Prokaryotes: the unseen majority

Surface-functionalized bacteria: Frontier explorations in next-generation live biotherapeutics

Screening robust living bacteria to produce living biotherapeutic products (LBPs) represents a burgeoning research field in biomedical applications. Despite their natural abilities to colonize bio-interfaces and proliferate, harnessing bacteria for such applications is hindered by considerable challenges in unsatisfied functionalities and safety concerns. Leveraging the high degree of customization and adaptability on the surface of bacteria demonstrates significant potential to improve therapeutic outcomes and achieve tailored functionalities of LBPs. This review focuses on the recent laboratory strategies of bacterial surface functionalization, which aims to address these challenges and potentiate the therapeutic effects in biomedicine. Firstly, we introduce various functional materials that are used for bacterial surface functionalization involving organic, inorganic, and biological materials. Secondly, the methodologies for achieving bacterial surface functionalization are categorized into three primary approaches including covalent bonding, non-covalent interactions, and hybrid techniques, while various advantages and limitations of different modification strategies are compared from multiple perspectives. Subsequently, the current status of the applications of surface-functionalized bacteria in bioimaging and disease treatments, especially in the treatment of inflammatory bowel disease (IBD) and cancer is summarized. Finally, challenges and pressing issues in the development of surface-functionalized bacteria as LBPs are presented.

Earth's most needed uncultivated aquatic prokaryotes

Aquatic ecosystems house a significant fraction of Earth's biosphere, yet most prokaryotes inhabiting these environments remain uncultivated. While recently developed genome-resolved metagenomics and single-cell genomics techniques have underscored the immense genetic breadth and metabolic potential residing in uncultivated Bacteria and Archaea, cultivation of these microorganisms is required to study their physiology via genetic systems, confirm predicted biochemical pathways, exploit biotechnological potential, and accurately appraise nutrient turnover. Over the past two decades, the limitations of culture-independent investigations highlighted the importance of cultivation in bridging this vast knowledge gap. Here, we collected more than 80 highly sought-after uncultivated lineages of aquatic Bacteria and Archaea with global ecological impact. In addition to fulfilling critical roles in global carbon, nitrogen, and sulfur cycling, many of these organisms are thought to partake in key symbiotic relationships. This review highlights the vital contributions of uncultured microbes in aquatic ecosystems, from lakes and groundwater to the surfaces and depths of the oceans and will guide current and future initiatives tasked with cultivating our planet's most elusive, yet highly consequential aquatic microflora.

Anthropogenic impacts on the terrestrial subsurface biosphere

The terrestrial subsurface is estimated to be the largest reservoir of microbial life on Earth. However, the subsurface also harbours economic, industrial and environmental resources, on which humans heavily rely, including diverse energy sources and formations for the storage of industrial waste and carbon dioxide for climate change mitigation. As a result of this anthropogenic activity, the subsurface landscape is transformed, including the subsurface biosphere. Through the creation of new environments and the introduction of substrates that fuel microbial life, the structure and function of subsurface microbiomes shift markedly. These microbial changes often have unintended effects on overall ecosystem function and are frequently challenging to manage from the surface of the Earth. In this Review, we highlight emerging research that investigates the impacts of anthropogenic activity on the terrestrial subsurface biosphere. We explore how humans alter the constraints on microbial life in the subsurface through drilling, mining, contamination and resource extraction, along with the resulting impacts of microorganisms on resource recovery and subsurface infrastructure.

Biofilm development on fractured rock in oligotrophic nitrate-rich groundwater: An in-situ bioreactor study

Biofilms drive all biogeochemical processes and represent the main mode of existence for active microbial life. Many past studies examined biofilm formation under static and eutrophic conditions, but those conditions are not representative of typical groundwater environments. In this study, we developed in situ bioreactors and methodologies to examine the influence of subsurface properties such as redox condition and lithology on the properties of naturally formed biofilms in two adjacent wells, a 30-m deep well completed in alluvium and a 120-m deep well in gneiss bedrock. The bulk chemistry of groundwater from the wells was similar, with neutral pH and abundant nitrate (21.9-24.6 mg/L), but redox conditions differed with depth (alluvial: oxic, gneiss bedrock: anoxic). Microbial community analysis revealed distinct clustering of biofilm community composition with the groundwater environment. Biofilm communities were consistently assembled by deterministic processes whereas planktonic communities had a higher influence of stochastic processes. Alluvial biofilms exhibited more diverse communities mainly composed of organotrophic aerobes capable of nitrate utilization. Bedrock biofilms indicated similar community compositions with groundwater where anaerobic denitrifiers coupled with sulfur oxidizers were dominant. Visualization and biomass quantification revealed distinct morphologies and development of biofilm along rock types and groundwater environments. Biofilm on gneiss surface had more biomass and formed a thin layered structure, compared to sandstone biofilm which had a randomly distributed pattern, implying that the morphology of biofilm was governed by the properties of the rock. Attached to unattached (planktonic) microbe ratios ranged from 3.9 × 103 to 1.2 × 104: 1 in the gneiss surface and 3.4 × 102 to 4.2 × 102: 1 in the sandstone surface in bedrock groundwater environment. Taken together, this study advances our understanding of subsurface biomass abundance and demonstrates that the in-situ bioreactors are effective for cultivating and analyzing of subsurface biofilms. Based on the specific field conditions tested, we found that biofilm can form stably on fractured rock surfaces within a year, with groundwater redox conditions shaping community composition and rock types determining biofilm volume and morphology. The methodologies presented here can be extended to other subsurface environments with varying groundwater geochemistry and lithology, which will help further refine estimates of microbial life and its role in subsurface ecosystems.

Biodiversity restated: > 99.9% of global species in Soil Biota

More than a decade of research led to the conclusion in 2022 that the Soil Biome is home to ~ 2.1 × 1024 taxa and thus supports > 99.9% of global species biodiversity, mostly Bacteria or other microbes, based upon topographic field data. A subsequent 2023 report tabulated a central value of just 1.04 × 1010 taxa claiming soils had 59 ± 15%, i.e., 44-74% (or truly 10-50%?) of the global total, while incidentally confirming upper values of ~ 90% for soil Bacteria. Incompatibility of these two studies is reviewed, supporting prior biodiversity data with the vast majority of species inhabiting soils, despite excluding viruses (now with ~ 5 × 1031 virions and 1026 species most, ~ 80%, in soils). The status of Oligochaeta (earthworms) and other taxa marked "?" in the 2023 paper are clarified. Although biota totals are increased considerably, inordinate threats of topsoil erosion and poisoning yet pertain with finality of extinction. Species affected include Keystone taxa, especially earthworms and microbes, essential for a healthy Soil foundation to sustain the Tree-of-Life inhabiting the Earth.

The role of kynurenine pathway metabolism mediated by exercise in the microbial-gut-brain axis in Alzheimer's disease

In recent years, the role of the microbiome-gut-brain axis in the pathogenesis of Alzheimer's disease (AD) has garnered increasing attention. Specifically, tryptophan metabolism via the kynurenine pathway (KP) plays a crucial regulatory role in this axis. This study reviews how exercise regulates the microbiome-gut-brain axis by influencing kynurenine pathway metabolism, thereby exerting resistance against AD. This paper also discusses how exercise positively impacts AD via the microbiome-gut-brain axis by modulating the endocrine, autonomic nervous, and immune systems. Although the specific mechanisms are not fully understood, research indicates that exercise may optimize tryptophan metabolism by promoting the growth of beneficial microbiota and inhibiting harmful microbiota, producing substances that are beneficial to the nervous system and combating AD. The aim of this review is to provide new perspectives and potential intervention strategies for the prevention and treatment of AD by exploring the links between exercise, KP and the gut-brain axis.

