This resource is a video abstract of a research paper created by Research Square on behalf of its authors. It provides a synopsis that's easy to understand, and can be used to introduce the topics it covers to students, researchers, and the general public. The video's transcript is also provided in full, with a portion provided below for preview:

"Deep shale formations underlie most of North America and are typically inhospitable to microbial life. However, hydrologic fracturing of shale creates space and injects moisture and nutrients into the system, thus allowing new microbial communities to form. These communities can cause problems by corroding infrastructure and souring the hydrocarbon steam. Understanding the behavior of these microbial communities could lead to better management techniques. Recently, researchers examined the microbial genomes and metabolic capacity of fractured shale wells in Oklahoma, USA. Oklahoma shale is much hotter and has lower salinity than the previously characterized formations in the eastern USA. This study found that the Oklahoma formations had greater microbial taxonomic and metabolic diversity than the eastern formations. Sampling over time revealed that this microbial community broke down complex polymers from the fracturing process and used them for nutrients..."

The rest of the transcript, along with a link to the research itself, is available on the resource itself.

This resource is a video abstract of a research paper created by Research Square on behalf of its authors. It provides a synopsis that's easy to understand, and can be used to introduce the topics it covers to students, researchers, and the general public. The video's transcript is also provided in full, with a portion provided below for preview:

"Phytoplankton communities play major roles in global biogeochemical cycles and marine food webs. However, the complex phytoplankton communities in polar vs. non-polar oceans haven’t been well characterized. To address this gap, researchers recently profiled the metagenome-assembled genomes (MAGs) of eukaryotic microbes and associated prokaryotes from the chlorophyll A maximum layer at 11 sites in the Arctic and Atlantic Oceans. Within each ocean, adjacent sampling sites had 51–88% of their MAGs in common, but the Arctic and Atlantic MAGs were clearly differentiated. Most species associations were between Prasinophytes and Proteobacteria. In addition, eukaryotic MAGs were more diverse in the Arctic, while prokaryotic MAGs were more diverse in the Atlantic. For both prokaryotes and eukaryotes, 70% of the detected protein families were shared between Arctic and Atlantic MAGs. but eukaryotic MAGs had more Arctic-only protein families, whereas prokaryotic MAGs had more Atlantic-only protein families..."

The rest of the transcript, along with a link to the research itself, is available on the resource itself.

This resource is a video abstract of a research paper created by Research Square on behalf of its authors. It provides a synopsis that's easy to understand, and can be used to introduce the topics it covers to students, researchers, and the general public. The video's transcript is also provided in full, with a portion provided below for preview:

"Antibiotic resistance is a growing threat to global public health. While antibiotic resistance genes (ARGs) can arise in many different environments, environments with heavy antibiotic use, such as livestock farms and hospitals, are of particular concern. ARGs can then spread to human pathogens via horizontal gene transfer and the inhalation of antibiotic-resistant bacteria presents a particularly dangerous route of exposure. Thus, a recent study characterized the resistome found in the fine particulate matter from hospital air. The hospital airborne particulate samples had nearly twice the ARG abundance of ambient urban air samples, and up to 30% of the hospital microbiome was from human-associated sources, which highlights the risk of potentially resistant pathogens. The resistome varied with clinical activities; in particular the abundance of β-lactam ARGs was associated with the number of in-ward β-lactam resistant cases..."

The rest of the transcript, along with a link to the research itself, is available on the resource itself.

This resource is a video abstract of a research paper created by Research Square on behalf of its authors. It provides a synopsis that's easy to understand, and can be used to introduce the topics it covers to students, researchers, and the general public. The video's transcript is also provided in full, with a portion provided below for preview:

"Dental calculus, or mineralized dental plaque, preserves various microfossils and biomolecules, including DNA. Dental calculus from ancient human remains therefore contains information about the oral microbiomes, health, and diets of our ancestors. However, little is known about the non-bacterial microbes in ancient calculus. In a new study, researchers used metagenomics to study calculus from 20 sets of human remains dating to the Neolithic period through the Early Middle Ages. Compared with modern calculus in publicly available datasets, the ancient calculus had a much higher abundance of archaea belonging to the phylum Euryarchaeota. Compared with modern calculus in publicly available datasets, the ancient calculus had a much higher abundance of archaea belonging to the phylum Euryarchaeota, specifically archaea in the genus Methanobrevibacter. The only known Methanobrevibacter species in modern calculus, M..."

