April 10, 2015

Pregnancy and birth microbiome

Maternal fucosyltransferase 2 status affects the gut bifidobacterial communities of breastfed infants – Zachery T Lewis – Microbiome

The Infant Nasopharyngeal Microbiome Impacts Severity of Lower Respiratory Infection and Risk of Asthma Development – Shu Mei Teo – Cell Host & Microbe

Mid-trimester amniotic fluid pro-inflammatory biomarkers predict the risk of spontaneous preterm delivery in twins: a retrospective cohort study – S M Lee – Journal of Perinatology

Risk for Preterm and Very Preterm Delivery in Women Who Were Born Preterm – Boivin, Ariane – Obstetrics & Gynecology

Human oral microbiome

Clinical and microbiological effects of probiotic lozenges in the treatment of chronic periodontitis: a 1-year follow-up study – Merve Tekce – Journal of Clinical Periodontology

Review: Beyond microbial community composition: Functional activities of the oral microbiome in health and disease – Ana E. Duran-Pinedo, Jorge Frias-Lopez – Microbes and Infection

Human gut microbiome

A randomized controlled trial to test the effect of multispecies probiotics on cognitive reactivity to sad mood – Laura Steenbergen – Brain, Behavior, and Immunity

Fungi inhabiting the healthy human gastrointestinal tract: a diverse and dynamic community – Heather E. Hallen-Adams – Fungal Ecology

Changes in human gut microbiota influenced by probiotic fermented milk ingestion – Tatsuya Unno – Journal of Dairy Science

Fecal Microbiota Transplantation Induces Remission in Patients with Active Ulcerative Colitis in a Randomized, Controlled Trial – Paul Moayyedi – Gastroenterology

Review: The Microbiota and Microbiome in Aging: Potential Implications in Health and Age-Related Diseases – Heidi J. Zapata – Journal of the American Geriatrics Society

Review: Gastric cancer and the microbiome – Nivedita Arora – Asian Pacific Journal of Tropical Disease

Review: The Role of Microbiota on the Gut Immunology – Yang Won Min – Clinical Therapeutics

Animal models of microbiome research

Editorial: Gut Microbiota: The Link to Your Second Brain – Vanessa Ridaura – Cell
Belongs to: Indigenous Bacteria from the Gut Microbiota Regulate Host Serotonin Biosynthesis – Jessica M. Yano – Cell

Inoculation of tannin-degrading bacteria into novel hosts increases performance on tannin-rich diets – Kevin D. Kohl – Environmental Microbiology

Crosstalk between Microbiota-Derived Short-Chain Fatty Acids and Intestinal Epithelial HIF Augments Tissue Barrier Function – Caleb J. Kelly – Cell Host & Microbe

Effect of a new recombinant Aeromonas hydrophila vaccine on the grass carp intestinal microbiota and correlations with immunological responses – Lei Liu – Fish & Shellfish Immunology

Colonization and induction of Th17 cells by segmented filamentous bacteria in the murine intestine – Adam M. Farkas – Journal of Immunological Methods

Animal microbiome

Microbiota and probiotics in canine and feline welfare – Łukasz Grześkowiak – Anaerobe

Isolation and use of beneficial microbiota from the digestive tract of lions-paw scallop Nodipecten subnodosus and winged pearl oyster Pteria sterna in oyster aquaculture – Fernando Abasolo-Pacheco – Aquaculture Research

Perspective: Does the Arthropod Microbiota Impact the Establishment of Vector-Borne Diseases in Mammalian Hosts? – Constance A. M. Finney – PLOS Pathogens

Plant and plant root microbiome

Seagrass biofilm communities at a naturally CO2-rich vent – Christiane Hassenrück – Environmental Microbiology Reports

Preferential Association of Endophytic Bradyrhizobia with Different Rice Cultivars and Its Implications for Rice Endophyte Evolution – Pongdet Piromyou – Applied and Environmental Microbiology

Niche partitioning in arbuscular mycorrhizal communities in temperate grasslands: a lesson from adjacent serpentine and nonserpentine habitats – Petr Kohout – Molecular Ecology

