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:

"Advancements in metagenomic technology have been a boon to research but may encroach on people’s expectation of privacy. A staggering amount of information can be derived from the cells we leave behind on everyday surfaces, and our ability to interpret this information to learn about YOU will only grow with time. While these advancements are not likely to ever be 100% accurate, they present a potential avenue for discrimination. Genetic privacy is not a new concept, and in the US and elsewhere, there are laws protecting people from some discrimination based on genomic-derived data, but metagenomics is not covered by the existing laws and requires its own ethical and legal scrutiny. Our world is rapidly becoming one with ubiquitous genetic, molecular, and data profiling. In that world, privacy will be difficult to protect unless statutes and laws are brought up to date with the advancement in biotechnology..."

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 gilthead sea bream is one of the most important fish farmed in the Mediterranean. Selecting for economically valuable genetic traits has helped improve bream farming efficiency. But little is known about the role played by intestinal microbes in selective breeding practices. To find out, researchers examined how genetic selection for different growth rates and diet affect intestinal bacteria in the gilthead sea bream. Bream were divided into three groups according to genetically selected growth rate: slow, intermediate, and fast, and were fed a plant-based diet, a sustainable alternative for the normally carnivorous gilthead sea bream. The plant-based diet significantly changed the microbial makeup of the slow- and intermediate-growth groups, with a much weaker effect observed for the fast-growth group. And when exposed to an intestinal parasite common to the gilthead sea bream, the fast-growth group showed significantly lower parasite intensity and abundance than the slow-growth group..."

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:

"Glaciers and ice sheets may seem dead and empty to the naked eye, but the dust that coats them, cryoconite, is a hotspot for microbes and microbe-driven biogeochemical cycling. However, little is known about the geographical diversity in cryoconite microbial communities. Most cryoconite research focuses on polar microbial communities, and reports on Asia’s high mountain glaciers are rare. A recent metagenomics study found key metabolic and light harvesting differences between polar and Asian alpine cryoconite microbiota. The Asian cryoconite community had more abundant genes for denitrification, suggesting that denitrification is enhanced there compared to polar regions. While Asian cryoconite is dominated by multiple cyanobacterial lineages that possess phycoerythrin, a green-light harvesting protein, polar cryoconite is dominated by a single cyanobacterial species (_Phormidesmis priestleyi_) that lacks phycoerythrin..."

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:

"Buried within glaciers is a history of ancient ecosystems, including microbes and viruses past. Some of the airborne microbes and viruses that populate our atmosphere are often carried by snowflakes or dust onto the surface of glaciers. By studying glacial ice cores, scientists can reconstruct histories of microbes and viruses and the climatic and environmental conditions they experienced. Two problems that plague current methods of analyzing ice cores are contamination and low microbe biomass. To address these challenges, researchers recently developed a method for decontaminating ice core surfaces and extracting clean inner ice to study microbes and viruses. When applied to ice from the Guliya ice cap on the Tibetan Plateau in China, the method revealed a unique viral community of mostly novel taxa, providing the first window into viral genomes, communities, and functions in ancient glacier environments..."

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:

"Chronic diarrhea is a messy disease that can even be fatal. In addition to being widespread in humans, it’s common in captive rhesus macaques, which are important research animals. However, the causes of chronic diarrhea are often murky. To learn more, researchers recently compared the gut microbiomes of rhesus macaques with and without chronic diarrhea. According to metagenomic sequencing, sick macaques had significant depletion of Lactobacillus bacteria but increased abundance of opportunistic pathogens and bacteria that degrade the protective intestinal mucus layer. Metabolic pathways related to virulence factor synthesis were also activated in macaques with diarrhea, whereas beneficial short-chain fatty acid pathways were enhanced in asymptomatic macaques. In addition, compared with those of asymptomatic macaques, the gut bacteria of sick macaques had higher expression of antibiotic resistance genes (ARGs) and greater resistance to most tested antibiotics..."

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:

"P-glycoprotein (P-gp) plays a critical role in gut health by transporting foreign substances and aiding communication between the innate immune system and the gut mucus barrier. However, the exact P-gp regulation mechanisms and the influence of the microbiome remain unclear. To learn more, a recent study investigated how the microbiome drives P-gp expression and function. In mice, specific vancomycin-sensitive gut bacteria were found to be necessary for normal P-gp expression, and recolonizing germ-free mice with these bacteria from donor mice restored gut P-gp levels. Certain metabolites produced by these bacteria synergistically increased P-gp expression and function in mice and a human cell line. In samples from humans with ulcerative colitis (UC), P-gp expression was reduced, particularly in lesion (involved) samples, and the levels of the anti-inflammatory P-gp substrate AEA 20:2, an endocannabinoid (eCB), were decreased..."

