June 18, 2016

Your Saturday Microbiome Digest: CSF metagenomics in multiple sclerosis, Caenorhabditis elegans responses to bacteria, and archaeal communities in permafrost.

Infection and microbes

Only microbial contamination foundMetagenomic Analysis of Cerebrospinal Fluid from Patients with Multiple Sclerosis – Karol Perlejewski – Advances in Experimental Medicine and Biology

Review: The regulation of host defences to infection by the microbiota – Rebecca L. Brown – Immunology

Animal and in vitro experiments

Microbial Community Transplant Results in Increased and Long-Term Oxalate Degradation – Aaron W. Miller – Microbial Ecology

Differential Utilization of Basic Proline-Rich Glycoproteins During Growth of Oral Bacteria in Saliva – Yuan Zhou – Applied and Environmental Microbiology

Caenorhabditis elegans responses to bacteria from its natural habitats – Buck S. Samuel – PNAS

Plant, root, and soil microbiome

Presence and persistence of viable, clinically relevant Legionella pneumophila bacteria in garden soil in the Netherlands – E. van Heijnsbergen – Applied and Environmental Microbiology

Size Matters: Assessing Optimum Soil Sample Size for Fungal and Bacterial Community Structure Analyses Using High Throughput Sequencing of rRNA Gene Amplicons – C. Ryan Pento – Frontiers in Microbiology

Monitoring fungi in ecological restorations of coastal Indiana, U.S.A. – Peter G. Avis – Restoration Ecology

Review: Resilience of Soil Microbial Communities to Metals and Additional Stressors: DNA-Based Approaches for Assessing “Stress-on-Stress” Responses – Hamed Azarbad – MDPI International Journal of Molecular Sciences

Water and extremophile microbiome

Archaeal communities of Arctic methane-containing permafrost – Victoria Shcherbakova – FEMS Microbiology Ecology

Microbial community diversity, structure, and assembly across oxygen gradients in meromictic marine lakes, Palau – Matthew S. Meyerhof – Environmental Microbiology

Bioreactor microbiology

An integrated metagenome and -proteome analysis of the microbial community residing in a biogas production plant – Vera Ortseifen – Journal of Biotechnology


Finds microbial interactions based on PubMed abstracts, so basically finding interactions that were already published (???)@MInter: Automated Text-mining of Microbial Interactions – Lim Kun Ming Kenneth – Bioinformatics

More microbiology

In situ replication rates for uncultivated bacteria in microbial communities – Christopher T Brown – bioRxiv

Pervasive Selection for Cooperative Cross-Feeding in Bacterial Communities – Sebastian Germerodt – PLOS Computational Biology

Microbes in the news

UWM professor taking a deeper dive on beach pollution data – Milwaukee-Wisconsin Journal Sentinel

The medical revolution that delves into humans’ inner aliens – Robert Matthews – The National

Brewing on the wild side: IU’s Dr. Matthew L. Bochman – Rita Kohn – Nuvo.net

Fecal bacteria and antibiotic resistance genes found in water samples from fly-in Northern Manitoba – Ian Graham – Thompson Citizen

CosmosID, BioCollective Collaborate on Microbiome Analysis Kit – GenomeWeb

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