Number of global change factors alters the relative roles of abundant and rare microbes in driving soil multifunctionality resistance

There is increasing evidence that ecosystems are affected by multiple global change factors,1,2,3 impeding the sustainability of multiple soil functions.4 Biodiversity can buffer ecosystem functions against environmental changes, a concept largely supported by insurance and portfolio theories.5,6 However, the role of soil biodiversity, especially the diversity of abundant and rare microbial taxa, in regulating soil multifunctionality resistance under an increasing number of global change factors remains poorly explored. Here, we assessed the effects of the diversity of abundant and rare microbial taxa on soil multifunctionality resistance under different numbers of global change factors using 650 microcosms. The increasing number of global change factors reduced the effects of the diversity of abundant and rare microbial taxa on soil multifunctionality resistance and shifted their relative importance. The diversity of abundant taxa showed stronger positive effects on soil multifunctionality resistance under one or two global change factors. However, the diversity of rare taxa had stronger effects under multiple co-acting global change factors. The resistance of abundant and rare microbial taxa was significantly associated with their respective diversity effects on soil multifunctionality resistance. These effects were represented by standardized slopes that evaluated the relationships between microbial diversity and multifunctionality resistance under varying numbers of global change factors. Our findings indicate a shift in the relative importance of the diversity of abundant and rare microbial taxa in regulating soil multifunctionality resistance with an increasing number of global change factors, providing new insights into the relationship between soil biodiversity and ecosystem stability under environmental disturbances.

S-layers: from a serendipitous discovery to a toolkit for nanobiotechnology

Prokaryotic microorganisms, comprising Bacteria and Archaea, exhibit a fascinating diversity of cell envelope structures reflecting their adaptations that contribute to their resilience and survival in diverse environments. Among these adaptations, surface layers (S-layers) composed of monomolecular protein or glycoprotein lattices are one of the most observed envelope components. They are the most abundant cellular proteins and represent the simplest biological membranes that have developed during evolution. S-layers provide organisms with a great variety of selective advantages, including acting as an antifouling layer, protective coating, molecular sieve, ion trap, structure involved in cell and molecular adhesion, surface recognition and virulence factor for pathogens. In Archaea that possess S-layers as the exclusive cell wall component, the (glyco)protein lattices function as a cell shape-determining/maintaining scaffold. The wealth of information available on the structure, chemistry, genetics and in vivo and in vitro morphogenesis has revealed a broad application potential for S-layers as patterning elements in a molecular construction kit for bio- and nanotechnology, synthetic biology, biomimetics, biomedicine and diagnostics. In this review, we try to describe the scientifically exciting early days of S-layer research with a special focus on the 'Vienna-S-Layer-Group'. Our presentation is intended to illustrate how our curiosity and joy of discovery motivated us to explore this new structure and to make the scientific community aware of its relevance in the realm of prokaryotes, and moreover, how we developed concepts for exploiting this unique self-assembly structure. We hope that our presentation, with its many personal notes, is also of interest from the perspective of the history of S-layer research.

Selected Mechanisms of Action of Bacteriophages in Bacterial Infections in Animals

Bacteriophages, as ubiquitous bacterial viruses in various natural ecosystems, play an important role in maintaining the homeostasis of the natural microbiota. For many years, bacteriophages were not believed to act on eukaryotic cells; however, recent studies have confirmed their ability to affect eukaryotic cells and interact with the host immune system. Due to their complex protein structure, phages can also directly or indirectly modulate immune processes, including innate immunity, by modulating phagocytosis and cytokine reactions, as well as acquired immunity, by producing antibodies and activating effector cells. They can therefore have a profound impact on the course of bacterial infections by stimulating and at the same time inhibiting the systemic pro-inflammatory response. This review article presents a characterization of the processes by which bacteriophages affect selected immune mechanisms in selected animal species. The results of our own experiments using calves are also presented as examples. The paper contains many new examples of potential uses of bacteriophages and their effects on eukaryotic cells, especially in the course of bacterial infections, which are extremely important in experimental treatments exploiting phages as alternatives to antibiotics. The positive results of the effects of bacteriophages on eukaryotic cells during infections open up promising new prospects for their use as natural tools in the treatment of bacterial, fungal, and viral diseases in animals and humans.

Microhabitat accessibility determines peptide substrate degradation by soil microbial community

Soil pore space, considered the most complex biomaterial that exists, generates a complex environment, that gives rise to a wide variety of properties, such as microbial diversity and carbon storage. Soils contain, at the same time, the largest carbon reservoir on earth and an immense amount of nutrient-limited microbial biomass. The reason why this carbon is not consumed by soil microbes is attributed to the complex nature of soil, which forms a labyrinth where carbon and microbes cannot be in direct contact. In the present study, by using microfluidics, we tested the effect of labyrinth-like structures of decreasing accessibility on the decomposing activity of soil microbial communities from a soil inoculum. The two parameters used to study the effect of microhabitat accessibility were either the turning angle in an array of channel-like pore structures or the fractal order in an array of maze-like pore structures. We found that in both cases, channels and mazes, decreasing accessibility produced a higher peptide substrate degradation. When we analyzed the degradation within the structures, we found that most of the activity is concentrated in the regions of intermediate accessibility. We think that the increased degradation activity in low accessibility mazes might be due to the reduced interactions within the microbial communities which leads to a reduction in competition. Lowered competition allows different communities with a wide range of metabolic strategies to cohabit in the structures, which resulted in a bulk increase of the peptide substrate degradation.IMPORTANCEThe role microbes have in the environment is highly influenced by the characteristics of their habitat. Here, we show that a complex habitat enhances the enzymatic activity of a soil microbial inoculum. This might occur due to a reduced competition in complex habitats, which allows a more diverse community to coexist and explore a wider variety of metabolic strategies. The different rates of enzymatic activity in different levels of complexity suggest emergent properties of microbial communities in complex microhabitats which could have important implication for microbial processes, such as soil carbon storage and nutrient cycling.

The Gut Microbiota-Related Antihyperglycemic Effect of Metformin

It is critical to sustain the diversity of the microbiota to maintain host homeostasis and health. Growing evidence indicates that changes in gut microbial biodiversity may be associated with the development of several pathologies, including type 2 diabetes mellitus (T2DM). Metformin is still the first-line drug for treatment of T2DM unless there are contra-indications. The drug primarily inhibits hepatic gluconeogenesis and increases the sensitivity of target cells (hepatocytes, adipocytes and myocytes) to insulin; however, increasing evidence suggests that it may also influence the gut. As T2DM patients exhibit gut dysbiosis, the intestinal microbiome has gained interest as a key target for metabolic diseases. Interestingly, changes in the gut microbiome were also observed in T2DM patients treated with metformin compared to those who were not. Therefore, the aim of this review is to present the current state of knowledge regarding the association of the gut microbiome with the antihyperglycemic effect of metformin. Numerous studies indicate that the reduction in glucose concentration observed in T2DM patients treated with metformin is due in part to changes in the biodiversity of the gut microbiota. These changes contribute to improved intestinal barrier integrity, increased production of short-chain fatty acids (SCFAs), regulation of bile acid metabolism, and enhanced glucose absorption. Therefore, in addition to the well-recognized reduction of gluconeogenesis, metformin also appears to exert its glucose-lowering effect by influencing gut microbiome biodiversity. However, we are only beginning to understand how metformin acts on specific microorganisms in the intestine, and further research is needed to understand its role in regulating glucose metabolism, including the impact of this remarkable drug on specific microorganisms in the gut.

The mOTUs online database provides web-accessible genomic context to taxonomic profiling of microbial communities

Determining the taxonomic composition (taxonomic profiling) is a fundamental task in studying environmental and host-associated microbial communities. However, genome-resolved microbial diversity on Earth remains undersampled, and accessing the genomic context of taxa detected during taxonomic profiling remains a challenging task. Here, we present the mOTUs online database (mOTUs-db), which is consistent with and interfaces with the mOTUs taxonomic profiling tool. It comprises 2.83 million metagenome-assembled genomes (MAGs) and 919 090 single-cell and isolate genomes from 124 295 species-level taxonomic units. In addition to being one of the largest prokaryotic genome resources to date, all MAGs in the mOTUs-db were reconstructed de novo in 117 902 individual samples by abundance correlation of scaffolds across multiple samples for improved quality metrics. The database complements the Genome Taxonomy Database, with over 50% of its species-level taxonomic groups being unique. It also offers interactive querying, enabling users to explore and download genomes at various taxonomic levels. The mOTUs-db is accessible at https://motus-db.org.

