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 life can be found in nearly every environment on earth. These tiny organisms can significantly impact their surroundings, be it deep-sea microbes influencing the ecology of the ocean floor or the human gut microbiome affecting health. Metagenomics, or the analysis of microbial DNA in different environments, has dramatically increased what is known about microbial life. These sequencing-based techniques are not dependent on culturing microbes, which can be an incredibly difficult undertaking. However, isolating and cultivating microbes remains important to both confirm and expand upon those results. Moreover, cultivated microbes could potentially be used as probiotics or biocontrol agents or for industrial purposes. To date, most environmental microbes remain uncultured, but metagenomic data can be leveraged to help researchers isolate and cultivate new ones..."

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:

"Phosphorus is essential for life to function. It is a critical component of the energy metabolism molecules, genetic materials, and cell structures of all life. Phosphorus only enters natural ecosystems through the slow weathering of stone. Then microbes help maintain and regulate phosphorus by cycling it between its organic and inorganic forms. Understanding microbial phosphorus cycling is critical to many fields of study, like ecology and agriculture. However, researchers lack a comprehensive understanding of the phosphorus cycling genes microbes use, but the recently developed curated phosphorus cycling database (PCycDB) could help close that gap. PCycDB covers 10 phosphorus metabolic processes and 139 gene families, including several that have been missed elsewhere. Testing PCycDB with simulated datasets revealed high annotation accuracy, positive predictive value, sensitivity, specificity, and negative predictive value..."

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:

"Most of the microorganisms in the human microbiome are commensals, contributing essential functions to their hosts, while in contrast, pathogenic microorganisms cause disease by invading, colonizing, and damaging their hosts. Virulence factors, including bacterial toxins, contribute to their pathogenicity, and antimicrobial resistance (AMR) genes allow them to evade otherwise curative treatments. A new tool seeks to improve our understanding of virulence factors and antimicrobial resistance genes. PathoFact is a tool for the contextualized prediction of virulence factors, bacterial toxins, and AMR genes. In an evaluation with simulated metagenomic datasets, PathoFact outperformed two other existing analysis workflows, and in a test with three case-control datasets representing infection and chronic disease, PathoFact identified virulence factors that were either secreted or not secreted..."

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

Microbes rule the reef. They determine both coral reef health and decline. Exploration of their diverse roles in these ecosystems has become possible only recently with the development of new research methods, such as metagenomics. Join San Diego State microbial ecologist Forest Rohwer as he builds his case for the role of microbes in the DDAMnation of coral reefs. His research expeditions to the remote Line Islands, including trips with Scripps scientists, have provided new insights into the mechanisms by which human activities can influence reef health; how we convert the essential microbial partners of a healthy coral reef ecosystem into coral killers. (28 minutes)

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 have diverse microbiomes, which have profound effects on their hosts. But it is not yet known if, or how, plant hosts influence their microbiomes. Recently, researchers comprehensively examined the influence maize has on its microbiomes. Plant developmental stage had a stronger influence on plant microbiomes than on soil microbiomes and the strongest effect was on the phylloplane. Phylloplane microbiomes were co-shaped by both plant growth and seasonal environmental factors, with the air as its important source. Phylloplane bacteria and fungi took on different roles in the early and late stages. In plant compartments, deterministic processes had the strongest effect on bacterial communities at the early stage and then on fungal communities at the late stage. The microbial interkingdom network and crop yield predication also followed this pattern - bacterial taxa played the most important role in the early stage and fungal taxa in the late stage, respectively..."

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:

"Every year, over 9 million metric tons of plastic waste enter the ocean and can harm its ecosystems. When it comes to marine microbes, most of the current research has focused on those that directly colonize the plastic particles. But plastic also leaches chemical additives into the water, which could impact planktonic microbes as well. So, researchers tested the impact of leachate from polyvinyl chloride (PVC), a common plastic, and zinc, a plastic additive, on a natural planktonic community. Some microorganisms, including both bacteria and eukaryotes, were impaired by exposure to plastic leachates. Photosynthetic microorganisms, the base of the food web, were particularly strongly affected, showing declines in photosynthetic efficiency, diversity, and abundance. Other important and normally highly abundant bacterial groups were also negatively impacted. In contrast, microorganisms that thrive in nutrient-rich environments, copiotrophs, dramatically increased in relative abundance..."

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:

"Fixing carbon through biological methanation is a promising technology for generating renewable energy. It remains unclear, however, how microbial species interact to generate biogas. To find out, researchers explored the community dynamics of microbes found in biofilms from four biogas reactors. Metagenomics revealed 59 species of microbes with five accounting for more than 70% of total abundance in the four reactors under investigation. Experiments showed that Firmicutes spp. GSMM966 and GSMM974 and Limnochordia sp. GSMM975 played a central role in biofilm formation. And metabolic reconstruction indicated complex metabolisms for the two dominant species M. wolfeii GSMM957 and Limnochordia sp. GSMM975. Simulations of the core biofilm community showed that these same species exhibit the highest increases in growth rate with increasing uptake. And cross-feeding interactions, not easily measured in vivo, were visualized..."