Soil microbiome

Microbial community dynamics during the early stages of plant polymer breakdown in paddy soil – Carl-Eric Wegner andWerner Liesack – Environmental Microbiology

Depth-related responses of soil microbial communities to experimental warming in an alpine meadow on the Qinghai-Tibet Plateau – B. Zhang – European Journal of Soil Science

Red Soils Harbor Diverse Culturable Actinomycetes That Are Promising Sources of Novel Secondary Metabolites – Xiaoxuan Guo – Applied and Environmental Microbiology

Water microbiome

Shifts in the meso- and bathypelagic archaea communities composition during recovery and short-term handling of decompressed deep-sea samples – Violetta La Cono –

Understanding diversity patterns in bacterioplankton communities from a sub-Antarctic peatland – María Victoria Quiroga – Environmental Microbiology Reports

The hidden seasonality of the rare biosphere in coastal marine bacterioplankton – Laura Alonso-Sáez- Environmental Microbiology

Bacterial community dynamics during polysaccharide degradation at contrasting sites in the Southern and Atlantic Oceans – Matthias Wietz – Environmental Microbiology

Extremophile microbiome

Nature special: Permafrost: overview articles and primary research from Nature papers, including role of microbes in permafrost soils

Metagenomic analysis of a high carbon dioxide subsurface microbial community populated by chemolithoautotrophs and bacteria and archaea from candidate phyla
Joanne B. Emerson – Environmental Microbiology

Food microbiology

Batch-to-batch uniformity of bacterial community succession and flavor formation in the fermentation of Zhenjiang aromatic vinegar – Zong-Min Wang – Food Microbiology

Microbial diversity and stability during primary cultivation and subcultivation processes of Tibetan kefir – Wei Gao – International Journal of Food Science & Technology

There is a serious problem with Figure 1: Tetragenococcus koreensis is part of the microbiota in a traditional Italian raw fermented sausage – C. Amadoro – Food Microbiology

Other  papers of interest

Development and utility of the FDA ‘GutProbe’ DNA microarray for identification, genotyping and metagenomic analysis of commercially available probiotics – J.N. Patro – Journal of Applied Microbiology

Increased Biodiversity in the Environment Improves the Humoral Response of Rats
Cinthia Pi – PLOS ONE

Microbes in the news

Bundle Of Joyful Microbes: Mom’s DNA Alters Baby’s Gut Bacteria – Michaeleen Doucleff – NPR Shots

Worms, germs lead to better immune function – Science Daily
What does the term microbiome mean? And where did it come from? A bit of a surprise .. – Jonathan Eisen – MicroBEnet

Leading expert on microbiome Rob Knight wins a 2015 Vilcek Prize for Creative Promise in Biomedical Science – PR NewsWire

Congrats: You Are Officially a Superorganism – Max Lugavere – Huffington Post

Genetically-Engineered Bacteria Can Keep Mice From Getting Fat – Sarah Zhang – Gizmodo

Your microbiome may hold keys to cancer treatment – Alexandra Ossola – Popular Science

Cheese: The latest piece of the French paradox puzzle? – Niamh Michail – Food Navigator

#BacteriaHysteria #BacteriaArePlural: How much bacteria is in your kid’s lunchbox? You might be surprised (and grossed out) – Alex Perez – ABC 7online

Science, publishing, and career

Wanted: staff-scientist positions for postdocs – Kendall Powell – Nature

Book review: Speaking of science – Scientific Babel: How Science Was Done Before and After Global English – Lynn K. Nyhart – Science

Gender Disparity in Peer Review? – Andrew Harrison – Publons

Citations are not enough: Academic promotion panels must take into account a scholar’s presence in popular media – London School of Economics and Political Science

Bik’s Picks

Incredible imprinting – ‘are you my mummy?’ – Biodetectives

Sea Turtle Toddlers’ ‘Lost Years’ Spent Swimming, Not Drifting In Seaweed Matts – Rebekah Marcarelli – HNGN.com

New species of ‘terror bird’ discovered – Sid Perkins – Science


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