Strain identity effects contribute more to Pseudomonas community functioning than strain interactions

Microbial communities can shape key ecological services, but the determinants of their functioning often remain little understood. While traditional research predominantly focuses on effects related to species identity (community composition and species richness), recent work increasingly explores the impact of species interactions on community functioning. Here, we conducted experiments with replicated small communities of Pseudomonas bacteria to quantify the relative importance of strain identity versus interaction effects on two important functions, community productivity and siderophore production. By combining supernatant and competition assays with an established linear model method, we show that both factors have significant effects on functioning, but identity effects generally outweigh strain interaction effects. These results hold irrespective of whether strain interactions are inferred statistically or approximated experimentally. Our results have implications for microbiome engineering, as the success of approaches aiming to induce beneficial (probiotic) strain interactions will be sensitive to strain identity effects in many communities.

Moving Toward Metaproteogenomics: A Computational Perspective on Analyzing Microbial Samples via Proteogenomics

Microbial sample analysis has received growing attention within the last decade, driven by important findings in microbiome research and promising applications in the biotechnological field. Modern mass spectrometry-based methodology has been established in this context, providing sufficient sensitivity, resolution, dynamic range, and throughput to analyze the so-called metaproteome of complex microbial mixtures from clinical or environmental samples. While proteomic analyses were previously restricted to common model organisms, next-generation sequencing technologies nowadays allow for the rapid and cost-efficient characterization of whole metagenomes of microbial consortia and specific genomes from non-model organisms to which microbes contribute by significant amounts. This proteogenomic approach, meaning the combined application of genomic and proteomic methods, enables researchers to create a protein database that presents a tailored blueprint of the microbial sample under investigation. This contribution provides an overview of the computational challenges and opportunities in proteogenomics and metaproteomics as of January 2018. For practical application, we first showcase an integrative proteogenomic method that circumvents existing reference databases by creating sample-specific transcripts. The underlying algorithm uses a graph network approach that combines RNA-Seq and peptide information. As a second example, we provide a tutorial for a simulation tool that estimates the computational limits of detecting microbial non-model organisms. This method evaluates the potential influence of error-tolerant searches and proteogenomic approaches on databases of interest. Finally, we discuss recommendations for developing future strategies that may help overcome present limitations by combining the strengths of genome- and proteome-based methods and moving toward an integrated metaproteogenomics approach.

Unveiling gut microbiota's role: Bidirectional regulation of drug transport for improved safety

Drug safety is a paramount concern in the field of drug development, with researchers increasingly focusing on the bidirectional regulation of gut microbiota in this context. The gut microbiota plays a crucial role in maintaining drug safety. It can influence drug transport processes in the body through various mechanisms, thereby modulating their efficacy and toxicity. The main mechanisms include: (1) The gut microbiota directly interacts with drugs, altering their chemical structure to reduce toxicity and enhance efficacy, thereby impacting drug transport mechanisms, drugs can also change the structure and abundance of gut bacteria; (2) bidirectional regulation of intestinal barrier permeability by gut microbiota, promoting the absorption of nontoxic drugs and inhibiting the absorption of toxic components; (3) bidirectional regulation of the expression and activity of transport proteins by gut microbiota, selectively promoting the absorption of effective components or inhibiting the absorption of toxic components. This bidirectional regulatory role enables the gut microbiota to play a key role in maintaining drug balance in the body and reducing adverse reactions. Understanding these regulatory mechanisms sheds light on novel approaches to minimize toxic side effects, enhance drug efficacy, and ultimately improve drug safety. This review systematically examines the bidirectional regulation of gut microbiota in drug transportation from the aforementioned aspects, emphasizing their significance in ensuring drug safety. Furthermore, it offers a prospective outlook from the standpoint of enhancing therapeutic efficacy and reducing drug toxicity, underscoring the importance of further exploration in this research domain. It aims to provide more effective strategies for drug development and treatment.

Microbial diversity and biogeochemical interactions in the seismically active and CO2- rich Eger Rift ecosystem

The Eger Rift subsurface is characterized by frequent seismic activity and consistently high CO2 concentrations, making it a unique deep biosphere ecosystem and a suitable site to study the interactions between volcanism, tectonics, and microbiological activity. Pulses of geogenic H2 during earthquakes may provide substrates for methanogenic and chemolithoautotrophic processes, but very little is currently known about the role of subsurface microorganisms and their cellular processes in this type of environment. To assess the impact of geologic activity on microbial life, we analyzed the geological, geochemical, and microbiological composition of rock and sediment samples from a 238 m deep drill core, running across six lithostratigraphic zones. We evaluated the diversity and distribution of bacterial and archaeal communities. Our investigation revealed a distinct low-biomass community, with a surprisingly diverse archaeal population, providing strong support that methanogenic archaea reside in the Eger subsurface. Geochemical analysis demonstrated that ion concentrations (mostly sodium and sulfate) were highest in sediments from 50 to 100 m depth and in weathered rock below 200 m, indicating an elevated potential for ion solution in these areas. Microbial communities were dominated by common soil and water bacteria. Together with the occurrence of freshwater cyanobacteria at specific depths, these observations emphasize the heterogenous character of the sediments and are indicators for vertical groundwater movement across the Eger Rift subsurface. Our investigations also found evidence for anaerobic, autotrophic, and acidophilic communities in Eger Rift sediments, as sulfur-cycling taxa like Thiohalophilus and Desulfosporosinus were specifically enriched at depths below 100 m. The detection of methanogenic, halophilic, and ammonia-oxidizing archaeal populations demonstrate that the unique features of the Eger Rift subsurface environment provide the foundation for diverse types of microbial life, including the microbial utilization of geologically derived CO2 and, when available, H2, as a primary energy source.

A global comparison of surface and subsurface microbiomes reveals large-scale biodiversity gradients, and a marine-terrestrial divide

Subsurface environments are among Earth's largest habitats for microbial life. Yet, until recently, we lacked adequate data to accurately differentiate between globally distributed marine and terrestrial surface and subsurface microbiomes. Here, we analyzed 478 archaeal and 964 bacterial metabarcoding datasets and 147 metagenomes from diverse and widely distributed environments. Microbial diversity is similar in marine and terrestrial microbiomes at local to global scales. However, community composition greatly differs between sea and land, corroborating a phylogenetic divide that mirrors patterns in plant and animal diversity. In contrast, community composition overlaps between surface to subsurface environments supporting a diversity continuum rather than a discrete subsurface biosphere. Differences in microbial life thus seem greater between land and sea than between surface and subsurface. Diversity of terrestrial microbiomes decreases with depth, while marine subsurface diversity and phylogenetic distance to cultured isolates rivals or exceeds that of surface environments. We identify distinct microbial community compositions but similar microbial diversity for Earth's subsurface and surface environments.

Taxonomic variability and functional stability across Oregon coastal subsurface microbiomes

The factors shaping microbial communities in marine subsurface sediments remain poorly understood. Here, we analyzed the microbiome of subsurface sediments within a depth range of 1.6-1.9 m, at 10 locations along the Oregon coast. We used metagenomics to reconstruct the functional structure and 16S rRNA gene amplicon sequencing to estimate the taxonomic composition of microbial communities, accompanied by physicochemical measurements. Functional community structure, in terms of the proportions of various gene groups, was remarkably stable across samples, despite the latter covering a region spanning over 300 km. In contrast, taxonomic composition was highly variable, especially at the level of amplicon sequence variants (ASVs) and operational taxonomic units (OTUs). Mantel correlation tests between compositional dissimilarities and geographic distances revealed only a moderate influence of distance on composition. Regression models predicting taxonomic dissimilarities and considering up to 20 physicochemical variables as predictors, almost always failed to select a significant predictor, suggesting that variation in local conditions does not explain the high taxonomic variability. Permutation null models of community assembly revealed that taxa tend to strongly segregate, i.e., exclude each other. We conclude that biological interactions are important drivers of taxonomic variation in subsurface sediments, and that this variation can decouple from functional structure.

