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 are more than just prokaryotes and viruses; they also contain important eukaryotes, including fungi and protists. However, eukaryotes are difficult to study using ‘shotgun’ metagenomics, as their signal is often overwhelmed by the prokaryotes. Some methods use eukaryote-specific marker genes, but they can’t detect eukaryotes that aren’t in the reference marker gene set, and such methods are not compatible with web-based tools for downstream analysis. But CORRAL (Clustering Of Related Reference ALignments) is designed to close those gaps. CORRAL identifies eukaryotes in metagenomic data based on alignments to eukaryote-specific marker genes and Markov clustering. It can detect microbial eukaryotes that are not included in the marker gene reference set. The process is even automated and can be carried out at scale. A recent paper demonstrates CORRAL’s sensitivity and accuracy with simulated datasets, mock community standards, and human microbiome datasets..."

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:

"Bacteria and other microorganisms cover nearly every surface on earth, including the surfaces we build and maintain. Ocean piers are unique sites at the intersection of terrestrial, aquatic, and human-built environments. Saltwater spray, inclement weather, and pollutants make piers a harsh environment for bacteria. Together, these factors suggest that piers house a unique microbiome. Researchers recently conducted a study to characterize the microbiomes found on pier surfaces. On nine piers along the coast of Hong Kong, the researchers found diverse microbiomes that were rich in novel bacterial species. Surface material (metal versus concrete) was the strongest factor influencing the bacterial community structure. Although the overall abundance was low, corrosion-associated bacteria were more prevalent on metal surfaces, and high-touch surfaces like handrails and poles had more human skin-associated microbes than other surfaces..."

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:

"Built environment microbiomes are shaped by their occupants and the outside environment. These microbiomes can have a profound impact on the health of its occupants. The International Space Station (ISS) is a uniquely sealed environment, with only the arrival of crewmembers and supplies introducing new microbes. Monitoring the ISS microbiome is important to ensure astronaut health and spacecraft integrity. So, a recent study used samples from two long-term projects, Microbial Tracking 1 and 2, which sampled the same surfaces over two 14-month-long periods. The ISS surface microbiome was dominated by microbes associated with human skin. The most represented groups were Staphylococcus and Malassezia among bacteria and fungi, respectively. Community abundances shifted over time, but did not differ between surfaces. Overall, the metabolism genes tended towards amino acid utilization rather than carbohydrate metabolism..."

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:

"Most microbial biomass in the ocean is found in the deep sea. Deep-sea microbes are important agents for organic matter (OM) recycling and storage, but it’s unclear how these organisms cope with the fluctuating OM supply in the deep ocean, especially in the deepest areas: the hadal trenches. To learn more, a new study examined the metabolic potential of microbes in the phylum Chloroflexi using sediment samples from the Mariana Trench. Metagenomic sequencing revealed 6 novel species, 4 novel genera, 1 novel family, and 1 novel order of Chloroflexi in the sediment. Based on the sequences, the associated microbes were primarily OM consumers that could degrade various organic carbon (OC), sulfur, and halogenated compounds and could even metabolize degradation-resistant types of OM, such as polyaromatic hydrocarbons (PAHs)..."

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 immune systems of fish and other animals follow circadian rhythms related to light/dark cycles. In aquaculture, the light period is commonly lengthened to enhance growth and control reproduction, but the effects on fish immunity are unclear and parasite infestations and infectious diseases remain major challenges to the industry, so a better understanding of fish immunity is needed. Microbial communities living on fish's skin - their microbiome - can help defend against parasites and pathogens, but it is currently unknown if they too have daily rhythms. To learn more, researchers recently characterized the circadian dynamics of clock genes, immune genes, and microbes in the skin of rainbow trout. They found that skin immune gene expression and the skin microbiome exhibited daily rhythms. These rhythms were affected by both a change in photoperiod and infestation with lice (Argulus foliaceus), and fish under constant light were less able to defend themselves against lice infestation..."

