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 growing problem worldwide—and in outer space. Spaceflight can promote biofilm formation and antimicrobial resistance development, and astronauts are especially vulnerable to infection due to the unique demands of spaceflight. To support future space travel, it is critical to understand exactly how spaceflight affects microbial diversity and virulence. To learn more, researchers recently used a machine learning algorithm to analyze sequencing data from the Microbial Tracking (MT)-1 mission, which sampled microbes at eight locations on the International Space Station during three flights. The model predicted the presence of hundreds of antibiotic resistance genes (ARGs) in the 226 bacterial strains isolated from the flights, including strains of the potentially very pathogenic bacterium Enterobacter bugandensis and the food poisoning-related bacterium Bacillus cereus..."

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

Biology is designed for multi-semester biology courses for science majors. It is grounded on an evolutionary basis and includes exciting features that highlight careers in the biological sciences and everyday applications of the concepts at hand. To meet the needs of today’s instructors and students, some content has been strategically condensed while maintaining the overall scope and coverage of traditional texts for this course. Instructors can customize the book, adapting it to the approach that works best in their classroom. Biology also includes an innovative art program that incorporates critical thinking and clicker questions to help students understand—and apply—key concepts.

By the end of this section, you will be able to:Define genomicsDescribe genetic and physical mapsDescribe genomic mapping methods

By the end of this section, you will be able to:Describe three types of sequencingDefine whole-genome sequencing

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:

"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..."

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

Fundamentals of Biology focuses on the basic principles of biochemistry, molecular biology, genetics, and recombinant DNA. These principles are necessary to understanding the basic mechanisms of life and anchor the biological knowledge that is required to understand many of the challenges in everyday life, from human health and disease to loss of biodiversity and environmental quality.
Course Format

This course has been designed for independent study. It consists of four units, one for each topic. The units can be used individually or in combination. The materials for each unit include:

Lecture Videos by MIT faculty.
Learning activities, including Interactive Concept Quizzes, designed to reinforce main concepts from lectures.
Problem Sets you do on your own and check your answers against the Solutions when you're done.
Problem Solving Video help sessions taught by experienced MIT Teaching Assistants.
Lists of important Terms and Definitions.
Suggested Topics and Links for further study.
Exams with Solution Keys.

Content Development

Eric Lander
Robert Weinberg
Tyler Jacks
Hazel Sive
Graham Walker
Sallie Chisholm
Dr. Michelle Mischke

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 honey bee gut microbiome has a critical influence on bee health and is transmitted among members of a colony through social interactions. The bee microbiome is made up of a core set of bacterial groups that show high diversity among individuals at the strain level. While this variation has been shown to be clearly associated with numerous environmental factors, bee genetics may also play an important role. Researchers recently used DNA sequencing techniques to better understand how bee genetics affect gut microbiome structure. The team examined the genomes of four subspecies of lab-reared honey bees with those of their associated microbiomes. They noted that the abundance of most core gut microbiota members was influenced by host subspecies and also found a clear link between a Bifidobacterium strain in the gut and brain neurotransmitter and gene expression 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:

"Non-alcoholic fatty liver disease (NAFLD) is a common metabolic disease that can progress to cirrhosis and hepatocellular carcinoma. Iron level is a known factor in the development of NAFLD, but the details of its involvement are unclear. To elucidate the mechanisms at play, researchers applied an integrative systems medicine approach. They examined the fecal metagenome, plasma and urine metabolome, and hepatic transcriptome in three human cohorts, confirming the findings in vitro and using mice. Serum ferritin levels, a marker of hepatic iron stores, was linked to liver fat accumulation and a decrease in gut microbial gene richness. Elevation in ferritin was also associated with changes in the abundance of several bacterial families. Those families were strongly correlated with iron-related liver genes. This iron-related microbiome signature was also associated with the degree of liver fat accumulation..."

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:

"Amphibians are one of the most vulnerable animal groups on the planet, with over 40% of their species threatened with extinction. A major driver of that vulnerability is the fungal pathogen _Batrachochytrium dendrobatidis_ (Bd). Bd is linked to the decline of at least 500 amphibian species, the greatest loss in biodiversity due to a pathogen ever recorded. The amphibian skin microbiome community structure has been linked to health outcomes of Bd infection, but the functional importance of the microbiota is not yet fully understood. To close this gap and potentially discover biomarkers or disease control methods, researchers investigated the microbiome of midwife toads. They examined both wild populations with naturally occurring Bd infection and controlled laboratory exposure. Infection with Bd led to changes in the microbial community structure, gene profile, and metabolic function in laboratory and wild toad populations..."

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 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 seeking to understand the difference between a healthy and unhealthy gut microbiome often turn to sequencing microbial DNA. Two main approaches are currently used: metabarcoding, also known as targeted amplicon sequencing, and shotgun sequencing of random fragments. While metabarcoding has limited resolution, full shotgun sequencing has improved resolution but comes with a higher cost, restricting the number of samples sequenced. As an alternative, researchers evaluated the use of Reduced Metagenome Sequencing (RMS) to estimate microbial community composition. RMS involves double-digested restriction-associated DNA sequencing, meaning that only a small fraction of genomes are sequenced. RMS read sets are different from both amplicon and shotgun data, making it difficult to use analysis pipelines for either method. A new analysis pipeline is proposed that uses fragment clustering and constrained ordinary least square deconvolution, allowing for estimates of 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:

"Much like the organisms that flood its instruments the microbiome research community is thriving. But researchers from the UK’s National Institute for Biological Standards and Control (NIBSC) say that it could be doing even better. They’ve developed the first reference reagents for microbiome DNA analysis, Gut-Mix-RR and Gut-HiLo-RR. It’s a move designed to promote standardization and reproducibility across the field of microbiome research as tests revealed drastic variations across shotgun sequencing taxonomic profilers, which could alter conclusions about interactions between different microbes . If researchers can reach a consensus on acceptable levels of errors and begin using the materials in their labs the reference reagents could help standardize downstream gut microbiome analyses. A large open-invite collaborative study for multiple laboratories is slated for later in 2020..."

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:

"Antibiotic-resistant bacteria like carbapenem-resistant Enterobacteriaceae (CRE) pose a serious threat to human health. Some resistant pathogens can exist alongside our commensal microbiota at undetectable levels. Antibiotic use can lead to outgrowth of these subclinically colonized bacteria. A recent study sought to better understand the interaction between the gut microbiota and CRE during subclinical colonization and outgrowth. First, researchers exposed wild-type mice to the CRE _K. pneumoniae_. While the levels of _K. pneumoniae_ were not detectable after exposure, the post-exposure microbiome was disrupted. Then, administration of an antibiotic cocktail, ampicillin, vancomycin, or azithromycin induced _K. pneumoniae_ outgrowth while reducing overall microbial diversity. Vancomycin only induced outgrowth in a subset of mice. The researchers found these outgrowth-susceptible mice had differences in mRNA stability pathways and xylose abundance..."

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