Microbial profiling of the East Siberian Sea sediments using 16S rRNA gene and metagenome sequencing

The Arctic Ocean is experiencing significant global warming, leading to reduced sea-ice cover, submarine permafrost thawing, and increased river discharge. The East Siberian Sea (ESS) undergoes more significant terrestrial inflow from coastal erosion and river runoff than other Arctic seas. Despite extensive research on environmental changes, microbial communities and their functions in the ESS, which are closely related to environmental conditions, remain largely unexplored. Here, we investigated microbial communities in ESS surface sediments spanning latitudes from 73°N to 77°N using 16S rRNA amplicon sequencing, and reconstructed 211 metagenome-assembled genomes (MAGs) using shotgun metagenome sequencing. Taxonomic analysis identified 209 bacterial MAGs, with the predominant phyla Pseudomonadota (n = 82), Actinobacteriota (n = 38), Desulfobacterota (n = 23), along with 2 archaeal MAGs of Thermoproteota. Notably, 86% of the MAGs (n = 183) could not be classified into known species, indicating the potential presence of novel and unidentified microorganisms in the ESS. This dataset provides invaluable information on the microbial diversity and ecological functions in the rapidly changing ESS.

A prescription for engineering PFAS biodegradation

Per- and polyfluorinated chemicals (PFAS) are of rising concern due to environmental persistence and emerging evidence of health risks to humans. Environmental persistence is largely attributed to a failure of microbes to degrade PFAS. PFAS recalcitrance has been proposed to result from chemistry, specifically C-F bond strength, or biology, largely negative selection from fluoride toxicity. Given natural evolution has many hurdles, this review advocates for a strategy of laboratory engineering and evolution. Enzymes identified to participate in defluorination reactions have been discovered in all Enzyme Commission classes, providing a palette for metabolic engineering. In vivo PFAS biodegradation will require multiple types of reactions and powerful fluoride mitigation mechanisms to act in concert. The necessary steps are to: (1) engineer bacteria that survive very high, unnatural levels of fluoride, (2) design, evolve, and screen for enzymes that cleave C-F bonds in a broader array of substrates, and (3) create overall physiological conditions that make for positive selective pressure with PFAS substrates.

Depth-dependent bacterial colonization on model chitin particles in the open ocean

Sinking particles transport carbon from the surface to the deep ocean. Microbial colonization and remineralization are important ecosystem services constraining ocean biogeochemistry by recycling and redistributing nutrients from the surface to the deep ocean. Fragmentation of particles by zooplankton and the resulting colonization by microorganisms before ingestion, known as 'microbial gardening', allows for trophic upgrading and increased microbial biomass for detritivorous zooplankton. Using model chitin particles incubated with seawater collected from the surface, mesopelagic and bathypelagic depths in the Northeast Atlantic Ocean, we determined particle-attaching bacterial communities to identify general and depth-specific candidates of particle colonization. Comparison of particle-attached communities at the amplicon sequence variant level showed that bacteria found on surface particles were also colonizers in the bathypelagic, in line with sinking particles promoting vertical connectivity. Bathypelagic particle-attached communities were most diverse. We propose that some particle colonizers attach to the surface and sink out with the particle, whilst other colonizers are depth-specific. This suggests that candidates for particle colonization differ with depth, which may be important when considering the implications for the delivery of ecosystem services, including carbon cycling and the role they play for zooplankton grazers.

Delayed Sowing Reduced Verticillium Wilt by Altering Soil Temperature and Humidity to Enhance Beneficial Rhizosphere Bacteria of Sunflower

Sunflower Verticillium Wilt (SVW) caused by Verticillium dahliae is a significant threat to sunflower production in China. This soilborne disease is difficult to control. It has been observed that delayed sowing reduces the severity of SVW on different varieties and across various locations. Soil was collected from multiple locations with different sowing dates to understand the underlying biological mechanisms driving this phenomenon. The soil bacterial community was characterized through 16S rRNA gene amplicon sequencing performed on the Illumina MiSeq platform, followed by comprehensive bioinformatics analysis. Microsclerotia numbers in soil were detected using both NP-10 selective medium and quantitative polymerase chain reaction (qPCR). By delaying the sowing date, the number of microsclerotia in soil and the biomass of V. dahliae colonized inside sunflower roots were reduced during the early developmental stages (V2-V6) of sunflowers. Amplicon sequencing revealed an increased abundance of bacterial genera, such as Pseudomonas, Azoarcus, and Bacillus in soil samples collected from delayed sowing plots. Five bacterial strains isolated from the delayed sowing plot exhibited strong antagonistic effects against V. dahliae. The result of the pot experiments indicated that supplying two different synthetic communities (SynComs) in the pot did increase the control efficiencies on SVW by 19.08% and 37.82% separately. Additionally, soil temperature and humidity across different sowing dates were also monitored, and a significant correlation between disease severity and environmental factors was observed. In conclusion, delayed sowing appears to decrease microsclerotia levels by recruiting beneficial rhizosphere bacteria, thereby reducing the severity of SVW.

Microfluidics for studying the deep underground biosphere: from applications to fundamentals

In this review, selected examples are presented to demonstrate how microfluidic approaches can be utilized for investigating microbial life from deep geological environments, both from practical and fundamental perspectives. Beginning with the definition of the deep underground biosphere and the conventional experimental techniques employed for these studies, the use of microfluidic systems for accessing critical parameters of deep life in geological environments at the microscale is subsequently addressed (high pressure, high temperature, low volume). Microfluidics can simulate a range of environmental conditions on a chip, enabling rapid and comprehensive studies of microbial behavior and interactions in subsurface ecosystems, such as simulations of porous systems, interactions among microbes/microbes/minerals, and gradient cultivation. Transparent microreactors allow real-time, noninvasive analysis of microbial activities (microscopy, Raman spectroscopy, FTIR microspectroscopy, etc.), providing detailed insights into biogeochemical processes and facilitating pore-scale analysis. Finally, the current challenges and opportunities to expand the use of microfluidic methodologies for studying and monitoring the deep biosphere in real time under deep underground conditions are discussed.

Acidic proteomes are linked to microbial alkaline preference in African lakes

Microbial amino acid composition (AA) reflects adaptive strategies of cellular and molecular regulations such as a high proportion of acidic AAs, including glutamic and aspartic acids in alkaliphiles. It remains understudied how microbial AA content is linked to their pH adaptation especially in natural environments. Here we examined prokaryotic communities and their AA composition of genes with metagenomics for 39 water and sediments of East African lakes along a gradient of pH spanning from 7.2 to 10.1. We found that Shannon diversity declined with the increasing pH and that species abundance were either positively or negatively associated with pH, indicating their distinct habitat preference in lakes. Microbial communities showed higher acidic proteomes in alkaline than neutral lakes. Species acidic proteomes were also positively correlated with their pH preference, which was consistent across major bacterial lineages. These results suggest selective pressure associated with high pH likely shape microbial amino acid composition both at the species and community levels. Comparative genome analyses further revealed that alkaliphilic microbes contained more functional genes with higher acidic AAs when compared to those in neutral conditions. These traits included genes encoding diverse classes of cation transmembrane transporters, antiporters, and compatible solute transporters, which are involved in cytoplasmic pH homeostasis and osmotic stress defense under high pH conditions. Our results provide the field evidence for the strong relationship between prokaryotic AA composition and their habitat preference and highlight amino acid optimization as strategies for environmental adaptation.