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:

"High-quality reference genomes are needed to understand the physiology and function of uncultured microbes in complex ecosystems. Metagenomics has been an incredibly useful tool for studying microbial communities, but assigning sequence assemblies accurately to genomes is difficult in microbial species or strains that lack a reference genome. These 'consensus genomes' have lower resolution than those generated from cultured isolates. Combining single-cell genomics with metagenomics may allow us to overcome these methodological weaknesses. Thus, researchers recently developed a framework called SMAGLinker, which integrates single-cell genomes from microfluidic droplets and uses them as guides for metagenome assembly. Compared to metagenomics alone, SMAGLinker showed more precise contig binning and higher recovery rates of rRNA and plasmids in a mock microbial community. In human gut and skin microbiota samples, SMAGLinker returned more genomes than the conventional metagenomics frameworks..."

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 mosquito microbiome is critical for mosquito development. Its influence on mosquito-borne pathogen transmission has resulted in increasing research interest. Although the mosquito microbiome has been extensively characterized, resulting in large amounts of data, neither standardized methods for mosquito microbiome research nor a curated data repository are available. With an overarching goal of collectively unravelling the role of the mosquito microbiome in mosquito biology, the authors created the Mosquito Microbiome Consortium to address this lack of standardized methods and data repository..."

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:

"Adherent-invasive E. coli, or AIEC, are bacteria that are abnormally abundant in the gut of individuals with Crohn’s disease, a chronic inflammatory disease that affects the lining of the gastrointestinal tract. To determine whether targeting AIEC could help relieve symptoms of Crohn’s disease, researchers recently explored the possibility of simply making these bacteria less sticky. The team applied a compound known as TAK-018 to gut samples gathered from patients. TAK-018 binds to the bacterial adhesin FimH, blocking bacteria clinging and interaction with cells along the intestinal wall. Tests revealed that TAK-018 not only prevented AIEC bacteria from adhering to intestinal tissue but also reduced inflammation, helping preserve the integrity of this important barrier. While more work is needed to understand how TAK-018 operates in the body, the drug is known to be safe and well-tolerated in patients and is currently undergoing phase II testing for the treatment of Crohn’s disease..."

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 plant microbiome plays integral roles in plant growth and health, and the soil environment of the roots, known as the rhizosphere, can recruit beneficial microbes to suppress soil-borne pathogens. However, the processes that regulate microbiome assembly and function both below- and aboveground during pathogen invasion are unclear. To learn more, researchers recently compared the microbiomes of different parts of chili pepper plants with or without Fusarium wilt disease (FWD). Sequencing analysis revealed that FWD affected the root/stem microbiomes (particularly the upper stem microbiome) more than the fruit microbiome. FWD also affected fungal communities more strongly than bacterial communities and made the roots and stems more susceptible to colonization by pathogenic fungi..."

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:

"When scientists want to understand microbial populations, they turn to metagenomics. The standard technique, shotgun metagenomics, produces nearly complete genomes, enabling researchers to predict traits within a species. Unfortunately, this method applies to broad populations, making it difficult to precisely link metabolic traits to individual species. Sequencing single cells addresses this shortcoming, but the information provided is often incomplete. Now, researchers have developed a way to target smaller populations for metagenomic sequencing. Before sequencing, the researchers added a critical sorting step using hybridization chain reaction fluorescence in-situ hybridization (HCR-FISH). Isolating a population of interest before the sorted cells were used for shotgun sequencing. The result was a more complete genome of a targeted species with low diversity. The technique provided the team enough precision to analyze metabolic features of bacteria sparsely found feeding on decaying diatom algae..."

