Course description: Critical reading of papers that leverage public data related to medical and environmental microbiology. Covers all types of publicly available microbial sequence and phenotypic data, including both metagenomics and traditional isolate-based genomes. Focuses on the key insights that were needed to arrive at a result that anyone with a computer would have had access to and how to frame good questions, in addition to methodological approaches and critiques. Senior undergraduates are welcome.

Format: Weekly discussions of papers, led by students. Each class will cover 1-2 published papers. When we discuss preprints, we will use the second half of class collaborating on a comment to be posted on the preprint server.

Assignments: For each discussed paper, post 1 or more questions in a google doc by 9p the night before. Lead discussion of 2-4 papers over the course of the semester (depending on class size) and participate in all class discussions.

Grading: Pass/Fail

Auditing: Graduate students and undergraduate students must register for the class to participate. Employees (postdocs, research technicians) interested in auditing the class will be expected to participate fully, including presenting papers and posting discussion questions. Please register your interest in auditing the class here.

Schedule:

https://docs.google.com/spreadsheets/d/1VXGT0DEKbI8Mbp8FVkyygwTQulYaqcZn4oDHMZRq5Ac

Piazza:

piazza.com/mit/fall2021/hsts56/home

List of potential papers :

Why highly expressed proteins evolve slowly

Meta-analysis of gut microbiome studies identifies disease-specific and shared responses

The Landscape of Type VI Secretion across Human Gut Microbiomes Reveals Its Role in Community Composition

Human gut bacteria contain acquired interbacterial defence systems

Systematic discovery of antiphage defense systems in the microbial pangenome

A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes

Resource conservation manifests in the genetic code

Convergent gain and loss of genomic islands drive lifestyle changes in plant-associated Pseudomonas

Consistent Metagenome-Derived Metrics Verify and Delineate Bacterial Species Boundaries

Genetic exchanges are more frequent in bacteria encoding capsules

Global landscape of phenazine biosynthesis and biodegradation reveals species-specific colonization patterns in agricultural soils and crop microbiomes

Evolutionary dynamics of bacteria in the gut microbiome within and across hosts

Two dynamic regimes in the human gut microbiome

Phylogenetic conservatism of functional traits in microorganisms

Why Genes Evolve Faster on Secondary Chromosomes in Bacteria

A widespread toxin−antitoxin system exploiting growth control via alarmone signaling

Public good exploitation in natural bacterioplankton communities

Host adaptation in gut Firmicutes is associated with sporulation loss and altered transmission cycle

Comparisons of dN/dS are time dependent for closely related bacterial genomes

Whole genome phylogenies reflect the distributions of recombination rates for many bacterial species

Preprints

A computational screen for alternative genetic codes in over 250,000 genomes

Borgs are giant extrachromosomal elements with the potential to augment methane oxidation

Systematic and quantitative view of the antiviral arsenal of prokaryotes