Being Sunday there aren’t that many publications to talk about. However the study by Zheng and colleagues makes up for it and is a must read! A bit like BCG for bladder cancer they engineered bacteria to induce an effective antitumor immune response, successfully treating tumors in several different mouse models with no evidence of toxicity. In another interesting study, Harach et al demonstrate microbial involvement in the development of Abeta amyloid pathology, and suggest that microbiota may contribute to the development of neurodegenerative diseases.

General microbiome

*Two-step enhanced cancer immunotherapy with engineered Salmonella typhimurium secreting heterologous flagellin – Jin Hai Zheng – Science Translational Medicine

Millennia of genomic stability within the invasive Para C Lineage of Salmonella enterica –  Zhemin Zhou – bioRxiv

A target-specific assay for rapid and quantitative detection of Mycobacterium chimaera DNA in environmental and clinical specimens – Enrique Zozaya-Valdes – bioRxiv

Human gut microbiome

*Reduction of Abeta amyloid pathology in APPPS1 transgenic mice in the absence of gut microbiota – T. Harach –  Scientific Reports

Gut bacteria may play a role in Alzheimer’s disease –  Science Daily

Water and extremophile microbiome 

A survey of microparasites present in adult migrating Chinook salmon (Oncorhynchus tshawytscha) in south-western British Columbia determined by high-throughput quantitative polymerase chain reaction – A L Bass – Journal of Fish Disease

Distinct Biogeographic Patterns for Archaea, Bacteria, and Fungi along the Vegetation Gradient at the Continental Scale in Eastern China – B Ma – mSystems

Bioinformatics

OptiClust: Improved method for assigning amplicon-based sequence data to operational taxonomic units – Sarah L Westcott – bioRxiv

 Microbes in the news 

Gut Microbiota Improved when Eating Whole Grains – Council Chronicle

Feeding probiotics to rats before stressing them out reduces disruption of gut microbiota – The Indian Express

Researchers develop new method that can rapidly profile resistome of gut microbial communities – News Medical

Changes in the gut microbiota during aging is associated with increased gut permeability and peripheral inflammation and may mediate cognitive decline. An overview of the gut microbiome in Crohn’s Disease and insight into how extremophiles might maintain protein folding. 

General microbiome

Whole genome sequence of lactic acid bacterium Pediococcus acidilactici strain S1 – Gun-Seok Park – Brazilian Journal of Microbiology

‘Pygmaiobacter massiliensis’ sp. nov., a new bacterium isolated from the human gut of a Pygmy woman – M. Bilen – NMNI

Human and rat gut microbiome composition is maintained following sleep restriction – Zhang SL – PNAS

Palaeogeographic variation in the Permian−Triassic boundary microbialites: A discussion of microbial and ocean processes after the end-Permian mass extinction – Stephen Kershaw – Journal of Palaeogeography

Assessment of bacterial profiles in aged, home-made Sichuan paocai brine with varying titratable acidity by PacBio SMRT sequencing technology – Jialu Cao – Food Control

Human gut microbiome

Differences in Gut Metabolites and Microbial Composition and Functions between Egyptian and U.S. Children Are Consistent with Their Diets  – V. Shankar – mSystems

*PrePrint:  Postmortem succession of gut microbial communities in human cadavers – Jennifer M DeBruyn – PeerJ Preprints

Substituting whole grains for refined grains in a 6-wk randomized trial has a modest effect on gut microbiota and immune and inflammatory markers of healthy adults – Vanegas SM – American Journal of Clinical Nutrition

Altered molecular signature of intestinal microbiota in irritable bowel syndrome patients compared with healthy controls: A systematic review and meta-analysis – Hai-Ning Liu – Digestive and Liver Disease

Animal experiments 

Revisiting Metchnikoff: Age-related Alterations in Microbiota-Gut-Brain Axis in the Mouse – Karen A. Scott – Brain, Behavior, and Immunity

Animal microbiome 

Immune system stimulation by the native gut microbiota of honey bees – Waldan K. Kwong – Royal Society for Open Science

Deep Sequencing Reveals Highly Variable Gut Microbial Composition of Invasive Fish Mossambicus Tilapia (Oreochromis mossambicus) Collected from Two Different Habitats – Swapnil Sopan Gaikwad – Indian Journal of Microbiology

The gastrointestinal tract microbiota of the Japanese quail, Coturnix japonica –  Ngare Wilkinson – Environmental Biotechnology

Plant, root, and soil microbiome

Hydrogen Peroxide and Strigolactones Signaling Are Involved in Alleviation of Salt Stress Induced by Arbuscular Mycorrhizal Fungus in Sesbania cannabina Seedlings – Cun-Cui Kong – Journal of Plant Growth Regulation

Potential Role of Plant-Associated Bacteria in Plant Metal Uptake and Implications in Phytotechnologies – Petra S. Kidd – Advances in Botanical Research

Application of bacteria from non-cultivated plants to promote growth, alter root architecture and alleviate salt stress of cotton – Ivelisse Irizarry – Journal of Applied Microbiology

Water and extremophile microbiome 

Molecular determinant of the effects of hydrostatic pressure on protein folding stability – Calvin R. Chen – Nature Communications

Microarray analysis of the benthic bacterium Shewanella piezotolerans WP3 at low temperature – Huahua Jian – Marine Genomics

Metagenomic exploration of microbial community in mine tailings of Malanjkhand copper project, India – Abhishek Gupta – Genomics Data

Illumina sequencing-based analysis of sediment bacteria community in different trophic status freshwater lakes – Yu Wan – Microbiology Open

Variations in airborne bacterial communities at high altitudes over the Noto Peninsula (Japan) in response to Asian dust events – Teruya Maki – Atmospheric Chemistry and Physics Discussions