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:

"Disturbances such as antibiotics and environmental toxicity can alter microbial communities in the gut Afterward, gut microbe species recover to different extents, resulting in altered proportions of the microbes post-disturbance Unfortunately, it is still unclear what shapes the composition of gut microbiota ecosystems during recovery A recent study evaluated these changes in yellow perch after exposure to toxic metals Researchers exposed the fish to cadmium chloride in the laboratory and then evaluated the microbes on their skin and gut surfaces DNA sequencing demonstrated that while gut microbes recovered well after exposure Skin microbes recovered incompletely, resulting in the proliferation of opportunistic pathogens Interestingly, the type of cadmium exposure also affected recovery Recovery was better in microbial communities after constant exposure, while gradually increasing exposure altered microbe levels to a greater extent Although further studies are needed to fully understand how microbe.."

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 characteristics of the world around us vary from one location to the next. This is also true of aquatic environments, where bottom-dwelling microorganisms must cope with variation in temperature, salinity, dissolved oxygen, and nutrients. Unfortunately, little is known about how these microbial communities and their functional genes respond to environmental changes. A team of researchers at Stockholm University recently set out to do just that by collecting samples of sediment at 59 sites spanning 1,145 km across the Baltic Sea. They characterized the environmental attributes and microbial community at each site using genetic sequencing and other laboratory techniques. The researchers found that salinity and dissolved oxygen content had the greatest effects on the microbes making up each community with the communities in oxygen-deficient “dead” zones being particularly dissimilar to those with higher dissolved oxygen content..."

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:

"BackgroundThe role of bacterial symbionts that populate octocorals (Cnidaria, Octocorallia) is still poorly understood. To shed light on their metabolic capacities, we examined 66 high-quality metagenome-assembled genomes (MAGs) spanning 30 prokaryotic species, retrieved from microbial metagenomes of three octocoral species and seawater. ResultsSymbionts of healthy octocorals were affiliated with the taxa Endozoicomonadaceae, Candidatus Thioglobaceae, Metamycoplasmataceae, unclassified Pseudomonadales, Rhodobacteraceae, unclassified Alphaproteobacteria and Ca. Rhabdochlamydiaceae. Phylogenomics inference revealed that the Endozoicomonadaceae symbionts uncovered here represent two species of a novel genus unique to temperate octocorals, here denoted Ca. Gorgonimonas eunicellae and Ca. Gorgonimonas leptogorgiae..."

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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:

"Multiple myeloma, or MM, is the second-most common malignancy of the blood. In MM, malignant plasma cells in the bone marrow crowd out healthy cells. The result is anemia, bone damage, and renal damage. Researchers have now discovered that part of that damage, especially to the kidneys, is caused by a microbial imbalance triggered by MM. Comparing fecal samples between 19 patients newly diagnosed with MM and 18 healthy controls revealed significant differences in the makeup of their gut microbiomes, with patients diagnosed with MM showing a high abundance of nitrogen-recycling bacteria. The accumulation of these bacteria could create a vicious cycle, where they cause a buildup of urea or ammonium (NH₄⁺) that leads to progressive kidney failure and worsening MM and cultivates more nitrogen-active bacteria. Data from a larger population could help clarify these findings and lead to new ways of diagnosing and treating multiple myeloma..."

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:

"Diarrhea is common among calves and causes huge losses to the global cattle industry. Fecal microbiota transplantation (FMT) is one promising approach to prevent and treat calf diarrhea. However, achieving success with FMT is difficult because of farm management differences, a lack of good donors, and the difficulty of recipient selection. To guide more effective FMT, a recent study investigated factors related to FMT success or failure in 20 donor–recipient pairs. The overall success rate for diarrhea improvement was 70%. Selenomonas bacteria were found in both donors and recipients when FMT was successful, suggesting that Selenomonas may be a biomarker of donor–recipient compatibility, and Sporobacter was identified as a potential biomarker for good donor selection. Pairs of correlations between specific microbial taxa and metabolites were also linked to success, and low levels of pre-FMT glycerol 3-phosphate, dihydroxyacetone phosphate, and isoamylamine were predicted to facilitate good results..."

