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 microbiome can both positively and negatively affect host health, with broader effects on ecosystems and evolution. Prokaryotic members of the microbiome are commonly studied by sequencing 16S rRNA fragments, but eukaryotic members are hard to study because their analogous 18S rRNA fragments are vastly outnumbered by those of the host. To solve this problem, researchers recently developed a new method, CRISPR-Cas Selective Amplicon Sequencing (CCSAS). In CCSAS, a single-guide RNA specific to the host taxon directs the enzyme Cas9 to cleave host 18S rRNA, preventing its amplification and detection, while the 18S rRNA of eukaryotic microbes like fungi and protists is left intact. The researchers tested the method by investigating the eukaryotic microbiome in settled oyster larvae (spat). CCSAS uncovered a diverse array of eukaryotic microbes with much less host (metazoan) fragment contamination than alternative methods..."

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:

"Designer rootstocks enable fruit trees to thrive under otherwise unbearable conditions, providing strong anchorage and defending against biological and nonbiological stressors. But what role does the root microbiome play in this assistive act? To find out, researchers used 16S rRNA sequencing to examine the rootstocks of Valencia orange trees in Florida. Results showed that the genetic makeup of different rootstocks determined how the root microbiome responded to compost treatment. The aspects of the root microbiome that were rootstock- specific included bacterial abundance, diversity, and community composition. These findings suggest that specific bacteria drive changes in nutrient concentrations accessed by different rootstocks. Understanding this intimate relationship is important to supporting overall plant health and could inspire research into how root microbes might affect other parts of trees..."

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:

"Aquaculture is a critical industry for human food production, and strategies to improve fish nutrition while protecting the environment can help maximize aquaculture output and sustainability. However, the roles of the gut microbiome in fish nutrition are not well understood. To support further research, scientists recently developed SalmoSim, an in vitro model of the Atlantic salmon gut and microbiome. The researchers linked three bioreactors seeded with gut material from adult farmed salmon to simulate the stomach (S), pyloric caecum (PC), and midgut (MG). When a fishmeal “diet” (FMD) was supplied, SalmoSim’s microbial community stabilized in approximately 20 days and was ecologically indistinguishable from the real fish microbiome used to inoculate the system. Switching from the FMD to a fishmeal-free diet (FMF) for 20 days did not affect most microbes (operational taxonomic units, OTUs) in either SalmoSim or real salmon..."

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:

"Disruption of the gut microbiome composition is associated with many metabolic, inflammatory, and infectious diseases in humans. Accurately profiling microbiomes at the strain level is important for gaining a clear understanding of the microbiome’s role in disease. However, the existing tools can’t reliably classify microbes at strain resolution, making it difficult to detect composition changes. A new bioinformatic tool, SameStr, addresses this difficulty by identifying strains that are shared between metagenomes according to the similarity of single-nucleotide variants (SNVs) in certain species-specific marker genes. In validation studies, SameStr was more sensitive than other tools in identifying shared strains among mock populations, while remaining robust against false-positives..."

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 Atacama Desert in northern Chile is the driest nonpolar desert on Earth. The almost complete lack of precipitation means that it can support very little life, especially in its hyperarid core. But this core region harbors expansive fields of ancient boulders that scientists think could shelter unique microbes from the extreme desert environment. To find out, researchers used DNA sequencing techniques to compare the microbes inhabiting the soil directly beneath the Atacama Desert boulders and in the open areas beside them. They found a substantial difference in these microbial communities, with significantly more archaea occupying the soil below the boulders than beside them. Remarkably, the team also discovered that many of these archaea belong to a completely new genus of Thaumarchaeota archaea, which they named Candidatus Nitrosodeserticola. These archaea harbor genes involved in ammonia oxidation, carbon fixation, acetate metabolism, and the ability to tolerate extreme environmental conditions..."

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 the age of antibiotic-resistant microbes, developing new anti-infective alternatives is crucial. A new study takes a novel approach – turning our gaze back on the microbes that colonize us. Commensal skin bacteria are fundamental to maintaining the skin barrier and protecting us from pathogenic microbes. While dysbiosis of the skin microbiome is associated with diseases such as psoriasis and atopic dermatitis, in healthy skin, skin commensals protect the host by supporting the immune system and impairing the growth or virulence of competitors. Researchers screened of over 3000 human skin isolates to evaluate bacterial competition. Their results revealed a strain of Staphylococcus hominis with activity against Gram-positive pathogens, mediated by a molecule called MP1. Using either a “probiotic” approach or nanoparticles could replicate the effect of MP1, reducing infection by the pathogenic bacteria Staphylococcus aureus in mice. While future studies will determine whether S..."

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

The goals of the Thermal Biology Institute's webpage are to present cutting-edge research focused on the biology of geothermal systems, to promote collaboration among researchers and resource agencies, and to advance public education on the biocomplexity of geothermal environments. Information is organized by topic including hot topics, research, current events, outreach, education, and electronic resources.