The Anti-Elixir Triad: Non-Synced Circadian Rhythm, Gut Dysbiosis, and Telomeric Damage

Aging is an inevitable life process which is accelerated by lifestyle and environmental factors. It is an irreversible accretion of molecular and cellular damage associated with changes in the body composition and deterioration in physiological functions. Each cell (other than stem cells) reaches the limit of its ability to replicate, known as cellular or replicative senescence, and consequently, the organs lose their physiological functions, resulting in overall impairment. Other factors that promote aging include smoking, alcohol, UV rays, sleep habits, food, stress, sedentary lifestyle, and genetic abnormalities. These stress factors can alter our endogenous clock (the circadian rhythm) and the microbial commensals. As a result of the effect of these stressors, the microorganisms that generally support human physiological processes become baleful. The disturbance of natural physiology instigates many age-related pathologies, such as cardiovascular diseases, chronic obstructive pulmonary disorder, cerebrovascular diseases, opportunistic infections, high blood pressure, cancer, diabetes, kidney diseases, dementia, and Alzheimer's disease. The present review covers the three most essential processes of the circadian clock; the circadian gene mechanism and regulation, the mitotic clock (which plays a vital role in the telomere's attrition) and the gut microbiota and their metabolome that drive aging and lead to age-related pathologies. In conclusion, maintaining a synchronized circadian rhythm, a healthy gut microbiome, and telomere integrity is essential for mitigating the effects of aging and promoting longevity. The interplay among these factors underscores the importance of lifestyle choices in enhancing overall health and lifespan.

Unraveling the Gut Microbiota: Implications for Precision Nutrition and Personalized Medicine

Recent studies have shown a growing interest in the complex relationship between the human gut microbiota, metabolism, and overall health. This review aims to explore the gut microbiota-host association, focusing on its implications for precision nutrition and personalized medicine. The objective is to highlight how gut microbiota modulate metabolic and immune functions, contributing to disease susceptibility and wellbeing. The review synthesizes recent research findings, analyzing key studies on the influence of gut microbiota on lipid and carbohydrate metabolism, intestinal health, neurobehavioral regulation, and endocrine signaling. Data were drawn from both experimental and clinical trials examining microbiota-host interactions relevant to precision nutrition. Our findings highlight the essential role of gut microbiota-derived metabolites in regulating host metabolism, including lipid and glucose pathways. These metabolites have been found to influence immune responses and gut barrier integrity. Additionally, the microbiota impacts broader physiological processes, including neuroendocrine regulation, which could be crucial for dietary interventions. Therefore, understanding the molecular mechanisms of dietary-microbiota-host interactions is pivotal for advancing personalized nutrition strategies. Tailored dietary recommendations based on individual gut microbiota compositions hold promise for improving health outcomes, potentially revolutionizing future healthcare approaches across diverse populations.

The attenuation of gut microbiota-derived short-chain fatty acids elevates lipid transportation through suppression of the intestinal HDAC3-H3K27ac-PPAR-γ axis in gestational diabetes mellitus

Gut flora is considered to modulate lipid transport from the intestine into the bloodstream, and thus may potentially participate in the development of GDM. Although previous studies have shown that the intestinal microbiota influences lipid transport and metabolism in GDM, the precise mechanisms remain elusive. To address this, we used a high-fat diet (HFD)-induced GDM mouse model and conducted 16s rRNA sequencing and fecal metabolomics to assess gut microbial community shifts and associated metabolite changes. Western blot, ELISA, and chromatin immunoprecipitation (ChIP) were utilized to elucidate how gut microbiota affect intestinal lipid transport and the insulin sensitivity of hepatic, adipose, and skeletal muscle tissues. We found that HFD impaired the oral glucose tolerance test (OGTT) and insulin tolerance test (ITT) in pregnant mice. 16s rRNA sequencing demonstrated profound compositional changes, especially in the relative abundances of Firmicutes and Bacteroidetes. Metabolomics analysis presented a decline in the concentration of short-chain fatty acids (SCFAs) in the GDM group. Western blot analyses showed an upregulation of HDAC3 and a concurrent reduction in H3K27 acetylation in the intestine. ChIP-qPCR showed that PPAR-γ was inhibited, which in turn activated lipid-transporter CD36. ELISA and insulin signaling pathway detection in insulin-target organs showed high concentrations of circulating fatty acids and triglycerides and insulin resistance in insulin-target organs. Our results suggest that gut microbiota is closely associated with the development of GDM, partly because decreased gut flora-associated SCFAs activate CD36 by suppressing the HDAC3-H3K27ac-PPAR-γ axis to transport excessive fatty acids and triglycerides into blood circulation, thereby dysregulating the insulin sensitivity of insulin target organs.

Hidden comet tails of marine snow impede ocean-based carbon sequestration

Gravity-driven sinking of "marine snow" sequesters carbon in the ocean, constituting a key biological pump that regulates Earth's climate. A mechanistic understanding of this phenomenon is obscured by the biological richness of these aggregates and a lack of direct observation of their sedimentation physics. Utilizing a scale-free vertical tracking microscopy in a field setting, we present microhydrodynamic measurements of freshly collected marine snow aggregates from sediment traps. Our observations reveal hitherto-unknown comet-like morphology arising from fluid-structure interactions of transparent exopolymer halos around sinking aggregates. These invisible comet tails slow down individual particles, greatly increasing their residence time. Based on these findings, we constructed a reduced-order model for the Stokesian sedimentation of these mucus-embedded two-phase particles, paving the way toward a predictive understanding of marine snow.

Subsurface Microbial Colonization at Mineral-Filled Veins in 2-Billion-Year-Old Mafic Rock from the Bushveld Igneous Complex, South Africa

Recent advances in subsurface microbiology have demonstrated the habitability of multi-million-year-old igneous rocks, despite the scarce energy supply from rock-water interactions. Given the minimal evolution coupled with exceedingly slow metabolic rates in subsurface ecosystems, spatiotemporally stable igneous rocks can sustain microbes over geological time scales. This study investigated a 2-billion-year-old mafic rock in the Bushveld Igneous Complex, South Africa, where ultradeep drilling is being executed by the International Continental Scientific Drilling Program (ICDP). New procedures were successfully developed to simultaneously detect indigenous and contaminant microbial cells in a drill core sample. Precision rock sectioning coupled with infrared, fluorescence, and electron microscopy imaging of the rock section with submicron resolution revealed microbial colonization in veins filled with clay minerals. The entry and exit of microbial cells in the veins are severely limited by tight packing with clay minerals, the formation of which supplies energy sources for long-term habitability. Further microbiological characterization of drilled rock cores from the Bushveld Igneous Complex will expand the understanding of microbial evolution in deep igneous rocks over 2 billion years.

Estimating the Importance of Viral Contributions to Soil Carbon Dynamics

Biogeochemical models for predicting carbon dynamics increasingly include microbial processes, reflecting the importance of microorganisms in regulating the movement of carbon between soils and the atmosphere. Soil viruses can redirect carbon among various chemical pools, indicating a need for quantification and development soil carbon models that explicitly represent viral dynamics. In this opinion, we derive a global estimate of carbon potentially released from microbial biomass by viral infections in soils and synthesize a quantitative soil carbon budget from existing literature that explicitly includes viral impacts. We then adapt known mechanisms by which viruses influence carbon cycles in marine ecosystems into a soil-explicit framework. Finally, we explore the diversity of virus-host interactions during infection and conceptualize how infection mode may impact soil carbon fate. Our synthesis highlights key knowledge gaps hindering the incorporation of viruses into soil carbon cycling research and generates specific hypotheses to test in the pursuit of better quantifying microbial dynamics that explain ecosystem-scale carbon fluxes. The importance of identifying critical drivers behind soil carbon dynamics, including these elusive but likely pervasive viral mechanisms of carbon redistribution, becomes more pressing with climate change.

An S-methyltransferase that produces the climate-active gas dimethylsulfide is widespread across diverse marine bacteria

Hydrogen sulfide (H2S), methanethiol (MeSH) and dimethylsulfide (DMS) are abundant sulfur gases with roles in biogeochemical cycling, chemotaxis and/or climate regulation. Catabolism of the marine osmolyte dimethylsulfoniopropionate (DMSP) is a major source of DMS and MeSH, but both also result from S-methylation of H2S via MddA, an H2S and MeSH S-methyltransferase whose gene is abundant in soil but scarce in marine environments. Here we identify the S-adenosine methionine (SAM)-dependent MeSH and H2S S-methyltransferase 'MddH', which is widespread in diverse marine bacteria and some freshwater and soil bacteria. mddH is predicted in up to ~5% and ~15% of seawater and coastal sediment bacteria, respectively, which is considerably higher than mddA. Furthermore, marine mddH transcript levels are similar to those for the most abundant DMSP lyase gene dddP. This study implies that the importance of H2S and MeSH S-methylation pathways in marine environments is significantly underestimated.