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 Antarctica, certain photosynthetic microorganisms produce enough food in the summer to sustain aquatic ecosystems through the long, dark winters. One species of photosynthetic Chlorobium bacteria dominates Ace Lake in East Antarctica, and its abundance changes drastically with the seasons. However, the importance and abundance fluctuations of this species in other Antarctic water bodies are unclear. To learn more, a recent metagenomics study examined Chlorobium sequences from Ace Lake that spanned seven years, plus sequences from two nearby marine basins. The species Candidatus (Ca.) Chlorobium antarcticum dominated all three aquatic systems, and its genome varied little. However, there was seasonal genomic variation in the ability to synthesize cobalamin, which is required for photosynthetic growth. Since most bacteria can’t synthesize their own cobalamin, Ca. Chlorobium antarcticum is likely a major source of cobalamin in these three ecosystems..."

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:

"Trendy health foods are taking off in the United States, but one new trend may do more harm than good. Unpasteurized, or “raw,” milk is purported to have probiotic health benefits. Unfortunately, despite the proposed benefits, contamination with pathogenic bacteria has occurred. and little is known about the extent of antibiotic-resistant microbes present in raw milk sold at retail stores. A new study evaluated the microbiomes of cow's milk samples using DNA sequencing and metagenomics. including over 2,000 retail milk samples from 5 states – both raw milk and milk pasteurized in different ways. Raw milk samples had the highest prevalence of viable bacteria, with Pseudomonadaceae dominating. Probiotic lactic acid bacteria levels were limited in raw milk, and storage outside of a refrigerator dramatically increased bacterial populations expressing antibiotic-resistance genes..."

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 candidate phyla radiation (CPR) is a lineage of bacteria with unusual ribosomal structures, reduced metabolic capacities, small genomes, and small cell sizes. Due to these traits, this phylum — also called Patescibacteria — is thought to be host-associated, and there are only a few cultivated representatives. Most CPR genomes originated from groundwater, but they also can be found in surface freshwater, where they remain largely understudied. To close this gap, a recent study examined CPRs from freshwater lakes in Europe and Asia with deep metagenomic sequencing, as well as the first use of Fluorescence in situ Hybridization followed by Catalyzed Reporter Deposition (CARD-FISH) to view CPRs in freshwater. Like previously described CPR members, the lineages in this study had reduced genome sizes, low abundance, and slow estimated replication rates..."

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:

"Methane production by microbes holds great promise for converting industrial waste to fuel. In the wild, this process involves the well-orchestrated transfer of hydrogen between organisms that break down carbon-rich matter and those that form methane. But that harmony presents a thermodynamic puzzle, as reactions that generate high concentrations of hydrogen can and do inhibit reactions that occur only at low hydrogen concentrations. To understand how these competing processes co-exist, researchers analyzed 17 methane-producing bioreactors using metagenomics. Altogether, they assembled genomes spanning 66 phyla of microorganisms, which were divided according to the compounds they most commonly broke down, such as sugars or amino acids. The team used those findings to understand how high- and low-hydrogen reactions occur side by side and produced a model describing how organisms may employ unique strategies to drive thermodynamically competitive metabolisms..."

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 sulfur cycle involves a series of complex aerobic and anaerobic transformations of sulfur-containing molecules. Sulfur transformations are fundamental to cellular and ecosystem-level processes, influencing biological carbon transfers and other biogeochemical cycles. Yet despite the importance of this pathway, the microbial communities and metabolic pathways involved remain poorly understood. A recent study examined these features in an extreme geochemical environment: isolated, ice-capped Lake A in the Canadian High Arctic. Using complementary molecular approaches, researchers found a sharp contrast in the microbial communities and metabolic potentials in the distinct water layers in Lake A. Throughout all layers, sulfur cycling genes were abundant. Oxidative processes were enriched in samples from oxygen-rich freshwater-like layers, while reductive reactions were enriched in the anoxic and sulfidic bottom layers..."

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 composition of our gut microbial community has been linked directly to our health, but researchers are only beginning to study the impact of its functional metabolic behavior, which can shift in response to external factors. Microbial production of H₂S in the gut is one such function, and it may be a colorectal cancer trigger. A recent study used publicly available datasets to examine the sulfur metabolism genes in our gut microbiota. Sulfur metabolism genes were more abundant and diverse than previously thought and were correlated with colorectal cancer. The researchers also examined two key sulfate reductases: dissimilatory sulfite reductases (Dsr) and anaerobic sulfite reductase (asr) and found that genes for asr were twice as abundant as genes for Dsr, suggesting that asr is a more important contributor to sulfate reduction in the human gut and found that genes for asr were twice as abundant as genes for Dsr, suggesting that asr is a more important contributor to sulfate reduction in the human 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:

"Scientists have created a “super” sourdough that could help breadmakers and microbiome researchers alike answer long-standing questions, including how a sourdough’s microbial makeup might make it more stable than others. The team created their synthetic sourdough by pulling bacteria and yeast from 8 spontaneously formed sourdoughs from around the world. These microbes fulfilled two criteria: 1) they occurred in 4 of the 8 spontaneous sourdoughs, and 2) they harbored at least 20 key genes associated with metabolic pathways critical to maintaining sourdough quality, including the fermentation and breakdown of different sugars. Seven species (5 bacteria, 2 yeasts) met these criteria, forming a global sourdough labeled “SDG.” Scientists compared SDG with a synthetic sourdough (SMC-SD43) modeled after one of the original 8 spontaneous sourdoughs..."

