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 laboratory and computational tools available to microbiome researchers have greatly improved in recent years, especially in assembling genomes from complex communities. Most of the research to date has focused on macrodiversity, which is classical ecology metrics like population abundance, α-diversity, and β-diversity. But microdiversity — population genetics metrics like single nucleotide polymorphisms (SNPs) and selective pressures — is important to consider. There are several technical and accessibility issues that hinder widespread analysis of microdiversity in metagenomic datasets, but the recently developed open-access software tool MetaPop is designed to close this gap. MetaPop provides a user-friendly interface to analyze both the macro- and microdiversity of microbial and viral community metagenomes. For small datasets, MetaPop can be run on a laptop, making it a practical choice for non-bioinformaticians or labs without access to high-powered computing..."

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.

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

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

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

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

"Cancer is a leading cause of mortality worldwide. Some types of cancer are linked to infection by viruses and bacteria, but many such links remain unexplored, indicating that other carcinogenic microbes are likely to exist. A recent study used a large, high-quality collection of 3025 whole-genome sequencing datasets to identify relationships between cancer, bacteria, and viruses. A custom-built pipeline based on the Kraken taxonomic sequence classification system software was used to identify bacterial and viral sequences in the datasets. A total of 3,534,707 read pairs matching 218 bacterial, viral, or phage species-level taxa were detected in tumor and matched healthy tissues. Of these, 27 taxa were identified to be linked to cancer. The findings support known associations between viruses, bacteria, and tumor and patient phenotypes and also reveal entirely new associations. For example, Pseudomonas spp..."

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 discipline of planetary protection, spacecraft are assembled in unique cleanrooms to prevent microbe transfer between planets. The cleanliness of these rooms has traditionally been assessed with the NASA standard spore assay (NSA), but advanced molecular techniques have revealed that this assay may be insufficient for contamination control. To learn more, researchers recently analyzed floor samples collected over 6 months from the Spacecraft Assembly Facility at NASA’s Jet Propulsion Laboratory. The NSA coupled with Sanger sequencing identified 16 genera of bacteria, 97% of which were spore-formers, primarily Bacillus subtilis and Virgibacillus pantothenticus. However, 16S rRNA amplicon sequencing detected 51 additional bacterial genera. When viable and dead organisms were differentiated, amplicon sequencing identified 46 viable non-spore-forming genera (86% of bacteria) and 8 viable spore-forming genera (14% of bacteria)..."

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

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

"Microbial phylogeography is the study of diversification and distribution of microorganisms across space and time, offering unique insights into eco-evolutionary processes that influence the ubiquity and diversity of microbial populations in the environment. However, our understanding of microbes lags far behind that of macroorganisms, primarily because many dominant microorganisms are difficult to culture. A recent study evaluated the microbial phylogeography of one tiny inhabitant of freshwater ecosystems. Bacterioplankton are common to many freshwater ecosystems despite the fact that these habitats are geographically disconnected, and better understanding their microdiversity is key to uncovering the eco-evolutionary processes behind their dominance. Using long-read amplicon sequencing, researchers evaluated pelagic bacterioplankton assemblages in 11 deep freshwater lakes in Japan and Europe..."

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

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

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

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

This micrograph was taken at 1000X total magnifcation on a brightfield microscope. The subject is Bacillus cereus cells were grown in broth culture for 48 hours at 30 degrees Celsius. The cells were heat-fixed to a slide and stained with malachite green (endospores) and safranin red (vegetative cells) prior to visualization.Image credit: Emily Fox

This micrograph was taken at 1000X total magnifcation on a brightfield microscope. The subject is Bacillus megaterium cells were grown in broth culture for 5 days at 30 degrees Celsius. The cells were heat-fixed to a slide and stained with malachite green (endospores) and safranin red (vegetative cells) prior to visualization.Image credit: Emily Fox

This micrograph was taken at 1000X total magnifcation on a brightfield microscope. The subject is Bacillus subtilis cells were grown in broth culture for 48 hours at 30 degrees Celsius. The cells were heat-fixed to a slide and stained with malachite green (endospores) and safranin red (vegetative cells) prior to visualization.Image credit: Emily Fox

This micrograph was taken at 1000X total magnifcation on a brightfield microscope. The subject is Bacillus subtilis cells were grown in broth culture for 5 days at 30 degrees Celsius. The cells were heat-fixed to a slide and stained with malachite green (endospores) and safranin red (vegetative cells) prior to visualization.Image credit: Emily Fox

This micrograph was taken at 100X total magnifcation on a brightfield microscope. The subject is Bacillus subtilis cells grown in broth culture overnight at 30 degrees Celsius. The cells were heat-fixed to a slide Gram stained prior to visualization.Image credit: Emily Fox

This micrograph was taken at 1000X total magnifcation on a brightfield microscope. The subject is unidentified coccus cells from a contaminant colony grown on nutrient agar at 30 degrees Celsius. The cells were heat-fixed to a slide and Gram stained prior to visualization.Image credit: Emily Fox

This micrograph was taken at 1000X total magnifcation on a brightfield microscope. The subject is Enterobacter aerogenes cells grown in broth culture overnight at 37 degrees Celsius. The cells were heat-fixed to a slide and Gram stained prior to visualization.Image credit: Emily Fox

This micrograph was taken at 1000X total magnifcation on a brightfield microscope. The subject is Escherichia coli cells were grown in broth culture for 48 hours at 30 degrees Celsius. The cells were heat-fixed to a slide and stained with malachite green (endospores) and safranin red (vegetative cells) prior to visualization. No endospores are seen, as E. coli does not form endospores.Image credit: Emily Fox

This micrograph was taken at 1000X total magnifcation on a brightfield microscope. The subject is Escherichia coli cells were grown in broth culture for 5 days at 30 degrees Celsius. The cells were heat-fixed to a slide and stained with malachite green (endospores) and safranin red (vegetative cells) prior to visualization. No endospores are seen, as E. coli does not form endospores.Image credit: Emily Fox

This micrograph was taken at 1000X total magnifcation on a brightfield microscope. The subject is Escherichia coli cells grown in broth culture overnight at 37 degrees Celsius. The cells were heat-fixed to a slide and Gram stained prior to visualization.Image credit: Emily Fox

This micrograph was taken at 400X total magnifcation on a brightfield microscope. The subject is Escherichia coli cells grown in broth culture overnight at 37 degrees Celsius. The cells were heat-fixed to a slide and Gram stained prior to visualization.Image credit: Emily Fox

This micrograph was taken at 1000X total magnifcation on a brightfield microscope. The subject is Escherichia coli cells and Mycobacterium smegmatis cells grown separately in broth culture at 37 degrees Celsius. The cells were heat-fixed to a slide and acid-fast stained using the Ziehl-Neelsen method prior to visualization. M. smegmatis (acid-fast) stains pink with carbol fuchsin. E.coli (non-acid-fast) stains blue with methylene blue counterstain.Image credit: Emily Fox