Category Archives: journal club

Exploration and critique of the literature

Get That Weak Staph Outta Here!

Certain skin commensal bacteria protect individuals against Staphylococcus aureus colonization We’re all covered in skin (hopefully) and our skin is covered with microbes. For the most part, this skin microbiome coexists with us and remains stable, despite our constant contact with other people and our environment. … Continue reading

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Delivery by C-section Has No Effect on the Infant Microbiome… Wait What?

Every paper on the infant microbiome starts with known determinants… infant diet (formula or breastfeeding), oral antibiotic use and delivery method. But a new paper just out from Kjersti Aagaard’s group, who you may remember as the placental microbiome folks, … Continue reading

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Why do people have such different microbiomes from one another?

Discussing a computational approach to answering what controls inter-individual variability in the human microbiome. Modulating human microbial communities continues to be an area of intense academic and entrepreneurial interest because of the role of the human microbiome in determining health and … Continue reading

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A network based approach to longitudinal analysis of the microbiota

Analysis of the microbiome over time is hard. You can treat the abundance of each bacterial taxa as a separate outcome and look at them all individually but then you lose interactions between them. Worse yet, you can treat each measurement … Continue reading

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Sign up now for the human microbiome journal club

Journal club continues this year with a powerpoint presentation and discussion from 3 – 4 pm in MUMC 3N10A, then continuing the discussion at the Phoenix for those who are interested. See the schedule here and sign up for empty spots! A … Continue reading

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Oligotyping to Achieve Increased Taxonomic Resolution of the Oral Microbiome

The development of novel bioinformatics tools has allowed for researchers to glean increasing amounts of information from next generation sequencing of 16S rRNA gene data. Current methods of sequence analysis have been limited to taxonomic identity up to genera or … Continue reading

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Summing up: Exploration of the Virome in Inflammatory Bowel Disease by Norman et al.

Last week we drew our attention to the virome as discussed in “Disease-specific alterations in the enteric virome in inflammatory bowel disease” (Norman et. al). Continuing on the thread of ‘other’ components of the microbiome from our discussion last month … Continue reading

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Response to May 29, 2015 Journal Club: “Modulation of Post-Antibiotic Bacterial Community Reassembly and Host Response by Candida Albicans” [Downward et al, 2013]

Although this is a slightly older paper, the role of fungi in the gut microbiota is becoming an increasingly prevalent topic of discussion among microbiome groups, making this discussion a timely one. This group also previously published two papers on … Continue reading

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Should we care about fungi? The mycobiome: an emerging field of the human microbiome research

With the advancement of next-generation sequencing in the last decade, our knowledge about the trillions of microbes that the human body harbours has exponentially increased. Microbiome research has mostly been focused on the study of bacteria notwithstanding that the classical … Continue reading

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Summing up: Bassis et al.’s take on the influence of the URT on other human-associated biogeographies.

Last week, Pat led us in the examination of a new paper from the Huffnagle group at the University of Michigan. This was the first meeting of McMaster’s HMBJC in a few months which meant a very lively discussion since … Continue reading

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