Interconnected influences of tumour and host microbiota on treatment response and side effects in nasopharyngeal cancer

This study elucidates the intricate relationship between nasopharyngeal carcinoma (NPC), a significant malignancy predominant in Asia with notable global incidence and mortality rates, and the host microbiota, including those of tumour, nasal, nasopharyngeal, oral, oropharyngeal, and gut communities. It underscores how the composition and diversity of microbiota are altered in NPC, delving into their implications for disease pathogenesis, treatment response, and the side effects of therapies. A consistent reduction in alpha diversity across oral, nasal, and gut microbiomes in NPC patients compared to healthy individuals signals a distinct microbial signature indicative of the diseased state. The study also shows unique microbial changes tied to different NPC stages, indicating a dynamic interplay between disease progression and microbiota composition. Patients with specific microbial profiles exhibit varied responses to chemotherapy and immunotherapy, underscoring the potential for treatment personalisation based on microbiota analysis. Furthermore, the side effects of NPC treatments, such as oral mucositis, are intensified by shifts in microbial communities, suggesting a direct link between microbiota composition and treatment tolerance. This nexus offers opportunities for interventions aimed at modulating the microbiota to alleviate side effects, improve quality of life, and potentially enhance treatment efficacy. Highlighting the dual potential of microbiota as both a therapeutic target and a biomarker for NPC, this review emphasises its significance in influencing treatment outcomes and side effects, heralding a new era in NPC management through personalised treatment strategies and innovative approaches.

Soil microbiome characterization and its future directions with biosensing

Soil microbiome characterization is typically achieved with next-generation sequencing (NGS) techniques. Metabarcoding is very common, and meta-omics is growing in popularity. These techniques have been instrumental in microbiology, but they have limitations. They require extensive time, funding, expertise, and computing power to be effective. Moreover, these techniques are restricted to controlled laboratory conditions; they are not applicable in field settings, nor can they rapidly generate data. This hinders using NGS as an environmental monitoring tool or an in-situ checking device. Biosensing technology can be applied to soil microbiome characterization to overcome these limitations and to complement NGS techniques. Biosensing has been used in biomedical applications for decades, and many successful commercial products are on the market. Given its previous success, biosensing has much to offer soil microbiome characterization. There is a great variety of biosensors and biosensing techniques, and a few in particular are better suited for soil field studies. Aptamers are more stable than enzymes or antibodies and are more ready for field-use biosensors. Given that any microbiome is complex, a multiplex sensor will be needed, and with large, complicated datasets, machine learning might benefit these analyses. If the signals from the biosensors are optical, a smartphone can be used as a portable optical reader and potential data-analyzing device. Biosensing is a rich field that couples engineering and biology, and applying its toolset to help advance soil microbiome characterization would be a boon to microbiology more broadly.

Isolation of hitherto-uncultivated microorganisms- Application of radical scavengers

The culture filtrates of the predominant bacterial strains isolated from soil samples have been shown to increase the microbial colony counts on agar plates used for the isolation of uncultured bacteria. One of the factors in the culture filtrates responsible for this increase was identified to be superoxide dismutase (SOD). The generation of reactive oxygen species (O2-, H2O2, and ・OH) was detected from conventional laboratory agar media. The use of agar media supplemented with radical scavengers (SOD, catalase, ascorbic acid, or rutin) effectively increased the colony counts and kinds of microbial strains that grew from soil samples. Taxonomical studies on these isolates revealed new taxa for phylum Actinomycetota; one family, three genera, and nine species were newly described. One of the strains, Patulibacter minatonensis KV-614T belonging to the new family Patulibacteraceae, was isolated on agar medium supplemented with SOD. P. minatonensis KV-614T represents a novel lineage within the phylum Actinomycetota. A polymerase chain reaction (PCR) study using specific primers for the detection of strains related to the genus Patulibacter, order Solirubrobacterales, showed a high distribution frequency, with detection in over 70% of the soil samples tested. These data suggest that the use of radical scavengers may facilitate the isolation of some hitherto-uncultivated microorganisms widely distributed in soil.

Profile of Bacterial Communities in Copper Mine Tailings Revealed through High-Throughput Sequencing

Mine-tailing dumps are one of the leading sources of environmental degradation, often with public health and ecological consequences. Due to the complex ecosystems generated, they are ideal sites for exploring the bacterial diversity of specially adapted microorganisms. We investigated the concentrations of trace metals in solid copper (Cu) mine tailings from the Ovejería Tailings Dam of the National Copper Corporation of Chile and used high-throughput sequencing techniques to determine the microbial community diversity of the tailings using 16S rRNA gene-based amplicon sequence analysis. The concentrations of the detected metals were highest in the following order: iron (Fe) > Cu > manganese (Mn) > molybdenum (Mo) > lead (Pb) > chromium (Cr) > cadmium (Cd). Furthermore, 16S rRNA gene-based sequence analysis identified 12 phyla, 18 classes, 43 orders, 82 families, and 154 genera at the three sampling points. The phylum Proteobacteria was the most dominant, followed by Chlamydiota, Bacteroidetes, Actinobacteria, and Firmicutes. Genera, such as Bradyrhizobium, Aquabacterium, Paracoccus, Caulobacter, Azospira, and Neochlamydia, showed high relative abundance. These genera are known to possess adaptation mechanisms in high concentrations of metals, such as Cd, Cu, and Pb, along with nitrogen-fixation capacity. In addition to their tolerance to various metals, some of these genera may represent pathogens of amoeba or humans, which contributes to the complexity and resilience of bacterial communities in the studied Cu mining tailings. This study highlights the unique microbial diversity in the Ovejería Tailings Dam, including the discovery of the genus Neochlamydia, reported for the first time for heavy metal resistance. This underscores the importance of characterizing mining sites, particularly in Chile, to uncover novel bacterial mechanisms for potential biotechnological applications.

Shaping the future of gastrointestinal cancers through metabolic interactions with host gut microbiota

Gastrointestinal (GI) cancers represent a significant global health challenge, driving relentless efforts to identify innovative diagnostic and therapeutic approaches. Recent strides in microbiome research have unveiled a previously underestimated dimension of cancer progression that revolves around the intricate metabolic interplay between GI cancers and the host's gut microbiota. This review aims to provide a comprehensive overview of these emerging metabolic interactions and their potential to catalyze a paradigm shift in precision diagnosis and therapeutic breakthroughs in GI cancers. The article underscores the groundbreaking impact of microbiome research on oncology by delving into the symbiotic connection between host metabolism and the gut microbiota. It offers valuable insights into tailoring treatment strategies to individual patients, thus moving beyond the traditional one-size-fits-all approach. This review also sheds light on novel diagnostic methodologies that could transform the early detection of GI cancers, potentially leading to more favorable patient outcomes. In conclusion, exploring the metabolic interactions between host gut microbiota and GI cancers showcases a promising frontier in the ongoing battle against these formidable diseases. By comprehending and harnessing the microbiome's influence, the future of precision diagnosis and therapeutic innovation for GI cancers appears more optimistic, opening doors to tailored treatments and enhanced diagnostic precision.

The global distribution and climate resilience of marine heterotrophic prokaryotes

Heterotrophic Bacteria and Archaea (prokaryotes) are a major component of marine food webs and global biogeochemical cycles. Yet, there is limited understanding about how prokaryotes vary across global environmental gradients, and how their global abundance and metabolic activity (production and respiration) may be affected by climate change. Using global datasets of prokaryotic abundance, cell carbon and metabolic activity we reveal that mean prokaryotic biomass varies by just under 3-fold across the global surface ocean, while total prokaryotic metabolic activity increases by more than one order of magnitude from polar to tropical coastal and upwelling regions. Under climate change, global prokaryotic biomass in surface waters is projected to decline ~1.5% per °C of warming, while prokaryotic respiration will increase ~3.5% ( ~ 0.85 Pg C yr-1). The rate of prokaryotic biomass decline is one-third that of zooplankton and fish, while the rate of increase in prokaryotic respiration is double. This suggests that future, warmer oceans could be increasingly dominated by prokaryotes, diverting a growing proportion of primary production into microbial food webs and away from higher trophic levels as well as reducing the capacity of the deep ocean to sequester carbon, all else being equal.