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:

"Tiny but tenacious, the tick is one of the most dangerous creatures on earth—and perhaps one of the most misunderstood. Because while typically associated with Lyme disease, ticks can actually harbor more than 120 different species of bacteria, each a unique source of infection. Unfortunately, the one-microbe, one-disease myth surrounding the tick extends well beyond the court of public opinion. The lack of broad-spectrum diagnostics in the clinic means that a single sufferer of tick-borne disease may spend up to $60,000, or 54,000 €, on more than 11 visits, doctors, and tests just to get a proper diagnosis. A 2018 blood analysis of 432 individuals showing symptoms of Lyme disease puts the problem in perspective—and calls for revamped screening procedures that decrease the probability of missed or misdiagnosis..."

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 that infect bacteria and archaea are abundant in human and environmental microbiomes. Their roles in manipulating, killing, and recycling microbes makes them key players in environmental processes and human health and disease, including inflammatory bowel diseases. In spite of their importance, the tools available for analyzing viral genomes are limited. Now, a new tool allows researchers to identify viruses and predict their functions using genomic data. VIBRANT (Virus Identification By iteRative ANnoTation), is the first software to use a hybrid machine learning and protein similarity approach. going beyond traditional limitations to maximize the identification of highly diverse viruses. In validation experiments with reference datasets, VIBRANT recovered higher-quality virus sequences and reduced false identification of non-viral genome fragments compared to other identification programs..."

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:

"Children in daycare centers are exposed to various bacteria and fungi. Exposure to certain indoor fungi can lead to adverse health effects, but the extent to which the fungal community, or mycobiome, affects children in daycares remains unclear. To learn more, a recent study investigated the indoor mycobiomes of two daycare centers in Norway over the course of a year. DNA metabarcoding of dust samples from the daycares revealed that less-used rooms had fungal communities similar to the outdoor mycobiome, which were markedly different from the communities in the main rooms. The less-used rooms tended to have more Basidiomycota species. while the main rooms had more Ascomycota species. The indoor mycobiome composition was also strongly affected by the outdoor climate, exhibiting clear seasonality..."

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:

"Interactions among probiotics, resident gut microbes and host factors affect probiotic engraftment and the resulting therapeutic effects. These interactions depend on gut-adaptive evolution of the probiotic strains, but the underlying processes—and their differences among host species—are unclear. In addition, the evolutionary effects of probiotics on native gut microbes are not well characterized. A recent genomics study examined the evolution and effects of the probiotic Lactiplantibacillus plantarum HNU082 (Lp082) in the human, mouse, and zebrafish gut. In all three species, Lp082 acquired single-nucleotide mutations. In vitro, the gut-adapted strains exhibited improved fitness related to carbohydrate utilization and acid tolerance and remained genetically stable for three months. In the human and mouse gut, Lp082 engraftment increased the numbers of mutations of the resident gut microbiota (GM) by 10- to 70-fold..."

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:

"Type 2 diabetes is a serious disease affecting the way the body converts food into energy, and an increasing number of people are diagnosed with the disorder each year. Those whose mothers had hyperglycaemia in pregnancy (HIP) are particularly at risk, and it is possible that the microbes living in the mother’s gut may be at least somewhat responsible. To find out more, researchers compared the metabolic characteristics and gut microbial communities of mice whose mothers had HIP. The mice were born either naturally or via cesarean section and were nursed by either their own mother or a foster mouse without HIP. Cesarean section birth and foster nursing prevented the transmission of gut microbes from biological mother to offspring. In fact, the gut microbial communities of fostered offspring were more closely related to those of their foster mothers than to those of their biological mothers, with increased relative abundances of Bifidobacterium species and short-chain fatty acid bacterial metabolites..."

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:

"Differential abundance analysis (DAA) is a key statistical method for comparing microbiome compositions under different conditions, such as health vs. disease. However, DAA is complicated by the use of relative, rather than absolute, abundance values and by a high risk of false positives, or detection of significant effects when there aren’t any. In addition, the existing DAA tools can produce very divergent results from the same data, making it difficult to select the best tool. To provide guidance, a new study comprehensively evaluated the currently available tools with simulations based on real data. The researchers found that none of the tools were simultaneously robust, powerful, and flexible. Therefore, they concluded that none were suitable for blind application to real microbiome datasets. To build a better path forward, the researchers designed a new tool, ZicoSeq that drew on the strengths of the other available DAA methods while addressing their major limitations..."

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 gut microbiome is altered in patients with inflammatory bowel disease and plays an important role in colitis development in mouse models. However, the roles of host-microbe interactions in intestinal inflammation remain unclear and are difficult to study because of interindividual microbiome variability. To address these issues, researchers recently used a reductionist model and multiomics to study host-microbe interactions in wild-type and colitis-prone Was-/- mice. Was-/- mice colonized with both altered Schaedler flora (ASF) and Helicobacter developed colitis, while those colonized with either type alone did not. Bacteria also infiltrated the colon mucus layer in Was-/- mice, and Helicobacter and mucosal Mucispirillum schaedleri were positively correlated with fecal levels of the intestinal inflammation marker LCN2. Consistent with this, fitness- and immunogenicity-enhancing M. schaedleri genes were upregulated in Was-/- mice..."

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