The rest of the transcript, along with a link to the research itself, is available on the resource itself.

This resource is a video abstract of a research paper created by Research Square on behalf of its authors. It provides a synopsis that's easy to understand, and can be used to introduce the topics it covers to students, researchers, and the general public. The video's transcript is also provided in full, with a portion provided below for preview:

"Deep-sea hydrothermal vents are extreme environments that typically form along mid-ocean ridges. Although hundreds of vent systems have been identified, those south of 14°S on the Mid-Atlantic Ridge remain relatively unexplored. To learn more, a recent study investigated the microbes inhabiting the newly discovered Deyin-1 vent in this area. Analysis of 219 metagenome-assembled genomes (MAGs) revealed a highly diverse and variable community. Most of the dominant microbes appeared capable of using reduced sulfur and hydrogen as primary energy sources, and many of the microbes seemed to use multiple energy pathways, indicating adaptability to fluctuating conditions. Multiple types of bacteria were also predicted to participate in the same metabolic pathways, suggesting functional redundancy within the community. Furthermore, the genome sequences suggested that a large proportion of microbes could both make their own food and consume other organisms..."

The rest of the transcript, along with a link to the research itself, is available on the resource itself.

This resource is a video abstract of a research paper created by Research Square on behalf of its authors. It provides a synopsis that's easy to understand, and can be used to introduce the topics it covers to students, researchers, and the general public. The video's transcript is also provided in full, with a portion provided below for preview:

"Methane production by microbes is a hot topic - Literally. Because of the potential to cause global warming, increased methane production is of great concern, but if properly controlled, it can also boost energy generation. Unfortunately, the basic mechanisms through which microbes generate methane remain unclear. To provide some clarity, researchers recently approached the problem using a combination of metagenomics and metatranscriptomics, which revealed that different microbes fill unique functional niches in methane-producing communities. In some cases, microbes worked against each other, but in others, they used metabolic and transcription processes that complemented each other, suggesting that methanogenic microbes form a complex community to reduce the biosynthetic burden. And interestingly, different hydrogen concentrations in methane-producing niches favored different types of methanogenic bacteria..."

The rest of the transcript, along with a link to the research itself, is available on the resource itself.

This resource is a video abstract of a research paper created by Research Square on behalf of its authors. It provides a synopsis that's easy to understand, and can be used to introduce the topics it covers to students, researchers, and the general public. The video's transcript is also provided in full, with a portion provided below for preview:

"Microbiomes share an intimate relationship with the organisms they colonize, even across evolutionary timescales. That’s the basis of a theory called phylosymbiosis. Phylosymbiosis holds that microbial communities evolve as their host evolves and has been confirmed to exist for certain insects and mammals. Researchers recently tested whether that relationship holds among fish. Approximately 420 million years ago, fish made an epic evolutionary split into elasmobranchs -- creatures with all-cartilage skeletons -- and bony fish. Since then, the two have accumulated vast differences in anatomy and physiology, most notably in their skin. That’s where the researchers zeroed in. For a small sample of fish, they used metagenomics to compare the makeup of microbial communities living on fish skin. Between fishes considered closely or distantly related in evolutionary terms, findings revealed that elasmobranchs displayed patterns of phylosymbiosis, while bony fish did not..."

The rest of the transcript, along with a link to the research itself, is available on the resource itself.

This resource is a video abstract of a research paper created by Research Square on behalf of its authors. It provides a synopsis that's easy to understand, and can be used to introduce the topics it covers to students, researchers, and the general public. The video's transcript is also provided in full, with a portion provided below for preview:

"The microorganisms that inhabit our food processing facilities influence the safety of our food. Overuse of antibiotics while raising food animals can lead to an accumulation of antimicrobial resistance genes in their gut microbiomes, which may jump to resident microbes at the processing plant. This means meat processing facilities may act as reservoirs of antimicrobial-resistant microbes. To test this, researchers monitored microbial communities and their resistance genes for one and a half years in a new pork processing plant. Early on, the plant harbored few bacterial families, but over time, the diversity increased, and the communities on different surfaces diverged. At the same time, the overall abundance and diversity of antimicrobial resistance genes rose. The sharing of resistance genes between microbes was primarily detected in the facility’s drains late in the observation period..."

