September 5, 2018

Today’s Digest is not short of articles from all aspects of microbiome research. Highlights include a study on population dynamics during cycles of feast and famine, guidelines for FMT, and a 7-year experiment on the effect of warming and elevated carbon dioxide on soil carbon dynamics.

General microbiology

Microalgae-bacteria symbiosis in microalgal growth and biofuel production: a review – Shuo Yao et al. – Journal of Applied Microbiology

Sketching the Human Microbiome Biogeography with DAR (Diversity-Area Relationship) Profiles – Zhanshan (Sam) Ma – Microbial Ecology

** Frequency- and Amplitude-Dependent Microbial Population Dynamics during Cycles of Feast and Famine – Jason Merritt & Seppe Kuehn – Physical Review Letters

Review: Ecological effects of cellular computing in microbial populations – Maia Baskerville et al. – Natural Computing

Antibiotics/Antibiotic resistance

Detection of antibiotics synthetized in microfluidic picolitre-droplets by various actinobacteria – Lisa Mahler et al. – Scientific Reports

Turning pig manure into biochar can effectively mitigate antibiotic resistance genes as organic fertilizer – Xue Zhou et al. – Science of The Total Environment

Comparative network analysis revealing the mechanisms of antibiotic resistance genes removal by leachate recirculation under different hydraulic loadings – Yinglong Sun et al. – Science of The Total Environment

Do plastics serve as a possible vector for the spread of antibiotic resistance? First insights from bacteria associated to a polystyrene piece from King George Island (Antarctica) – Pasqualina Laganà et al. – International Journal of Hygiene and Environmental Health

Forensic microbiome

Combining human STR and microbial population profiling: two case reports – Frederike C.A. Quaak et al. – FSI Genetics

Human lung microbiome

Review: The Genetics and Genomics of Asthma – Saffron A.G. Willis-Owen et al. – Annual Review of Genomics and Human Genetics

Human gut microbiome

In vitro: Impact of combining acerola by-product with a probiotic strain on a gut microbiome model – Fernanda Bianchi et al. – International Journal of Food Sciences and Nutrition

Changes in the Gut Microbiota of Urban Subjects during an Immersion in the Traditional Diet and Lifestyle of a Rainforest Village – Kelly V. Ruggles et al. – mSphere

Letter: Primum non nocere: is faecal microbiota transplantation doing harm to patients with IBS? – Paul Enck – Gut

Changes in gut microbiota and plasma inflammatory factors across the stages of colorectal tumorigenesis: a case-control study – Yongzhen Zhang et al. – BMC Microbiology

** The use of faecal microbiota transplant as treatment for recurrent or refractory Clostridium difficile infection and other potential indications: joint British Society of Gastroenterology (BSG) and Healthcare Infection Society (HIS) guidelines – Benjamin H. Mullish et al. – Journal of Hospital Infection

Fecal microbiota transplantation: a promising strategy in preventing the progression of non-alcoholic steatohepatitis and improving the anti-cancer immune response – Vaihere Delaune et al. – Expert Opinion on Biological Therapy

Review: Modulation of the immune system by the gut microbiota in the development of Type 1 Diabetes – James A. Pearson et al. – Human Vaccines & Immunotherapeutics

Human gut-microbiome-brain axis

Altered Schaedler flora mice: An old defined microbiota animal model to study the new science of microbiota-gut-brain axis – J.M.Lyte et al. – Behavioural Brain Research

Animal experiments

Molecular networks affected by neonatal microbial colonization in porcine jejunum, luminally perfused with enterotoxigenic Escherichia coli, F4ac fimbria or Lactobacillus amylovorus – Paolo Trevisi et al. – PLoS One

Effects of Natural Flavonoid-Isoorientin on Growth Performance and Gut Microbiota of Mice – Li Xuan et al. – Journal of Agricultural and Food Chemistry

Host diet mediates a negative relationship between abundance and diversity of Drosophila gut microbiota – Berra Erkosar et al. – Ecology and Evolution

