Microbiome digest, November 28, 2014

Human gut microbiome

Effects of Surgical and Dietary Weight Loss Therapy for Obesity on Gut Microbiota Composition and Nutrient Absorption – Antje Damms-Machado – BioMed Research International

Collateral damage from oral ciprofloxacin versus nitrofurantoin in outpatients with urinary tract infections: a culture-free analysis of gut microbiota – Andrew J. Stewardson – Clinical Microbiology and Infection

Potential of fecal microbiota for early-stage detection of colorectal cancer – Georg Zeller – Molecular Systems Biology

Does the microbiota play a role in the pathogenesis of autoimmune diseases? – Mairi H McLean – Gut

The gut microbiota and inflammatory bowel disease – Katsuyoshi Matsuoka and Takanori Kanai – Seminars in Immunopathology

Metagenomic analysis of the gastric microbiota cultivable from a patient 

with gastritis concomitant with Barrett’s esophagus – Andrés Julián Gutiérrez-Escobar – Rev Gastroenterol Peru

Gut microbiota in patients with type 2 diabetes mellitus – Kristine H Allin – European Journal of Endocrinology

Gut brain axis: diet microbiota interactions and implications for modulation of anxiety and depression – Ruth Ann Luna, Jane A Foster

Behçet’s syndrome patients exhibit specific microbiome signature – Clarissa Consolandi – Autoimmunity Reviews

Animal microbiome

Complete genome sequence and comparative genome analysis of Klebsiella oxytoca HKOPL1 isolated from giant panda feces – Jingwei Jiang – BMC Research Notes

Few highly abundant operational taxonomic units dominate within rumen methanogenic archaeal species in New Zealand sheep and cattle – Henning Seedorf – Applied and Environmental Microbiology

Chironomid Microbiome – Malka Halpern, Yigal Senderovich – Microbial Ecology

Plant microbiome

Understanding and engineering beneficial plant–microbe interactions: plant growth promotion in energy crops – Kerrie Farrar – Plant Biotechnology Journal

Soil and sludge microbiome

Global diversity and geography of soil fungi – Leho Tedersoo – Science

Effects of the Biocontrol Agent Aspergillus flavipes on the Soil Microflora and Soil Enzymes in the Rooting Zone of Pepper Plants Infected with Phytophthora capsici – Hui Wang – Journal of Phytopathology

Plant diversity predicts beta but not alpha diversity of soil microbes across grasslands worldwide – Suzanne M. Prober – Ecology Letters

Soil chemical properties affect the reaction of forest soil bacteria to drought and rewetting stress – Marcin Chodak – Annals of Microbiology

Cyanobacteria and algae of buried soils and their modern analogues – A. D. Temraleeva – Paleontological Journal

Diversity and efficiency of anthracene-degrading bacteria isolated from a denitrifying activated sludge system treating municipal wastewater – Spyridon Ntougias – International Biodeterioration & Biodegradation

Water microbiome

Profile of bacterial communities in South African mine-water samples using Illumina next-generation sequencing platform – Jitendra Keshri – Applied Microbiology and Biotechnology

Temporal and Vertical Distribution of Bacterioplankton at the Gray’s Reef National Marine Sanctuary – Xinxin Lu – Applied and Environmental Microbiology

Identification of Microorganisms in Hydrocarbon-Contaminated Aquifer Samples by Fluorescence In Situ Hybridization (CARD-FISH) – Schattenhofer Martha – Springer Protocols Handbooks

Food microbiology

Influence of pig rennet on proteolysis, organic acids content and microbiota of Pecorino di Farindola, a traditional Italian ewe’s raw milk cheese – Tofalo Rosanna – Food Chemistry


Alternative for USEARCH: VSEARCH: Open and free 64-bit multithreaded tool for processing metagenomic sequences, including searching, clustering, chimera detection, dereplication, sorting, masking and shuffling – Github

svaseq: removing batch effects and other unwanted noise from sequencing data – Jeffrey T. Leek – Nucleic Acids Research

Phages and viruses

Automated classification of tailed bacteriophages according to their neck organization – Anne Lopes – BMC Genomics


Metabolic fate of neutral human milk oligosaccharides in exclusively breast-fed infants –
Viktoria Dotz – Molecular Nutrition & Food Research


Transcriptome analysis reveals novel regulatory mechanisms in a genome-reduced bacterium – Pavel V. Mazin – Nucleic Acids Research

More microbiology

In vivo treatment of Helicobacter pylori infection with liposomal linolenic acid reduces colonization and ameliorates inflammation – Soracha Thamphiwatana – PNAS USA

Microbes in the news

How bacteria in your gut could be making you fat, allergic, or anxious – Susannah Locke – Vox

Interview with Dan Knights: UMN professor solves problems from ‘gut bugs’ to Rubik’s Cube – Richard Chin – Twin Cities

Artificial Sweeteners May Have Despicable Impacts on Gut Microbes – Sheena Faherty – Scientific American

The Human Microbiome, An Issue of Clinics in Laboratory Medicine – Google eBook

Science and art

It’s a microbial world – protozoa pancakes

Bik’s Picks

Detection of fraudulent addition of bovine whey in Ricotta cheese by iso-electric focusing
– Fabio Fuselli – Journal of Science of Food and Agriculture

DNA survives critical entry into Earth’s atmosphere – Science Daily

Bill Nye: ‘Science is true, whether or not you believe it’ – Brad Wheeler – The Globe and Mail

The Best Gifts of 2014 for Science Geeks – Smithsonian.com



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