In a multi-week experiment, students monitor the core temperatures of two compost piles, one control and one tended, to see how air and water affect microbial activity. They daily aerate and wet the "treated" pile and collect 4-6 weeks' worth of daily temperature readings. Once the experiment is concluded, students plot and analyze their data to compare the behavior of the two piles. They find that the treated pile becomes hotter, an indication that more microbes are active and releasing heat. Through this activity, students see that microbes play a role in composting and how composting can be used as a carbon management process.

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:

"Genetics can affect many aspects of human health, in part by influencing the composition of the gut microbiome. The associations between genetic variants and individual microbial taxa are often investigated with genome-wide association studies (GWASs). However, typical GWASs have low statistical power, because they require extensive multiple testing and can’t account for inherent data structure. To help solve this problem, researchers recently developed a new approach: a covariate-adjusted kernel RV (KRV) framework. This framework compares pairwise similarity in genetic profiles to pairwise similarity in microbial profiles therefore reducing the multiple testing burden without obscuring the data structure. In simulation studies, the KRV framework had greater statistical power than other microbiome GWAS approaches in a range of scenarios..."

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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:

"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..."

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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:

"Antibiotic resistance is a global threat to public health, causing an estimated 700,000 deaths each year. Soil is an important reservoir of antibiotic resistance genes (ARGs), but the potential risk of ARGs in different ecosystems and the effect of land use changes are unknown. In a recent study, researchers investigated ARG types and amounts in three native soil ecosystems: Alaskan tundra, US Midwestern prairie, and Amazon Rainforest. They found high ARG diversity and abundance in all three ecosystems. A total of 10 regulatory and 55 non-regulatory ARGs were identified that were shared by all 26 metagenomes in the three ecosystems. No significant differences were observed in ARG diversity or abundance between native prairie and agricultural soil, while conversion of Amazon rainforest to pasture increased ARG abundance..."

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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:

"Animal health is of utmost importance in the production of milk, meat, and other animal products. Although vitamin supplements can help ensure livestock remain as healthy as possible, they are often expensive, driving up the cost of production. To help reduce these costs, a team of researchers set out to better understand how the essential vitamins B and K₂ are produced by microbes in the gastrointestinal tracts of ruminants, which are animals with complex digestive tracts composed of multiple distinct compartments to help them break down their plant-based diets. The team used genetic data from previous studies to identify 1,135,807 genes and 2366 full genomes involved in B or K₂ vitamin biosynthesis in the gastrointestinal tracts of seven ruminant species. They also found that most of this biosynthesis took place in the stomach compartments rather than other regions and that a high-grain diet enhanced most vitamin biosynthesis but inhibited cobalamin synthesis..."

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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:

"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..."

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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:

"The next time you swat away that fly buzzing around your head, consider this: an international team of researchers has shown that common houseflies and blowflies are more than just annoying insects. Covered with hundreds of different bacterial species, they’re also a type of airborne delivery service, transporting pathogens from organic decaying matter right to your countertops, food…and body. Although flies have been long known to spread disease, the researchers show that we’ve previously underestimated both the number and diversity of microbes that each insect can transmit. The team devised a new optimized way to collect flies without cross-contaminating them with other microorganisms and used the method to amass 116 flies from urban, rural, and natural sites on three continents..."

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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:

"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..."

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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:

"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..."

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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:

"Gas biofilters can help remove harmful volatile organic compounds (VOCs) from the air through the action of microorganisms immobilized on the filler surface. However, unchecked growth of these microbes can clog the filters, reducing filtration performance. Quorum quenching (QQ) is known to impair bacterial biofilm formation by disrupting bacterial communication, but it’s unclear whether it can prevent microbial clogging of gas biofilters. To find out, researchers recently operated gas biofilters with and without the QQ bacterium Rhodococcus sp. BH4 in parallel. Both the normal biofilter and the QQ biofilter removed aromatic compounds from the air, but the QQBF accumulated less biomass and functioned more stably. The bacteria in the QQBF made lower amounts of extracellular polymeric substances (EPSs) thus producing a less-adhesive biofilm that degraded more easily . The QQ biofilter also had lower abundance of quorum-sensing bacteria and quorum-sensing genes. Although the mechanism of Rhodococcus sp..."

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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:

"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..."

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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:

"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..."