The rest of the transcript, along with a link to the research itself, is available on the resource itself.

This resource is a video abstract of a research paper created by Research Square on behalf of its authors. It provides a synopsis that's easy to understand, and can be used to introduce the topics it covers to students, researchers, and the general public. The video's transcript is also provided in full, with a portion provided below for preview:

"Microbiome research has consistently been placed in the spotlight over the past two decades, and has shown tremendous promise in the fields of medicine, environmental science, food production, and agriculture. Life on Earth does not exist without microbes, and we may benefit from learning more about them. Yet, there is no common understanding amongst researchers of what a 'microbiome’ actually is. Researchers are now proposing a common definition of ‘microbiome’ to ensure better, more robust research across different disciplines. The authors build on the historical definition offered by Whipps and colleagues in 1988 using new research insights. Additionally, they highlight the importance of microbiomes as drivers for the health of many eukaryotic hosts, including humans and plants. The proposed amendments to the definition specify the elements of microbiome composition and their interactions..."

The rest of the transcript, along with a link to the research itself, is available on the resource itself.

This resource is a video abstract of a research paper created by Research Square on behalf of its authors. It provides a synopsis that's easy to understand, and can be used to introduce the topics it covers to students, researchers, and the general public. The video's transcript is also provided in full, with a portion provided below for preview:

"Amphibians are one of the most vulnerable animal groups on the planet, with over 40% of their species threatened with extinction. A major driver of that vulnerability is the fungal pathogen _Batrachochytrium dendrobatidis_ (Bd). Bd is linked to the decline of at least 500 amphibian species, the greatest loss in biodiversity due to a pathogen ever recorded. The amphibian skin microbiome community structure has been linked to health outcomes of Bd infection, but the functional importance of the microbiota is not yet fully understood. To close this gap and potentially discover biomarkers or disease control methods, researchers investigated the microbiome of midwife toads. They examined both wild populations with naturally occurring Bd infection and controlled laboratory exposure. Infection with Bd led to changes in the microbial community structure, gene profile, and metabolic function in laboratory and wild toad populations..."

The rest of the transcript, along with a link to the research itself, is available on the resource itself.

This resource is a video abstract of a research paper created by Research Square on behalf of its authors. It provides a synopsis that's easy to understand, and can be used to introduce the topics it covers to students, researchers, and the general public. The video's transcript is also provided in full, with a portion provided below for preview:

"In Greek, the word _eudora_ means “she of good gifts”. It was the name given to various mythological sea nymphs, patrons of, among other things, sailing and bountiful catches. Now, Eudora also refers to a group of newly discovered bacteria from the ocean that promise similar rewards. A recent study reveals that _Candidatus_ Eudoremicrobium holds the genetic blueprints for producing an array of natural products with potential applications in medicine and biotechnology. And they’re likely not the only ones. Numerous microbes yet to be characterized across the vast ocean could harbor similar treasures. The key to finding them lies in applying the tools of microbiomics. Microbiomics refers to the study of microbiomes using tools like DNA sequencing to reconstruct the genomes of microbes directly from the wild. This approach is becoming popular among scientists whose job is to mine the natural world for medically or technologically important compounds, such as antibiotics. One big reason why is access..."

The rest of the transcript, along with a link to the research itself, is available on the resource itself.

This resource is a video abstract of a research paper created by Research Square on behalf of its authors. It provides a synopsis that's easy to understand, and can be used to introduce the topics it covers to students, researchers, and the general public. The video's transcript is also provided in full, with a portion provided below for preview:

"Wastewater treatment plants are a critical piece of infrastructure that depend on microbes, both resident and incoming. Incoming microbes can be beneficial but may include parasites that need to be removed. Resident microbes, meanwhile, help break down organic waste. While much is known about bacteria in wastewater treatment plants, eukaryotes are frequently overlooked. Recently, researchers examined the whole microbiome of 10 wastewater treatment plants in Switzerland. They utilized metagenomics to measure which microbes were present and metatranscriptomics to analyze their activity. Bacteria were the most numerous— but eukaryotes, particularly protists, showed the most activity, and there was a surprising number and range of active parasites, which were particularly prevalent in the inflow. Network analysis suggested predation by resident microbes likely helped remove parasites..."

