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 ecology research, population density is an important metric for community analysis studies. Yet even though microbiomes are small ecosystems, microbiome studies rarely report the bacterial density. To evaluate the significance of bacterial density in gut microbiome research, a recent retrospective study examined rectal swabs from hospitalized patients. The authors found that bacterial density had important methodologic significance, as it predicted vulnerability to sequencing contamination. Specifically, low-bacterial-density specimens had higher levels of sequencing contamination. Clinical factors like age, exposure to antibiotics, and comorbidities also varied with bacterial density. Older patients and those with multiple co-morbidities had high bacterial density, while antibiotic exposure correlated with low density. Lastly, bacterial density showed potential as a prognostic indicator, as the density at time of admission correlated with subsequent infection..."

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:

"Trees support so much life on Earth – but one important component might easily be overlooked. The phyllosphere – the aerial surfaces of plants, including leaves – is a microbial habitat for diverse microorganisms. Phyllosphere bacteria play key roles in plant health, human health, and ecosystem function, but unfortunately, not much is known about how plants and their associated microbes influence each other. A recent study evaluated this relationship in a diverse neotropical forest. Using shotgun metagenomics, researchers found that the metabolic functions of phyllosphere microbes varied based on their tree hosts. While overall there was low variability in plant-associated microbes, suggesting that certain microbes form a “core microbiota” for neotropical trees, bacterial metabolism and membrane transport functions varied between plant species..."

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:

"Bathyarchaeota is a newly proposed phylum of archaeal organisms. Its diverse members inhabit anoxic environments such as hot springs, salt marshes, mangrove sediments, and the sub-seafloor. While Bathyarchaeota is believed to be an important driver of the global carbon cycle, little is known about the phylum's true metabolic potential. A new study constructed nine metagenome-assembled genomes of Bathyarchaeota using mangrove and mudflat sediments of the Futian and Mai Po Nature Reserves. Comparative analyses of these genomes expanded the role of this phylum in phototrophy, autotrophy, and the nitrogen and sulfur cycles. and findings suggested the Bathyarchaeotal subgroup can sense light and thrive in micro-oxygen conditions. The results provide insight into the metabolic abilities and diverse lifestyles of members of Bathyarchaeota and highlight the crucial role of this newly proposed phylum in global biochemical cycles..."

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:

"Although invisible to the naked eye, beds are teeming with microbial life, which might influence how the human body’s own microbial communities form and develop, especially in infancy. To explore this hypothesis, researchers analyzed 577 dust samples from the beds of infants, as well as 542 airway samples from a child cohort study. The diversity of bacteria and fungi detected in bed dust correlated with one another, suggesting an interplay between the two types of organisms in bed dust. Additionally, the microbial makeup of bacterial and fungal communities in bed dust was influenced by different environmental factors. Bacterial communities were influenced by type of home, living environment, sex of siblings, and pets, whereas fungal communities were influenced by type of home and sampling season. There was limited evidence of microbial transfer between bed dust and infant airways..."

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:

"Plants lack the nervous system of animals and are usually firmly rooted in the ground, making it easy to think of them as being unaware of the world around them. But evidence suggests that plants can indeed sense and actively respond to their environment. When under attack by microbial pathogens, some plants have been shown to recruit beneficial microbes to aid in their defense. A recent study uncovered this phenomenon in tangerine trees infected with the fungus that causes melanose, one of the most destructive diseases of citrus plants worldwide. Researchers identified the microorganisms living on infected and uninfected leaves with both culture-based and DNA sequencing techniques. They found that the infected and uninfected leaves hosted distinct microbial communities, with the microbes occupying infected leaves having beneficial and antifungal characteristics..."

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:

"Next-generation sequencing (NGS) studies have led to dramatic improvements in our understanding of human microbiomes. However, this method is based on the presence of DNA and cannot distinguish between living and dead microbes on its own. Environments like our skin are hostile and have high microbe turnover, which leads to significant amounts of DNA from dead microbes, which can lead to inaccurate community estimations in NGS studies. To overcome this, researchers tested the feasibility of pre-treatment with Benzonase to digest unprotected DNA. They used both mock bacterial communities and skin microbiome samples with inactivated bacteria or bacteria-free DNA spiked-in. Benzonase (BDA) pre-treatment reduced the levels of DNA from dead bacteria in both mock and natural communities. It also reduced the amount of host DNA in samples with high human-to-microbial DNA ratios without obvious impact on the microbial profile..."