Applications of polysaccharides in enzyme-triggered oral colon-specific drug delivery systems: A review

Enzyme-triggered oral colon-specific drug delivery system (EtOCDDS1) can withstand the harsh stomach and small intestine environments, releasing encapsulated drugs selectively in the colon in response to colonic microflora, exerting local or systematic therapeutic effects. EtOCDDS boasts high colon targetability, enhanced drug bioavailability, and reduced systemic side effects. Polysaccharides are extensively used in enzyme-triggered oral colon-specific drug delivery systems, and its colon targetability has been widely confirmed, as their properties meet the demand of EtOCDDS. Polysaccharides, known for their high safety and excellent biocompatibility, feature modifiable structures. Some remain undigested in the stomach and small intestine, whether in their natural state or after modifications, and are exclusively broken down by colon-resident microbiota. Such characteristics make them ideal materials for EtOCDDS. This article reviews the design principles of EtOCDDS as well as commonly used polysaccharides and their characteristics, modifications, applications and specific mechanism for colon targeting. The article concludes by summarizing the limitations and potential of ETOCDDS to stimulate the development of innovative design approaches.

A Procedure for Testing for Tokyo Type 1 Open-Ended Evolution

Tokyo Type 1 open-ended evolution (OEE) is a category of OEE that includes systems exhibiting the ongoing generation of adaptive novelty and ongoing growth in complexity. It can be considered as a necessary foundation for Tokyo Type 2 OEE (ongoing evolution of evolvability) and Tokyo Type 3 OEE (ongoing generation of major transitions). This article brings together five methods of analysis to form a procedure for testing for Tokyo Type 1 OEE. The procedure is presented as simply as possible, isolated from the complexities of any particular evolutionary system, and with a clear rationale for each step. In developing these steps, we also identify five key challenges in OEE. The last of these (achieving a higher order of complexity growth within a system exhibiting indefinitely scalable complexity) can be considered a grand challenge for Tokyo Type 1 OEE. Promising approaches to this grand challenge include also achieving one or both of Tokyo Types 2 and 3 OEE; this can be seen as one answer to why these other types of OEE are important, providing a unified view of OEE.

Phagotrophy in the nitrogen-fixing haptophyte Braarudosphaera bigelowii

Biological nitrogen fixation provides fixed nitrogen for microbes living in the oligotrophic open ocean. UCYN-A2, the previously known symbiont of Braarudosphaera bigelowii, now believed to be an early-stage B. bigelowii organelle that exchanges fixed nitrogen for fixed carbon, is globally distributed. Indirect evidence suggested that B. bigelowii might be a mixotrophic (phagotrophic) phototrophic flagellate. The goal of this study was to determine if B. bigelowii can graze on bacteria using several independent approaches. The results showed that B. bigelowii grazed on co-occurring bacteria at a rate of 5-7 cells/h/B. bigelowii and that the overall grazing rate was significantly higher at nighttime than at daytime. Bacterial abundance changes, assessed with 16S rRNA gene amplicon sequencing analysis, may have indicated preferential grazing by B. bigelowii on specific bacterial genotypes. In addition, Lysotracker™ staining of B. bigelowii suggested digestive activity inside B. bigelowii. Carbon and nitrogen fixation measurements revealed that the carbon demand of B. bigelowii could not be fulfilled by photosynthesis alone, implying supplementation by heterotrophy. These independent lines of evidence together revealed that B. bigelowii engages in phagotrophy, which, beyond serving as a supplementary source of carbon and energy, may also facilitate the indirect assimilation of inorganic nutrients.

Metabolites mediate the causal associations between gut microbiota and NAFLD: a Mendelian randomization study

BACKGROUND

Although gut microbiota and serum metabolite composition have been observed to be altered in patients with non-alcoholic fatty liver disease (NAFLD), previous observational studies have demonstrated inconsistent results. As this may be influenced by factors such as confounders and reverse causality, we used Mendelian randomization to clarify the causal effect of gut microbiota and blood metabolites on NAFLD.

METHODS

In this research, we performed a two-step Mendelian randomization analysis by utilizing genome-wide association study (GWAS) data obtained from MiBioGen and UK Biobank. To mitigate potential errors, we employed False Discovery Rate (FDR) correction and linkage unbalanced regression (LDSC) analysis. Sensitivity analyses including cML-MA and bidirectional Mendelian randomization were performed to ensure the robustness of the results.

RESULTS

In this study, a total of nine gut microbiota and seven metabolites were found to be significantly associated with NAFLD. MR analysis of the above findings revealed a causal relationship between Ruminococcus2 and cysteine-glutathione disulfide (OR = 1.17, 95%CI = 1.006-1.369, P = 0.041), as well as 3-indoleglyoxylic acid (OR = 1.18, 95%CI = 1.011-1.370, P = 0.036). For each incremental standard deviation in Ruminococcus2 abundance, there was a corresponding 26% reduction in NAFLD risk (OR = 0.74, 95%CI = 0.61-0.89, P = 0.0012), accompanied by a 17% increase in cysteine-glutathione disulfide levels (OR = 1.17, 95%CI = 1.01-1.37, P = 0.041) and an 18% increase in 3-indoleglyoxylic acid levels (OR = 1.18, 95%CI = 0.81-1.00, P = 0.036). The proportion mediated by cysteine-glutathione disulfide is 11.2%, while the proportion mediated by 3-indoleglyoxylic acid is 7.5%.

CONCLUSION

Our study suggests that increased abundance of specific gut microbiota may reduce the risk of developing NAFLD, and this relationship could potentially be mediated through blood metabolites.

Microbiota-associated mechanisms in colorectal cancer

Colorectal cancer (CRC) is one of the most common cancers worldwide, ranking third in terms of incidence and second as a cause of cancer-related death. There is growing scientific evidence that the gut microbiota plays a key role in the initiation and development of CRC. Specific bacterial species and complex microbial communities contribute directly to CRC pathogenesis by promoting the neoplastic transformation of intestinal epithelial cells or indirectly through their interaction with the host immune system. As a result, a protumoural and immunosuppressive environment is created conducive to CRC development. On the other hand, certain bacteria in the gut microbiota contribute to protection against CRC. In this chapter, we analysed the relationship of the gut microbiota to CRC and the associations identified with specific bacteria. Microbiota plays a key role in CRC through various mechanisms, such as increased intestinal permeability, inflammation and immune system dysregulation, biofilm formation, genotoxin production, virulence factors and oxidative stress. Exploring the interaction between gut microbiota and tumourigenesis is essential for developing innovative therapeutic approaches in the fight against CRC.

From shells to sequences: A proof-of-concept study for on-site analysis of hemolymphatic circulating cell-free DNA from sentinel mussels using Nanopore technology

Blue mussels are often abundant and widely distributed in polar marine coastal ecosystems. Because of their wide distribution, ecological importance, and relatively stationary lifestyle, bivalves have long been considered suitable indicators of ecosystem health and changes. Monitoring the population dynamics of blue mussels can provide information on the overall biodiversity, species interactions, and ecosystem functioning. In the present work, we combined the concept of liquid biopsy (LB), an emerging concept in medicine based on the sequencing of free circulating DNA, with the Oxford Nanopore Technologies (ONT) platform using a portable laboratory in a remote area. Our results demonstrate that this platform is ideally suited for sequencing hemolymphatic circulating cell-free DNA (ccfDNA) fragments found in blue mussels. The percentage of non-self ccfDNA accounted for >50 % of ccfDNA at certain sampling Sites, allowing the quick, on-site acquisition of a global view of the biodiversity of a coastal marine ecosystem. These ccfDNA fragments originated from viruses, bacteria, plants, arthropods, algae, and multiple Chordata. Aside from non-self ccfDNA, we found DNA fragments from all 14 blue mussel chromosomes, as well as those originating from the mitochondrial genomes. However, the distribution of nuclear and mitochondrial DNA was significantly different between Sites. Similarly, analyses between various sampling Sites showed that the biodiversity varied significantly within microhabitats. Our work shows that the ONT platform is well-suited for LB in sentinel blue mussels in remote and challenging conditions, enabling faster fieldwork for conservation strategies and resource management in diverse settings.

