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
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