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 analysis frequently plays an important role in development pipelines for human fecal microbiome-related products, but validation and standardization of the methods used to extract DNA and assemble sequence libraries for these studies is currently lacking. To close this gap, researchers recently characterized existing protocols for accuracy and precision. First, they tested the quantification accuracy by using a defined mock community of bacteria. Then, the protocols that performed as expected were evaluated for both within- and inter-laboratory precision metrics. The protocols were also tested against the MOSAIC Standards Challenge samples. Lastly, they defined performance metrics for the recommended protocols to provide best-practice guidance. The uptake of the recommendations generated here should improve reproducibility in human metagenomic research and therefore facilitate development and commercialization of human microbiome-related products..."

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:

"HIV infection remains unacceptably common among women in sub-Saharan Africa. One possible contributing factor is the composition of the vaginal microbiota, as African, Caribbean and other Black (ACB) women have an increased rate of bacterial vaginosis (BV), which is associated with increased HIV risk. Targeting the vaginal microbiota and treating BV could help prevent HIV among women. In the absence of BV, the vaginal microbiota is predominated by one of several _Lactobacillus_ species that provide different levels of BV and HIV protection. _L. crispatus_ is associated with exclusion of BV-associated bacteria and reduced HIV risk while _L. iners_, the most common species among ACB women, seems less protective. The reduced protection provided by _L. iners_ is supported by genomic differences, such as the absence of a gene encoding an HIV-trapping D-lactate isomer and the presence of genes encoding pro-inflammatory cytotoxins..."

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 microbial community, called the gut microbiota, plays an important role in health for both humans and animals. The bacterial members of this community are the most numerous and consequently get the most attention in research. However, there are often overlooked but important fungi, viruses, archaea, and protozoa in the microbiota too. The fungal subset of a microbiota is called the mycobiota, and it is particularly understudied in birds. To close this gap, a recent study comprehensively characterized the mycobiota of chickens bred for meat. While gut bacterial communities typically stabilize with age, the chicken mycobiota was dynamic over time with no clear pattern of successive changes and low overall diversity. The upper gastrointestinal (GI) tract mycobiota was more diverse than the lower tract mycobiota, and just 25 core fungal groups accounted for more than 85% of the fungal population in each section of the GI 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:

"Birds can carry and transmit viruses to humans and other animals. Thus, understanding the viral community hosted by birds could help us predict future outbreaks of human disease. A recent metagenomics study took a broad look at the viruses found in the gut of wild and captive birds. The dataset included samples from over 3,000 birds that represented over 87 species and 10 different phylogenetic orders and the researchers characterized genomes from numerous viral families including astroviruses, coronaviruses, parvoviruses, and adenoviruses. Examining trends, they found that wild birds had higher viral diversity than captive birds. There was also evidence of potential cross-species transmission between wild birds and domestic poultry. Further analysis of the viral genomic sequences revealed differences in virus distribution patterns between wild and captive birds. Different phylogenetic orders of birds and geographic sites also had distinct distribution patterns..."

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:

"Bogs are unique ecosystems, which have important ecological functions in carbon storage, climate stability, water quality, and biodiversity. The bog microbiome, composed mostly of bacteria that live in association with bog plants, plays key roles in these functions. However, the differences in associated bacteria between vascular plants and the non-vascular bryophytes that predominate in bogs remain unclear. Researchers recently used shotgun metagenomics to investigate the microbes associated with 12 representative bog species. Vascular plants tended to be colonized by specific bacteria, while bryophytes exhibited greater bacterial species richness and diversity. The two plant groups also had different marker species. The gene profiles of vascular plant- and bryophyte-associated microbes revealed functional differences, including differences in nitrogen cycling..."

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:

"Bacterial predators are a vital selective force in bacterial communities. Predation releases nutrients that power biogeochemical cycling. Bacterial predators are typically classified as “obligate” predators, which MUST feed on bacteria to survive, and “facultative” predators, which can subsist on a non-bacteria diet. The discovery of a new group of bacterial predators, however, proposes a revision to this classification system. These are Bradymonabacteria. Analyses of their feeding behavior and genetic makeup revealed that Bradymonabacteria adopt living strategies between those of obligate and facultative predators. Like obligate predators, for example, they possess multiple metabolic deficiencies that are shored up only by predation, while their large genomes suggest that Bradymonabacteria could effectively tolerate the absence of prey..."