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 spread of antibiotic resistance is one of the most pressing threats facing global health. Every year, approximately 700,000 deaths worldwide can be traced to antibiotic resistance. That makes it crucial to identify antibiotic resistance genes (ARGs) and their transmission between humans and the environment. Unfortunately, because they rely on curated databases and are not sensitive to certain mutations, many methods can overlook novel ARGs. Now, a new machine learning method called HMD-ARG could provide researchers with a more powerful alternative. Taking sequence encoding as input, it determines whether an input sequence is an ARG, what antibiotic family the ARG is resistant to, its mechanism of resistance, and whether it is intrinsic or acquired, and even the sub-class of antibiotic the ARG resists, if it happens to be a beta-lactamase, all without querying against existing sequence databases. The HMD-ARG database is the largest of its kind..."

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:

"Genomics research has greatly increased understanding of the human gut microbiome, but the existing reference databases remain insufficient, failing to map up to half of the sequences obtained in human gut studies. To solve this problem, researchers recently created HumGut, a comprehensive global reference database for the genomes of gut microbes in healthy humans. The researchers built the database by comparing nearly half a million publicly available prokaryote genomes with over 3,500 gut metagenomes from healthy humans worldwide, and retaining the prokaryote genomes that closely matched the sequences in healthy human guts. HumGut was approximately the same size as the recently released UHGG collection and half the size of a standard reference database. However, HumGut outperformed both other databases in classifying metagenomic reads from human gut samples, resulting in a lower percentage of unclassified reads..."

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:

"Recent advances in DNA sequencing technology have made it possible to investigate community-wide changes in microbes that live on and within the human body. Unfortunately, different studies can have different results, often due to systemic biases introduced at various stages of sequence-based microbiome studies. Sample collection can introduce biases depending on the source site and method of collection. Consistent collection methods are essential, and care must be taken when choosing storage methods, times, and reagents. Increasing the usage of benchmark samples and technical replicates may also help to mitigate batch effects during sample collection and processing. Additional bias can arise during DNA extraction due to differing extraction efficiencies, contamination, and the introduction of DNA from non-living organisms. Introducing steps to this process to reduce contamination and measure inter-plate and inter-assay variability will help to reduce these effects..."

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:

"Soil and sediment microorganisms are remarkably diverse and are critical for ecosystem health. However, they are underrepresented in public databases, and assembling new metaproteomic datasets is challenging, which makes it difficult to characterize the microorganisms in specific soil samples. To increase the outputs of soil metaproteomic studies, a recent study compared various database construction strategies. Search strategies using either sample-specific metagenomic databases or public databases produced comparable peptide-spectrum matches for a floodplain soil core. However, a two-step cascaded search combining both types of databases led to greater peptide-spectrum matching. The combination strategy also improved functional annotation of the peptides, and the resulting metaproteome (MetaP) annotations correlated well with the metagenome (MetaG) annotations..."

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:

"Many animals live in symbiosis with beneficial microbes. These beneficial associations are stable over time because of partner fidelity between the animals and their microbes over multiple generations. Long-term fidelity in terrestrial host animals is well understood, but fidelity in marine symbioses, particularly in hosts with multiple symbionts, is understudied. To learn more, researchers recently examined partner fidelity between the gutless marine worm Olavius algarvensis and its seven bacterial symbionts. Fidelity varied considerably across the seven symbionts. Fidelity was highest for the two sulphur-oxidizing symbionts that provide the worms with most of their nutrition. In contrast, fidelity was lower or non-existent for other less-abundant, nutritionally less important symbionts. This variability in fidelity was unexpected, because O. algarvensis pass their symbionts directly to their offspring from one generation to the next..."

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:

"Immunotherapy is one of the most powerful weapons for fighting cancer. This approach re-activates the anti-tumor activity of compromised immune cells, but one glaring weakness is that it can over-activate the immune system, leading to adverse events that can range from mild headache to anaphylaxis. That has some researchers turning to the gut for solutions. The intestinal microbiome is a complex ecosystem that regulates our physiology and psychology, both in health and in diseases such as cancer. Growing evidence suggests that certain microbes could be harnessed to boost anti-cancer immunotherapies. These microbes could secrete molecules that promote the spread of immune cells that target tumors or enhance immune cells’ ability to recognize cancer. Bolstered by recent advancements in sequencing techniques, microbiome research could be the perfect complement to cancer immunotherapy..."

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 protects ecosystems from pollution, including dangerous heavy metal contaminants. Nitrogen and phosphorus can be removed from wastewater by denitrifying phosphorus removal sludge (DPRS). This artificial ecosystem contains many different microbes active in anaerobic, anoxic, and aerobic processes. However, heavy metal pollution can stop DPRS from reaching its full potential. So researchers examined DPRS microbiomes in response to Cr(VI), Ni(II), and Cd(II) contamination. Using metaproteomics, they found that different microbial groups adopted different resistance mechanisms. Nitrospira improved its oxygen utilization, and Nitrosomonas produced more enzymes under heavy metal stress. Phosphorus-accumulating bacteria also produced polyphosphate, which could support community-wide detoxification, and showed a variety of other resistance responses, illuminating different microbial responses to pollutants and how diversity within a community keeps it healthy..."