The rest of the transcript, along with a link to the research itself, is available on the resource itself.

This resource is a video abstract of a research paper created by Research Square on behalf of its authors. It provides a synopsis that's easy to understand, and can be used to introduce the topics it covers to students, researchers, and the general public. The video's transcript is also provided in full, with a portion provided below for preview:

"Viruses might be small, but they drive ecological change across the planet. That includes helping lock otherwise harmful carbon away in soil. Unfortunately, little is known about soil viruses worldwide. A recent study extensively examined the viral microbiome of a Minnesotan peatland from the experimental site SPRUCE. Peatlands are the largest natural terrestrial reservoirs of carbon on earth and, as such, are a critical component of the carbon cycle. The makeup of viral communities in the SPRUCE peat varied with sample depth, water content, and carbon chemistry factors. Of the 4,326 distinct virus types identified from SPRUCE, only 164 had been previously detected in other soils and those matches were almost exclusively from other peatlands. Peatlands are a very wet, but otherwise terrestrial, ecosystem. However, none of the previously detected aquatic viruses matched SPRUCE viruses, which suggests a terrestrial and aquatic ‘species’ divide..."

The rest of the transcript, along with a link to the research itself, is available on the resource itself.

This resource is a video abstract of a research paper created by Research Square on behalf of its authors. It provides a synopsis that's easy to understand, and can be used to introduce the topics it covers to students, researchers, and the general public. The video's transcript is also provided in full, with a portion provided below for preview:

"Metagenomic techniques can be used to create microbial gene “catalogs” for different environments. First, shotgun sequencing reads are assembled, and genes are then predicted from the assembled reads. Typically, the reads are assembled either for individual samples separately or for all samples together (co-assembly). However, neither method is ideal, so a new study investigated if a third combined method, mix-assembly, could be a better choice. For mix-assembly, the genes from the individual assemblies were clustered according to their encoded proteins. The resulting nonredundant genes were then clustered with the genes from the co-assembly according to their encoded proteins to yield the final gene set. Compared with the other methods, mix-assembly produced a larger nonredundant gene set for metagenomic samples from the Baltic Sea. Mix-assembly also yielded more genes that were complete and more genes whose functions could be annotated..."

The rest of the transcript, along with a link to the research itself, is available on the resource itself.

This resource is a video abstract of a research paper created by Research Square on behalf of its authors. It provides a synopsis that's easy to understand, and can be used to introduce the topics it covers to students, researchers, and the general public. The video's transcript is also provided in full, with a portion provided below for preview:

"As the human population grows, so does the competition for resources between people and livestock. To meet the growing demand for dairy under these conditions, we need to optimize feed efficiency in dairy cattle. In ruminants, feed efficiency is determined by the ability of the rumen, and the microbes within it, to break down complex plant fibers. But the details of how the rumen microbiome contributes to feed efficiency are poorly understood. To close this gap, researchers examined the ruminal metagenomics, metatranscriptomics, and metabolomics of dairy cows with varying feed efficiency. Co-occurrence network analysis revealed that ‘high-efficiency’ animals had stronger and more numerous associations between microbes than animals with low feed efficiency. High-efficiency animals also showed positive interactions between members of the Selenomonas and Succinivibrionaceae bacterial families..."

The rest of the transcript, along with a link to the research itself, is available on the resource itself.

This resource is a video abstract of a research paper created by Research Square on behalf of its authors. It provides a synopsis that's easy to understand, and can be used to introduce the topics it covers to students, researchers, and the general public. The video's transcript is also provided in full, with a portion provided below for preview:

"Octocorals are found worldwide and are a significant part of the biodiversity in temperate marine biomes. Like most animals, corals have complex interactions with microbes, which likely have critical impacts on their health. However, very little is known about the structure and function of the octocoral microbiome or the interactions with their host. A new study examined the microbiome diversity and secondary metabolism of different octocoral species and healthy versus unhealthy tissue. Healthy octocorals have a microbiome that is distinct from the surrounding environment, host genus-specific, and defined by so-far uncultured groups of bacteria. In contrast, the microbiome of necrotic coral tissue shows large shifts in its community structure compared to healthy tissue and is colonized by seawater bacteria. Functional analysis showed that healthy corals were enriched in microbial genes associated with antiviral defense, host-symbiont recognition, micronutrient acquisition and heat-stress response..."