Animal microbiome

Effects of clove (Syzygium aromaticum) oil on quail growth, carcass traits, blood components, meat quality, and intestinal microbiota – Mohamed M A Hussein et al. – Poultry Science

The effect of lavender (Lavandula angustifolia) essential oil as a drinking water supplement on the production performance, blood biochemical parameters, and ileal microflora in broiler chickens – Michalina Adaszyńska-Skwirzyńska & Danuta Szczerbińska – Poultry Science

Review: Factors Influencing Individual Variation in Farm Animal Cognition and How to Account for These Statistically – Emily V. Bushby et al. – Frontiers in Veterinary Science

Broad Bean (Vicia faba L.) Induces Intestinal Inflammation in Grass Carp (Ctenopharyngodon idellus C. et V) by Increasing Relative Abundances of Intestinal Gram-Negative and Flagellated Bacteria – Zhifei Li et al. – Frontiers in Microbiology

Factors shaping the gut bacterial community assembly in two main Colombian malaria vectors – Priscila Bascuñán et al. – Microbiome

Alterations in honey bee gut microorganisms caused by Nosema spp. and pest control methods – Tsiri Diaz et al. – Pest Management Science

Plant, root and soil microbiome

** Elevated CO2 and warming cause interactive effects on soil carbon and shifts in carbon use by bacteria – Yolima Carrillo et al. – Ecology Letters

The role of wetland microorganisms in plant-litter decomposition and soil organic matter formation: a critical review – Stephanie A Yarwood – FEMS Microbiology Ecology

Strong succession in arbuscular mycorrhizal fungal communities – Cheng Gao et al. – ISME J

Manipulation of the rhizosphere bacterial community by biofertilizers is associated with mitigation of cadmium phytotoxicity – Meng Wang et al. – Science of The Total Environment

Multi-substrate induced microbial respiration, nitrification potential and enzyme activities in metal-polluted, EDTA-washed soils – Guixiang Zhou et al. – Scientific Reports

Divergent accumulation of microbial necromass and plant lignin components in grassland soils – Tian Ma et al. – Nature Communications

Microbial Community Composition In Take-All Suppressive Soils – Paola Duran et al. – Frontiers in Microbiology

Differential biodiversity responses between kingdoms (plants, fungi, bacteria and metazoa) along an Alpine succession gradient – Matteo Montagna et al. – Molecular Ecology

Water and extremophile microbiome

Steep redox gradient and biogeochemical cycling driven by deeply sourced fluids and gases in a terrestrial mud volcano – Yueh-Ting Lin et al. – FEMS Microbiology Ecology

Pigmented microbial eukaryotes fuel the deep sea carbon pool in the tropical Western Pacific Ocean – Dapeng Xu – Environmental Microbiology

Biofilm Formation and Degradation of Commercially Available Biodegradable Plastic Films by Bacterial Consortiums in Freshwater Environments – Tomohiro Morohoshi et al. – Microbes and Environments

Dynamics and Functional Potential of Stormwater Microorganisms Colonizing Sand Filters – Andrea Naimah Fraser et al. – Water

Review: Lignin depolymerization and utilization by bacteria – Rong Xu et al. – Bioresource Technology

Microbes in the industry

From systems biology to metabolically engineered cells — an omics perspective on the development of industrial microbes – Judith Becker &Christoph Wittmann – Current Opinion in Microbiology

Phages and viruses

High-Resolution Temporal and Spatial Patterns of Virome in Wastewater Treatment Systems – Yulin Wang et al. – Environmental Science & Technology


Limitations of Correlation-Based Inference in Complex Virus-Microbe Communities – Ashley R. Coenen & Joshua S. Weitz – mSystems

A Sensitive Thresholding Method for Confocal Laser Scanning Microscope Image Stacks of Microbial Biofilms – Ting L. Luo et al. – Scientific Reports

A steam-based method to investigate biofilm – Jason Tasse et al. – Scientific Reports

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