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:

"Non-alcoholic fatty liver disease (NAFLD) is a common metabolic disease that can progress to cirrhosis and hepatocellular carcinoma. Iron level is a known factor in the development of NAFLD, but the details of its involvement are unclear. To elucidate the mechanisms at play, researchers applied an integrative systems medicine approach. They examined the fecal metagenome, plasma and urine metabolome, and hepatic transcriptome in three human cohorts, confirming the findings in vitro and using mice. Serum ferritin levels, a marker of hepatic iron stores, was linked to liver fat accumulation and a decrease in gut microbial gene richness. Elevation in ferritin was also associated with changes in the abundance of several bacterial families. Those families were strongly correlated with iron-related liver genes. This iron-related microbiome signature was also associated with the degree of liver fat accumulation..."

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 are critical drivers of biogeochemical cycles and are the most abundant organisms in frigid regions. Identifying the genomic traits of cold-loving microbes may help explain their physiology and adaptation, but recognizing which genomic traits are important for environmental adaptation is challenging. A new study compared the genomes of Arthrobacter bacteria isolated from the Tibetan Plateau with published genomes of related bacteria and defined a new group of Arthrobacter that live in polar and alpine environments. In the laboratory, the bacteria in this group grew comparatively rapidly at 0 °C. Compared to bacteria from warmer environments, the polar/alpine bacteria had different genomic and amino acid compositions, and their predicted proteins had different stability levels and functions..."

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:

"Amplicon sequencing has made the business of identifying bacteria directly from environmental samples routine work, but there’s much room for improvement. Long-read sequencing technologies have helped cover the information gaps that plague short-read sequencing, but obtaining accurate results from complex metagenomes remains a challenge. A new study reports how LoopSeq can help boost microbial detection accuracy. Building on previous synthetic long-read (SLR) technologies, LoopSeq uses barcode-based molecular counting to construct accurate long reads from short-read sequences. Experiments confirmed that LoopSeq produces long reads with low error rates. In fact, LoopSeq produced more error-free reads of different lengths compared with other commercially available long-read technologies, and in a real-world test of six samples of US retail meat. LoopSeq could differentiate between strains within species of bacteria identified by the CDC as potential foodborne pathogens..."

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 human gut is home to a diverse community of microbes. Variations in the makeup of this community between individuals have been linked to diseases such as inflammatory bowel disease, diabetes, and cancer. Efforts to understand these differences have revealed three community types, or enterotypes, in humans, each representing the dominance of a single microbe. But because microbes co-mingle with many partners, studying the gut microbiome solely in terms of enterotypes misses on the highly nuanced nature of microbial interactions. Researchers recently addressed that shortcoming using a machine learning technique called latent Dirichlet allocation, or LDA. Their goal was to determine whether and how recurring microbial partnerships, or assemblages, are linked to the three enterotypes. Using gut metagenomic data gathered from 861 healthy adults across 12 countries LDA revealed three assemblages corresponding to each enterotype as well as a fourth wild-card assemblage that could be found in any gut..."

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:

"Ruminants have long been important in agriculture due to their ability to convert fibrous plant substrates into foods we can digest, like milk and meat. This unique digestive ability is directly tied to their gastrointestinal microbiome, which has made their microbiome a subject of interest to nutritionists, microbiologists, and physiologists. However, most microbiome research to date has focused on the rumen, and we lack a comprehensive map of the microbial diversity throughout their gastrointestinal tract (GIT). A recent study characterized the microbiome across the GIT by sampling 10 GIT regions in 7 ruminant species. In addition to common agricultural species, they sampled water buffalo, yak, roe deer, and water deer. Using this data, they constructed a microbial reference catalog with over 154 million nonredundant genes and over 10,000 metagenome-assembled genomes. They identified 8,745 uncultured candidate species, which encode genes that play key roles in ruminant digestion..."

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:

"Metagenomics is a powerful technique for studying complex microbial communities. The key computational step in this method is clustering genomic sequences from mixed samples into potential microbial genomes, but accurately classifying sequences from complex metagenomes remains challenging. Some tools depend on k-mer frequency and coverage, but such methods struggle to distinguish between similar genomes. Methods that address the similar genomes problem, like ones that rely on single-copy marker genes, in turn struggle with complex datasets. The newly developed MetaDecoder balances these challenges by using both types of methods broken into two steps. First, MetaDecoder simplifies the dataset by generating preliminary groups of sequences with the Dirichlet Process Gaussian Mixture Model (DPGMM). Then, these preliminary clusters are clustered further with a k-mer frequency probabilistic model and a modified Gaussian Mixture Model of single-copy marker gene coverage..."

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:

"Increasing evidence of gut microbe-metabolite-host health interactions has prompted increasing research on the human gut microbiome and metabolome. Statistical and machine learning-based methods have been widely used to identify microbial metabolites that can be modulated to improve gut health, but whether the findings of individual studies are applicable across studies remains unclear. In a recent meta-analysis, researchers searched for metabolites whose levels in the human gut could be reliably predicted from microbiome composition, using a machine learning approach with data processed from 1733 samples in 10 independent studies. While the predictability of many metabolites varied considerably among studies, the search identified 97 robustly well-predicted metabolites that were involved in processes such as bile acid transformation and polyamine metabolism..."

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