The rest of the transcript, along with a link to the research itself, is available on the resource itself.

This resource is a video abstract of a research paper created by Research Square on behalf of its authors. It provides a synopsis that's easy to understand, and can be used to introduce the topics it covers to students, researchers, and the general public. The video's transcript is also provided in full, with a portion provided below for preview:

"Classifying organisms is easier, cheaper, and more accurate than ever thanks to state-of-the-art gene sequencing techniques and powerful machine learning algorithms. Now, researchers report a method that boosts classification resolution beyond the genus level, a well-known barrier faced by 16S rRNA gene sequencing. The principles behind the method are simple: make classification algorithms smarter by training them on richer genetic reference databases. That starts with collecting high-quality genetic datasets for a given habitat, and then identifying reference sequences within these datasets. These sequences help capture the natural genetic variability within each group of organisms in the selected habitat. The team tested their method by creating a training set for a familiar microbial habitat: the aerodigestive tract..."

The rest of the transcript, along with a link to the research itself, is available on the resource itself.

This resource is a video abstract of a research paper created by Research Square on behalf of its authors. It provides a synopsis that's easy to understand, and can be used to introduce the topics it covers to students, researchers, and the general public. The video's transcript is also provided in full, with a portion provided below for preview:

"The deepest parts of the world’s oceans hold many mysteries, one of which involves its tiniest residents. Tiny prokaryotes called Thaumarchaeota survive in the extreme environment of the deep oceans. While the metabolic functions of Thaumarchaeota that live in shallower depths are fairly well described, those that live in the deepest sea zone – hadal water – are less well known. Now, a new study provides insight into the metabolism and cellular adaptations of deep-sea Thaumarchaeota. Using metagenomics to evaluate seawater samples from the Mariana Trench, researchers found that Thaumarchaeota present in the hadal zone were distinct from those in shallower depths. Hadal zone Thaumarchaeota depended on genes involved in bioenergetics, including those horizontally transferred from other extremophiles, to survive, and their unique genetic makeup revealed the potential to import a wide range of organic compounds..."

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This resource is a video abstract of a research paper created by Research Square on behalf of its authors. It provides a synopsis that's easy to understand, and can be used to introduce the topics it covers to students, researchers, and the general public. The video's transcript is also provided in full, with a portion provided below for preview:

"Biopesticides are widely available insect control applications derived from plant, animal, or bacterial proteins. They do not leave harmful residues and are more target-specific than chemical pesticides, but long-term use has led to resistance. Insecticidal protein genes (IPGs) are frequently found encoded in the genomes of arthropod pathogens, especially in the large plasmids found in soil bacteria. However, there are often several similar IPGs found on the same plasmid, which fragments their assembly. Further complicating the search, existing prediction tools analyze one contig at a time, and many IPGs are spread across multiple contigs, but the structure of the genome assembly graph can be used to combine multiple contigs. A new tool, ORFograph, uses this ‘graph-aware’ technique to predict IPGs. Benchmarking ORFograph on genomic and metagenomic datasets yielded both known IPGs that were “hidden” in assembly graphs and potential novel IPGs that had evaded existing tools..."

The rest of the transcript, along with a link to the research itself, is available on the resource itself.

This resource is a video abstract of a research paper created by Research Square on behalf of its authors. It provides a synopsis that's easy to understand, and can be used to introduce the topics it covers to students, researchers, and the general public. The video's transcript is also provided in full, with a portion provided below for preview:

"Isoprene is the most abundantly produced biogenic volatile organic compound (BVOC) on earth.,with annual global emissions rivaling those of methane. Unfortunately, surprisingly little is known about how isoprene is degraded in the environment. A recent study reveals a new set of bacteria that can metabolize isoprene. Researchers used DNA isotope probing to study microbes that degrade isoprene derived from oil palm trees. Among the new genera they discovered were Novosphingobium, Pelomonas, Rhodoblastus, Sphingomonas and Zoogloea. Metagenomic analysis further demonstrated that oil palm soil harboured more and more-diverse isoprene-degrading bacteria than leaves. That finding suggests that oil palm soils could be a bigger sink for isoprene than previously thought. Understanding the distribution and identity of isoprene degraders in the environment is crucial. to determine the extent to which microbes mitigate the effects of this abundant but neglected climate-active gas..."

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