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 microbiome is now known to play important roles in health and disease, but while microbiome research on European and North American populations has increased exponentially, African populations may be underrepresented. The relative lack of data could impair medical progress for Africans and obscure important treatment targets. To characterize the knowledge gaps, researchers recently searched the literature for next-generation sequencing studies published through April 1, 2020, that included African samples. Thirty-three out of 54 African countries were represented in the 168 studies found, primarily South Africa, Kenya, and Uganda. Only 26.8% of studies focused on diseases of significant public health concern in Africa. Among studies with intercontinental collaboration, the USA was the most common collaborator, and the first and last authors of most studies were not affiliated with African institutions. In addition, the primary funders were American or European institutions..."

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:

"A recent study examined toothbrushes to understand how microbes from our bodies interact with our environment. Toothbrushes are a unique component of the built environment that comes into daily contact with our bodies and water. Researchers characterized the metagenomes of toothbrushes from 34 individuals and found that toothbrush microbiomes resemble microbial communities in the mouth. Toothbrush-associated microbes were less diverse than those in people's mouths, but they had broader antimicrobial resistance gene (ARG) profiles, and microbial community makeup correlated with factors linked to personal health, dental hygiene, and bathroom features. Although this small pilot study must be expanded to confirm the findings, these results suggest that microbes on the surfaces we touch are affected by our health and behavior and that understanding how we can influence these microbes will help us make better decisions about cleaning and maintenance to promote a healthy environment..."

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:

"Bacteriophages are everywhere, influencing everything from microbial evolution to biogeochemical cycling. Phages, however, remain among the least understood members of complex microbiomes. Do the tools used to identify phages introduce biases? A recent study compared ten of the most widely used bioinformatics tools designed to detect phages from metagenomics data. Overall, tool performance varied substantially in the analysis of different benchmarking datasets. For a set of artificial RefSeq contigs, PPR Meta and VirSorter2 showed the highest performance. Kraken2 showed the highest accuracy for a mock community benchmark. And generally, k-mer tools performed better than similarity- or gene-based tools. The study offers insight into the biases introduced by different tools, offers guidance into which one is best suited for different use cases, and suggests that rather than relying on any one tool, researchers may do well to combine different ones to suit their research needs..."

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

This is a seminar based on research literature. Papers covered are selected to illustrate important problems and approaches in the field of computational and systems biology, and provide students a framework from which to evaluate new developments.
The MIT Initiative in Computational and Systems Biology (CSBi) is a campus-wide research and education program that links biology, engineering, and computer science in a multidisciplinary approach to the systematic analysis and modeling of complex biological phenomena. This course is one of a series of core subjects offered through the CSB Ph.D. program, for students with an interest in interdisciplinary training and research in the area of computational and systems biology.

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 community of microorganisms that colonize our gut is an adaptive one. It changes with environment, disease, and major life events. But one life event that has remained underexplored by microbiome science is pregnancy, especially in women with type 1 diabetes, which poses a health risk to both mother and fetus. To address this gap, researchers recently examined gut microbiome composition across 70 pregnancies, 36 of them involving women with type 1 diabetes. Women with diabetes demonstrated a shift towards a more pro-inflammatory gut microbiome during pregnancy, showing an increase in bacteria that produce lipopolysaccharides, which promote inflammation; decreased concentrations of short-chain fatty acids, which protect against inflammation; and increased serum levels of the protein I-FABP, an indicator of organ wall damage. These changes could contribute to pregnancy complications in women with type 1 diabetes, but might be modified through the diet..."

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:

"Since the 1970s, 16S ribosomal RNA sequencing has been the primary means of identifying bacteria in environmental samples of unknown composition. Among the most powerful tools for this sequencing is the Quantitative Insights Into Microbial Ecology (QIIME) package whose newest release, QIIME 2, boasts one of the highest classification accuracies for simulated metagenomes from the human gut, ocean, and soil. But a recent study suggests that even more powerful tools are available namely Kraken 2 and Bracken. Compared with QIIM2, Kraken 2 and Bracken were up to 100 times faster in generating the well-known Greengenes and SILVA 16S rRNA databases and up to 300 times faster at classification while using 100 times less RAM. Overall, Kraken 2 and Bracken produced more accurate 16S rRNA profiling results than QIIME2. Extremely fast, efficient, and accurate, Kraken 2 and Bracken could provide robust solutions for identifying and classifying bacterial species from a variety of environmental samples..."

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