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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:

"Phytoplankton communities play major roles in global biogeochemical cycles and marine food webs. However, the complex phytoplankton communities in polar vs. non-polar oceans haven’t been well characterized. To address this gap, researchers recently profiled the metagenome-assembled genomes (MAGs) of eukaryotic microbes and associated prokaryotes from the chlorophyll A maximum layer at 11 sites in the Arctic and Atlantic Oceans. Within each ocean, adjacent sampling sites had 51–88% of their MAGs in common, but the Arctic and Atlantic MAGs were clearly differentiated. Most species associations were between Prasinophytes and Proteobacteria. In addition, eukaryotic MAGs were more diverse in the Arctic, while prokaryotic MAGs were more diverse in the Atlantic. For both prokaryotes and eukaryotes, 70% of the detected protein families were shared between Arctic and Atlantic MAGs. but eukaryotic MAGs had more Arctic-only protein families, whereas prokaryotic MAGs had more Atlantic-only protein families..."

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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:

"Dental calculus, or mineralized dental plaque, preserves various microfossils and biomolecules, including DNA. Dental calculus from ancient human remains therefore contains information about the oral microbiomes, health, and diets of our ancestors. However, little is known about the non-bacterial microbes in ancient calculus. In a new study, researchers used metagenomics to study calculus from 20 sets of human remains dating to the Neolithic period through the Early Middle Ages. Compared with modern calculus in publicly available datasets, the ancient calculus had a much higher abundance of archaea belonging to the phylum Euryarchaeota. Compared with modern calculus in publicly available datasets, the ancient calculus had a much higher abundance of archaea belonging to the phylum Euryarchaeota, specifically archaea in the genus Methanobrevibacter. The only known Methanobrevibacter species in modern calculus, M..."

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Students design systems that use microbes to break down a water pollutant (in this case, sugar). They explore how temperature affects the rate of pollutant decomposition.

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:

"Indoor microbes can release harmful volatile organic compounds (VOCs), but how environmental factors and microbial community composition impact microbial VOC emissions is unclear. To learn more, researchers recently subjected drywall and carpet to different equilibrium relative humidity levels and quantified microbial communities and microbial VOC emissions. Fungus grew in dusty carpet when the humidity was >75% and in inoculated painted drywall when the humidity was >85%. The dust sample collection site and the material type significantly affected the fungal and bacterial species compositions. In dusty carpet, increased humidity was associated with decreased microbial species diversity. Abundant VOCs were likely released from the materials and dust themselves, but some microbial VOCs, such as C₁₀10H₁₆H⁺ (monoterpenes) and C₂H₆SH⁺ (dimethyl sulfide and ethanethiol), were released from microbes that grew in dusty carpet. At 95% humidity, dusty carpet produced 5..."

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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:

"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)..."

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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:

"Microbiome research has consistently been placed in the spotlight over the past two decades, and has shown tremendous promise in the fields of medicine, environmental science, food production, and agriculture. Life on Earth does not exist without microbes, and we may benefit from learning more about them. Yet, there is no common understanding amongst researchers of what a 'microbiome’ actually is. Researchers are now proposing a common definition of ‘microbiome’ to ensure better, more robust research across different disciplines. The authors build on the historical definition offered by Whipps and colleagues in 1988 using new research insights. Additionally, they highlight the importance of microbiomes as drivers for the health of many eukaryotic hosts, including humans and plants. The proposed amendments to the definition specify the elements of microbiome composition and their interactions..."

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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:

"The gut microbiome (GM) plays an integral role in overall human health, yet over 70% of human GM species have never been cultured, and these microbes may hold important clues into the function of the human GM and GM-host interactions. To address this gap, researchers recently cultured 10,558 bacterial isolates representing 400 GM species from 239 healthy human donors. Of the 400 cultured species, 102 new species were identified and characterized, 28 new genera and 3 new families were proposed, and 115 genomes were newly sequenced. These data were used to construct the human Gut Microbial Biobank, an open-access resource containing taxonomic and genetic information on over 80% of the dominant microbial taxa in the human gut. Although numerous gut microbes remain uncultured, the Gut Microbial Biobank sheds new light on the identities and functions of the microbes composing the human GM and has potential applications in the development of next-generation probiotics..."

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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:

"Microbial communities strongly affect biogeochemical cycles, ecosystems, and human health. Although studying microbial functions in these incredibly diverse communities was once difficult, new approaches are making it easier. One such approach, metaproteomics, enables scientists to study changes in the expression of microbial proteins over space and time and provides important insights into gene-protein links and microbial functions. The new Metaproteomics Initiative seeks to establish a central hub for the discussion, standardization, and improvement of metaproteomics methods in order to foster interdisciplinary collaboration and advancement of this relatively new field of microbiome research. This initiative, sponsored by the European Proteomics Association, will feature a website, a social media presence, and various platforms and resources for education and communication..."

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