguard health both on Earth and beyond.
Niranjan Nagarajan
Tackling the global spread of AMR using genome-resolved metagenomics and AI
We live in a microbial world estimated to contain more than a million species, and yet humanity’s adversarial relationship with microbes is shaped by a small fraction of pathogenic species and the pervasive use of antimicrobial agents. Efforts to eradicate microbes often have limited success, with disinfected environments being rapidly recolonized, and antibiotic treatment increasingly selecting for resistant pathogens. The global rise in antimicrobial resistance (AMR) rates for common pathogens (e.g. ESKAPE) is recognized as a pre-eminent threat to healthcare systems. As the range of effective antibiotics shrinks we approach a tipping point where no antibiotic works for a pathogen, putting at risk the lives of millions of vulnerable patients in hospitals worldwide. Already >1 million deaths/year are attributed to AMR, and by 2050 the UN projects that AMR will be responsible for more deaths every year than all cancers (>10 million deaths/year).
We need new approaches to track the transmission of antibiotic resistance across microbes and to understand how we can leverage ecological functions to reduce AMR reservoirs. We propose that the emerging field of genome-resolved metagenomics aided by long-read sequencing [Bertrand et al, Nature Biotechnology 2019] can transform our ability to do microbial surveillance, and we showcase its application in tracking pathogens through hospital environments [Chng et al, Nature Medicine 2020] as well as the gut microbiome [Kang et al, Nature Microbiology 2022]. In order to decipher how microbial communities assemble and can provide colonization resistance against pathogens, we have developed new AI/modelling approaches that can provide mechanistic insights based on high-throughput metagenomic datasets [Li et al, Microbiome 2019; Li et al, PLoS Computational Biology 2021]. Together with other data mining approaches [Chng et al, Nature Ecology and Evolution 2020], we are now leveraging these to understand how microbiomes recover from the impact of antibiotics and how new classes of biotherapeutics can be developed to prevent the spread of antimicrobial resistant pathogens.
Jennifer Pett-Ridge
Pursuing Wild Microbes: Microbiome Interactions and Ecophysiological Traits that Shape the Persistence of Soil Carbon
Since the dawn of agriculture, cultivated soils have lost a vast amount of carbon to the atmosphere. Much of the organic matter stored in soil is microbial necromass, shaped by the traits of diverse organisms. To understand how microorganisms lead to stable persistent soil carbon, it is critical to understand how microbial ecophysiological traits are linked to soil organic matter formation, and how cross-kingdom interactions—involving bacteria, fungi, archaea, protists, microfauna and viruses—shape soil carbon availability and loss. Yet our current ability to predict ecosystem processes from microbiome data is poor. Why? I will suggest several key reasons, and will present results from studies where we have used quantitative stable isotope probing (SIP) and metagenomics/transcriptomics to assess growth and mortality of wild microbial and viral communities and show how niche differentiation in specific soil microhabitats (space and time) drives the soil carbon cycle.
Karthik Raman
Algorithmic Adventures in Microbial Ecosystems: Disentangling Complexities with Metabolic Modelling
In this talk, we explore complex microbial communities and the interactions therein using advanced computational methods and mathematical modelling. We focus on scalable algorithms and tools developed, notably the Panera algorithm, which generates Pan Genus Metabolic Models (PGMMs) to surmount uncertainties in the composition of communities. Panera enables us to better understand the metabolic capabilities across genera, by accounting for species variations. The talk will also broadly focus on network-based approaches to capture microbial interactions, illustrating the utility of graph-based approaches to elucidate metabolic exchanges and dependencies within communities. We apply these methodologies to investigate diverse environments, from deep-sea (hydrothermal vents) to outer space (the International Space Station)! The methodologies include genome-scale metabolic modelling, Metabolic Support Index (MSI), and the MetQuest algorithm, which enable us to interrogate complex microbial communities, quantifying interspecies support and metabolic interactions. Overall, our work seeks to build novel methodologies for understanding microbial interactions in microbiomes, leveraging them for clinical, industrial and environmental applications, broadly impacting health and sustainability.
Srivatsan Raman
Decoding, Understanding, and Engineering Bacteriophages at Scale with High-Throughput Tools
Bacteriophage research has emerged as an exciting new frontier in microbiology due to the role of phages in shaping microbiomes and as a potential therapy against drug-resistant bacterial infections. Over the decades, phage biologists have painstakingly isolated and characterized thousands of natural phages. Though invaluable in their scope, these studies often lack a molecular understanding of how sequence changes drive phage function. A major impediment to advancing phage biology from empirical observations to molecular function is the lack of high-throughput methods to systematically and comprehensively profile sequence-function relationships at the genome and gene levels. Traditional phage assays, such as plaque assays, simply do not scale for large functional genomics studies.