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:

"Natural microbial systems are all around us, from nutrient-rich soil to churning seawater to our own bodies. These complex systems include bacteria, archaea, viruses, and microbial eukaryotes. One of the best methods available for analyzing these systems is shotgun sequencing, which generates vast quantities of DNA sequence data. However, current data annotation methods don't include a dedicated way to find eukaryotic sequences. Now, researchers have introduced a bioinformatics method called EukDetect. EukDetect uses a database of over 500,000 universal marker genes from 241 conserved gene families across thousands of eukaryotes. Broad taxonomic coverage and accurate identification of low-abundance and high-similarity sequences were possible with EukDetect, and bacterial contamination was no obstacle to identifying eukaryotic species. EukDetect highlights information that could be missed or obscured in standard shotgun sequence analysis..."

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:

"Blue-green algae, or cyanobacteria, are photosynthetic bacteria that live in water and are important oxygen producers. Human-driven changes are a major factor causing seasonal cyanobacterial blooms, which can cause mass death of aquatic animals. Bacteria-infecting viruses, called phages, could potentially be used to control these outbreaks with minimal environmental disruption. But to date few freshwater ‘cyanophages’ have been isolated or had their genomes sequenced. Recently, researchers isolated a strain of cyanobacteria from Lake Chaohu, a massive lake in China with seasonal cyanobacterial blooms. Using the new cyanobacteria strain, they isolated five new freshwater cyanophages with varying tail structures from the same lake. While viruses can have RNA genomes or even single-stranded DNA genomes, all five isolated phages had double-stranded DNA genomes. Further analysis suggested that they all use different DNA packaging mechanisms and are evolutionarily distinct..."

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:

"Microorganisms exist in nearly every part of our planet, including areas that can barely support life. The McMurdo Dry Valleys of Antarctica were considered lifeless until microbial communities were found inside porous rocks. Little is known about the evolution, diversity, and genetics of these exclusive cryptoendolithic life-forms. Recently, researchers used sequencing technology to generate microbial metagenomes from Antarctic rocks. They obtained 497 bacterial genomes from 269 previously uncharacterized candidate species. “Candidatus Jiangella antarctica” may be adapted to severe conditions, as it was found in all samples and contained additional genes. Most of the new species diverged from their known relatives 1.2 billion to 410 million years ago, long before the origin of modern Antarctica, and the Antarctic bacteria are functionally distinct from their closest known relatives, suggesting that groups of cold-adapted bacteria arrived when Antarctica became cold, spread, and diversified..."

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:

"Flavonoids are ubiquitous, nutritionally non-essential natural products of plants and they are frequently used to promote health. However, flavonoid metabolism and the impact of flavonoids on gut microbiomes are not well understood. Bamboo is particularly flavonoid rich, making giant pandas, with their all-bamboo diet, a unique research target. A recent study examined the diet, feces, and plasma of giant pandas to get a comprehensive view of flavonoid metabolism and its impact on the gut microbiome. The researchers found that bamboo leaves had more flavonoids than bamboo shoots. They also found that only a small fraction of dietary flavonoids were absorbed into the bloodstream and that the gut microbiota extensively utilized and transformed the flavonoids. The seasonal shifts in the flavonoid profile of bamboo drove changes to the gut microbial composition..."

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:

"Terrestrial fungi are well known as decomposers, breaking down dead matter to return nutrients to the soil. However, the roles of fungi in the ocean are less well understood. Oceanic fungi occur with other microbes throughout the water column, where they break down carbohydrates. A recent study examined the role of these marine fungi in recycling proteins, which represent more than half of living and dead marine biomass. Researchers performed a multi-omics analysis of all oceanic fungal-affiliated enzymes that break down proteins (peptidases). They found that the abundance, diversity, and expression of fungal peptidases increased with ocean depth, similar to fungal carbohydrate-degrading enzymes (CAZymes). This indicates a strong link between the carbon and nitrogen cycles in the open ocean. In-depth analysis of the most widely utilised fungal proteases revealed that the majority of pelagic fungal communities are dominated by saprotrophy rather than parasitism..."

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