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 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:

"In terrestrial and freshwater ecosystems, fungi are essential for nutrient cycling, releasing carbon dioxide into the atmosphere and inorganic nitrogen and phosphorus into the soil. In contrast, in marine environments, fungi are often considered to be associated with debris and less essential to the element cycle than other microbes such as prokaryotes and phytoplankton. A recent study sought to better understand the role of open-sea, or pelagic, fungi in carbon cycling in the ocean. Using multi-omics techniques and existing genomic datasets, researchers performed a global analysis of carbohydrate-active enzymes (CAZymes) – key enzymes in carbon cycling – in ocean fungi. They found that pelagic fungi are active in carbohydrate degradation, as indicated by a high ratio of CAZyme transcripts..."

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:

"_Clostridioides difficile_ infection (CDI), the most common hospital-acquired infection in the U.S., can cause severe diarrhea and even death, and more than 15% of infected individuals experience recurrent infection within 8 weeks. CDI is related to gut microbiome imbalance, but the factors that influence recurrence are not well understood. To identify potential predictors of recurrence, researchers sequenced and metabolically profiled the gut microbiomes of 53 patients with CDI over time. Compared to patients with no recurrence, patients with recurrent CDI had slower recovery of gut microbial diversity, and depletion of important anaerobic microbes, such as certain _Clostridium_ species. The patients with recurrent CDI also had delayed recovery of microbial metabolites in the gut, which was likely associated with dysfunction of the microbiome or of the host tissue..."

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 skin is the interface between the human body and the environment, and the different features in distinct skin regions, such as different temperatures, humidity levels, gland densities, and pH values, create a variety of niches that can support a diverse skin microbiome. This microbiome includes bacteria, archaea, viruses, fungi, and even mites. A healthy skin microbiome helps maintain skin homeostasis, protects against pathogens, communicates with and trains the immune system, and affects wound healing. However, the skin microbiome can be influenced by many factors, including intrinsic factors like aging and extrinsic factors like cosmetic. Recent advances in molecular biology techniques and next-generation sequencing have drastically increased our understanding of the microorganisms that live on our skin, but the microbes are often still difficult to culture and study..."

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:

"Spaceflight affects the human body in numerous ways, but one underexplored area is the mouth. The mouth is home to rich populations of bacteria and fungi which, studies have hinted, can undergo shifts during long and even short space missions. For the first time, researchers have tracked changes in the oral microbiome during and after spaceflight and examined how those changes might reawaken dormant viruses — a phenomenon long known to affect astronauts. The team analyzed saliva samples from 10 male astronauts for microbial makeup and for the presence of Epstein-Barr, herpes simplex, and varicella zoster virus. Only Epstein-Barr virus counts appeared to track with changes in microbial composition during spaceflight. For example, increased virus counts coincided with increased numbers of bacteria of the genus Gracilibacteria, while low counts coincided with increased numbers of members of Oribacteria and Hemophilus..."

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 factors affect the evolution of species, but a new influence has recently been recognized. Gut microbes – tiny residents of the intestinal tracts of all animals – have wide-ranging effects on the physiology of their hosts and scientists are increasingly appreciating that diversification may actually be correlated with changes in the gut microbiota. However, the extent to which gut microbes evolve along with a host species remains unclear. A recent study examined this correlation using an ideal model – a system where evolution repeated itself in different geographic settings. Beginning with two groups of Nicaraguan cichlid fish that evolved in parallel in different crater lakes researchers sequenced microbes from fish guts and lake water to determine whether species diverged in parallel. They found that bacterial communities in fish were distinct from those in lake water..."

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:

"Skin microbes play fundamental roles in maintaining balance in the skin. An imbalance – microbial dysbiosis – is associated with the onset and progression of many common skin diseases. To better understand the functions of skin microbes, a recent study aimed to develop a catalog of skin microbiome reference genes. Using a sample of 822 skin samples from Han Chinese individuals, combined with 538 previously obtained North American samples, researchers constructed the integrated Human Skin Microbial Gene Catalog, or iHSMGC, comprising over 10 million genes. Using the catalog, they found that skin commensals such as Staphylococcus are an important reservoir of antibiotic resistance genes (ARGs). Microbe- and skin site-specific ARG signatures were identified, as were differences between populations. Two patterns of microbial networks – “cutotypes” – were identified in the newly analyzed samples, with Moraxella osloensis and Cutibacterium acnes serving as markers of the cutotypes..."

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.