My laboratory has been at the forefront of developing high-throughput tools for phage genome engineering. In this presentation, I will describe our efforts to elucidate sequence-function relationships in phages through deep mutational scanning and genome-scale experiments using pooled selection experiments coupled to deep sequencing. I will talk about (a) understanding the sequence drivers of specificity and virulence encoded by the receptor-binding protein in phages and (b) categorizing phage genes as essential, non-essential, or conditionally essential across a wide range of hosts through genome-scale screens. Compared to traditional phage assays, our approach represents increased throughput by nearly four orders of magnitude. In addition to being a powerful tool to investigate phage biology, these high throughput approaches enable the design of synthetic phages with programmable properties against bacterial pathogens.
Shilpi Sharma
It takes four to tango: Harnessing the nexus between plants, microbiomes, soil, and environment for agricultural sustainability
The major impediment to agriculture worldwide is feeding the increasing population on continuously deteriorating arable land. The plant is no longer viewed as an independent entity but as a holobiont with its associated microbiomes, the latter being crucial for determining the host’s fitness. The interrelationship between the host plant, its associated microbiome, the soil, and the environment is being deciphered, and then harnessed by the group as a holistic approach for minimizing the use of chemicals. Engineering of the plant-associated microbiomes has shown promise as a sustainable approach to increasing plant productivity and maintaining soil health, especially for climate-resilient agriculture. In this context, the group adopts both top-down and bottom-up approaches of tailoring the microbiomes associated with plant roots. Using novel strategies of generating the optimal microbiomes as “next generation bioformulations”, the group has been attempting to mitigate biotic and abiotic stresses in agriculture.
Shruthi Sridhar Vembar
Malaria in India viewed through the lens of parasite, vector and microbiome diversity
Malaria, caused by eukaryotic parasites of the genus and transmitted by female Anopheline mosquitoes, remains prevalent in tropical and sub-tropical regions of the world, with an increasing risk of spread to temperate regions, owing to climate change. In recent years, studies in Africa have linked malaria transmission and severity to gut microbiota, both in the case of the human host and the vector. However, the impact of the microbiota on malaria in India, which bears the highest disease burden within Asia, is not known. This is where our interest lies, to explore malaria in India from a genomic and metagenomic perspective. To this end, we have performed population genomics studies to evaluate the genomic architecture of sp. in India. We have also begun population genomic and metagenomic studies of the two primary vectors of Indian malaria, (found in urban areas) and (found in rural and peri-urban areas). is especially interesting to study: it has five sibling species A, B, C, D and E, of which A, C , D and E can transmit malaria but not B. Whether this is due to genetic or microbiota differences is not clear, and this is an aspect we are currently investigating. Overall, alterations to the vector microbiota could emerge as a strategy to block transmission.
Paul Wilmes
From molecules to impact: Systems ecology of the human microbiome
The human microbiome, through its emergent properties, contributes essential functions to its host. Recent large-scale metagenomic studies have provided insights into its functional potential but have mostly focused on taxa-centric views. However, the functional repertoire which is actually contributed to human physiology remains largely unexplored. For example, the human microbiome produces a complex biomolecular cocktail in the form of small molecules, nucleic acids, and (poly-)peptides, recently defined as the expobiome. This cocktail has many bioactive properties but these have so far eluded systematic study. This overall gap in knowledge is limiting our understanding of the role of the human microbiome in governing human physiology and how changes to the microbiome impact chronic diseases including metabolic and neurological conditions through the triggering and exacerbation of disease pathways. Furthermore, without mechanistic understanding of the microbiome’s molecular complex, we are unable to rationally design microbiome-targeted therapies. In this context, the microbiome also represents a treasure trove for leads for the development of future diagnostic and therapeutic applications for chronic diseases. I will describe the current state of understanding of the functional microbiome in contrast to taxonomic views with a specific focus on microbiome-derived molecules in neurodegenerative diseases. Ranging from systematic integrated multi-omic analyses of the microbiome-borne molecular complex to mechanistic studies in novel experimental systems, a clear roadmap towards translating the functional ecology of the gut microbiome into novel diagnostic applications and drugs will be drawn.
Tanja Woyke
Genomics at the intersection of microbial communities and single cells
Microbial and viral diversity remains largely unexplored in laboratory settings. This underscores the continued importance of cultivation-independent methods for studying the genetic make-up of microbial and viral dark matter across diverse ecosystems. Metagenomics and single-cell sequencing are indispensable tools in microbiome research, offering insights into both the microbial identities present and the potential functions. In this presentation, I will discuss several studies conducted in my lab that use these approaches. While we use shotgun metagenomics, our focus also extends beyond traditional bulk techniques, as we try to find the needles in the haystack. To achieve this, we employ sorting and genome sequencing of individual environmental cells, using labeled probes or substrates as bait for targeted capture and investigations. Additionally, we explore genome sequences of microeukaryotes at the single-cell level, treating them as micro-consortia that may host bacterial endosymbionts or viral entities like giant viruses or virophages. This holistic approach helps us make predictions about inter-organismal interactions in the wild.