Beneficial Effects of Probiotic Lactobacillus paraplantarum BGCG11 on Pancreatic and Duodenum Function in Diabetic Rats

Diabetes mellitus, as a chronic metabolic disorder, significantly impacts the pancreas and among other organs, affects duodenal function. Emerging evidence suggests that probiotics can exert beneficial effects on gut health and metabolism. In our previous research, we evaluated the probiotic Lactobacillus paraplantarum BGCG11 primarily for its protective properties against diabetic rats' damaged liver and kidneys. In this work, we further examined the effects of probiotic strain BGCG11 on the function of the duodenum and pancreas in diabetic rats. We explored the potential mechanisms underlying the probiotic's effects, focusing on general indicators of diabetes, the architecture and morphology of pancreatic islets, duodenal integrity (measuring the transfer of fluid and serum zonulin level), and the modulation of gut microbiota composition. Our findings reveal the protective and regulatory roles of L. paraplantarum BGCG11 in mitigating diabetes-induced pancreatic and duodenal dysfunction regardless of its application time (pre- or post-treatment), highlighting its therapeutic potential in managing diabetes-related gastrointestinal complications.

The mystery of rich human gut antibiotic resistome in the Yellow River with hyper-concentrated sediment-laden flow

Human gut antibiotic resistome widely occur in anoxic environments characterized by high density of bacterial cells and frequent transmission of antibiotic resistance genes (ARGs). Such resistome is greatly diluted, degraded, and restrained in the aerobic habitats within most natural rivers (regarded as "terrestrial guts") connecting continents and the oceans. Here we implemented a large-scale monitoring campaign extending 5,200 km along the Yellow River, and provide the first integral biogeographic pattern for both ARGs and their hosts. We identified plentiful ARGs (24 types and 809 subtypes) and their hosts (24 phyla and 757 MAGs) in three media (water, suspended particulate matter (SPM), and sediment). Unexpectedly, we found diverse human gut bacteria (HGB) acting as supercarriers of ARGs in this oxygen-rich river. We further discovered that numerous microhabitats were created within stratified biofilms that surround SPMs, particularly regarding the aggregation of anaerobic HGB. These microhabitats provide numerous ideal sinks for anaerobic bacteria and facilitate horizontal transfer of ARGs within the stratified biofilms, Furthermore, the stratification of biofilms surrounding SPMs has facilitated synergy between human gut flora and denitrifiers for propagation of ARGs in the anoxic atmospheres, leading to high occurrence of human gut antibiotic resistome. SPMs play active roles in the dynamic interactions of river water and sediment, thus accelerating the evolution of riverine resistome and transmission of human gut antibiotic resistome. This study revealed the special contribution of SPMs to the propagation of ARGs, and highlighted the necessity of making alternative strategies for sustainable management of large rivers with hyper-concentrated sediment-laden flows.

Advancements in prokaryotic systematics and the role of Bergey's International Society for Microbial Systematicsin addressing challenges in the meta-data era

Prokaryotes are ubiquitous in the biosphere, important for human health and drive diverse biological and environmental processes. Systematics of prokaryotes, whose origins can be traced to the discovery of microorganisms in the 17th century, has transitioned from a phenotype-based classification to a more comprehensive polyphasic taxonomy and eventually to the current genome-based taxonomic approach. This transition aligns with a foundational shift from studies focused on phenotypic traits that have limited comparative value to those using genome sequences. In this context, Bergey's Manual of Systematics of Archaea and Bacteria (BMSAB) and Bergey's International Society for Microbial Systematics (BISMiS) play a pivotal role in guiding prokaryotic systematics. This review focuses on the historical development of prokaryotic systematics with a focus on the roles of BMSAB and BISMiS. We also explore significant contributions and achievements by microbiologists, highlight the latest progress in the field and anticipate challenges and opportunities within prokaryotic systematics. Additionally, we outline five focal points of BISMiS that are aimed at addressing these challenges. In conclusion, our collaborative effort seeks to enhance ongoing advancements in prokaryotic systematics, ensuring its continued relevance and innovative characters in the contemporary landscape of genomics and bioinformatics.

Chemosynthesis: a neglected foundation of marine ecology and biogeochemistry

Chemosynthesis is a metabolic process that transfers carbon to the biosphere using reduced compounds. It is well recognised that chemosynthesis occurs in much of the ocean, but it is often thought to be a negligible process compared to photosynthesis. Here we propose that chemosynthesis is the underlying process governing primary production in much of the ocean and suggest that it extends to a much wider range of compounds, microorganisms, and ecosystems than previously thought. In turn, this process has had a central role in controlling marine biogeochemistry, ecology, and carbon budgets across the vast realms of the ocean, from the dawn of life to contemporary times.

Comparative analysis of microbiome inhabiting oxygenated and deoxygenated habitats using V3 and V6 metabarcoding of 16S rRNA gene

We examine how oxygen levels and the choice of 16S ribosomal RNA (rRNA) tags impact marine bacterial communities using Next-Generation amplicon sequencing. Analyzing V3 and V6 regions, we assess microbial composition in both Oxygen minimum zones (OMZ) and non-OMZ (NOMZ) areas in the Arabian Sea (AS) and the Central Indian Ocean basin (CIOB) respectively. Operational taxonomic units (OTUs) at 97% similarity showed slightly higher richness and diversity with V6 compared to V3. Vertical diversity patterns were consistent across both regions. NOMZ showed greater richness and diversity than OMZ. AS and CIOB exhibited significant differences in bacterial community, diversity, and relative abundance at the order and family levels. Alteromonadaceae dominated the OMZ, while Pelagibacteraceae dominated the NOMZ. Synechococcaceae were found exclusively at 250 m in OMZ. Bacteria putatively involved in nitrification, denitrification, and sulfurylation were detected at both sites. Dissolved oxygen significantly influenced microbial diversity at both sites, while seasonal environmental parameters affected diversity consistently, with no observed temporal variation.

Swimming towards each other: the role of chemotaxis in bacterial interactions

Chemotaxis allows microorganisms to direct movement in response to chemical stimuli. Bacteria use this behaviour to develop spatial associations with animals and plants, and even larger microbes. However, current theory suggests that constraints imposed by the limits of chemotactic sensory systems will prevent sensing of chemical gradients emanating from cells smaller than a few micrometres, precluding the utility of chemotaxis in interactions between individual bacteria. Yet, recent evidence has revealed surprising levels of bacterial chemotactic precision, as well as a role for chemotaxis in metabolite exchange between bacterial cells. If indeed widespread, chemotactic sensing between bacteria could represent an important, but largely overlooked, phenotype within interbacterial interactions, and play a significant role in shaping cooperative and competitive relationships.

A metagenomic assessment of bacterial community in spices sold open-air markets in Saint-Louis, Senegal

Natural spices play an essential role in human nutrition and well-being. However, their processing on different scales can expose them to potential sources of contamination. This study aimed to describe the bacterial community genomic footprint in spices sold in Senegal. Spice samples were collected in August 2022 in Saint-Louis, Senegal. The genomic region coding bacterial 16S rRNA was then amplified and sequenced using Oxford Nanopore Technology (ONT). Sequencing was carried out on two batches of samples, one containing part of the "Local Spices or Herbs" (n = 10), and the other, a mixture of 7 spices, Curcuma, Thyme and the other part of the "Local Spices or Herbs" (n = 39). Results showed high bacterial diversity and the predominance of Escherichia coli and Salmonella enterica in samples, with total reads of 65,744 and 165,325 for the two batches, respectively. The sample category "Homemade mixture of food condiments ", which includes all "Local Spices or Herbs" samples, showed remarkable bacterial diversity. These were followed by Curcuma, a blend of 7 spices and thyme. Also, the different categories of spices studied show similarities in their bacterial composition. These results highlight the microbial community's highly diverse genomic profile, including pathogenic bacteria, in spice samples.