Phages and viruses

Viruses comprise an extensive pool of mobile genetic elements in eukaryote cell cultures and human clinical samples – Thannesberger J – The FASEB Journal

Techniques

Community-level physiological profiling analyses show potential to identify the copiotrophic bacteria present in soil environments – Salvador Llado – PLOS one

Cultivation-Free Raman Spectroscopic Investigations of Bacteria – Björn Lorenz – Trends in Microbiology

*Review:  Proteomics Tracing the Footsteps of Infectious Disease – Todd M Greco – Molecular and Cellular Proteomics

Metabolomics as a Challenging Approach for Medicinal Chemistry and Personalized Medicine – Michel Fredérich – Journal of Medical Chemistry

An integrative Bayesian Dirichlet-multinomial regression model for the analysis of taxonomic abundances in microbiome data – Wadsworth WD – BMC Bioinformatics

Microbes on the market 

General microbiome

*Review: Gut microbiota and acute coronary syndromes: ready for use in the emergency room? – Trøseid M. – Eur Heart J

Review: Fecal Microbiota Transplant versus Oral Vancomycin Taper: Important Undiscussed Limitations. – Jansen JW – Clin Infect Dis

Review: Fecal Microbiota Transplantation: do we need harmonization? – Galpérine T – Clin Infect Dis

Fecal microbiota transplantation in patients with slow-transit constipation: A randomized, clinical trial. – Tian H – PLoS One

Listeriolysin S: a bacteriocin from epidemic Listeria monocytogenes strains that targets the microbiota. – Quereda-Torres JJ – Gut Microbes

*Possible Alternative Predictors of Failure of Fecal Microbiota Transplant for Therapy of Recurrent C difficile Infection. – Bodiwala V – Am J Gastroenterol

Repeated fecal microbiota transplantations attenuate diarrhea and lead to sustained changes in the fecal microbiota in acute, refractory gastrointestinal graft-versus-host-disease. – Spindelboeck W – Haematologica

Review: Gastrointestinal Immune and Microbiome Changes During Parenteral Nutrition. – Pierre JF –  Am J Physiol Gastrointest Liver Physiol.

Microbiome sharing between children, livestock and household surfaces in western Kenya. – Mosites E – PLoS One

Pregnancy and early life

Oral yeast colonization throughout pregnancy. – Rio R – Med Oral Patol Oral Cir Bucal

Review: Human Milk Oligosaccharides and the Preterm Infant: A Journey in Sickness and in Health. – Moukarzel S – Clin Perinatol

Loss of cutaneous microbial diversity during first three weeks of life in very low birth weight infants. – Salava A – Exp Dermatol

The Fecal Microbial Community of Breast-fed Infants from Armenia and Georgia. – Lewis ZT – Sci Rep

Antibiotic resistance potential of the healthy preterm infant gut microbiome. – Rose G – PeerJ

Multi-site human microbiome

Review: From Evolutionary Advantage to Disease Agents: Forensic Reevaluation of Host-Microbe Interactions and Pathogenicity. – Rivera-Pérez JI – Microbiol Spectr

Human respiratory microbiome

*Microbes Associate with Host Innate Immune Response in Idiopathic Pulmonary Fibrosis. – Huang Y – Am J Respir Crit Care Med

Human gut microbiome

Review: The Enigmatic Gut in Cystic Fibrosis: Linking Inflammation, Dysbiosis, and the Increased Risk of Malignancy. – Garg M – Curr Gastroenterol Rep

Involvement of gut microbiota in the association between GLP-1/GLP-1 receptor expression and gastrointestinal motility. – Yang M – Am J Physiol Gastrointest Liver Physiol

*Novel insight into the role of microbiota in colorectal surgery. – Bachmann R – Gut

*Race-dependent association of sulfidogenic bacteria with colorectal cancer. –  Yazici C – Gut

Review: The “gut microbiota” hypothesis in primary sclerosing cholangitis. – Pontecorvi V – Ann Transl Med

Review: The development and role of microbial-host interactions in gut mucosal immune development. – Stokes CR – J Anim Sci Biotechnol

Yogurt Containing Lactobacillus gasseri Mitigates Aspirin-Induced Small Bowel Injuries: A Prospective, Randomized, Double-Blind, Placebo-Controlled Trial. – Suzuki T – Digestion

Animal experiments 

Dietary fibres modulate the composition and activity of butyrate-producing bacteria in the large intestine of suckling piglets – Mu C – Antonie Van Leeuwenhoek

Drunk Bugs: Chronic Vapour Alcohol Exposure Induces Marked Changes in the Gut Microbiome in Mice. – Peterson VL – Behav Brain Res

Microscopic Evaluation of the Effect of Oral Microbiota on the Development of Bisphosphonate-Related Osteonecrosis of the Jaws in Rats. – Silveira FM – J Oral Maxillofac Res

Animal microbiome

The bovine colostrum microbiome and its association with clinical mastitis. – Lima SF – J Dairy Sci

Bacterial bile salt hydrolase: an intestinal microbiome target for enhanced animal health. – Geng W – Anim Health Res Rev

Functional analysis for gut microbes of the brown tree frog (Polypedates megacephalus) in artificial hibernation. – Weng FC – BMC Genomics

Plant, root, and soil microbiome

Dairy propionibacteria prevent the proliferative effect of plant lectins on SW480 cells and protect the metabolic activity of the intestinal microbiota in vitro. – Zárate G – Anaerobe

Probiotics / prebiotics

Review: Potential Beneficial Effects of Probiotics on Human Migraine Headache: A Literature Review. – Dai YJ – Pain Physician

Bioinformatics

Robust Inference of Genetic Exchange Communities from Microbial Genomes Using TF-IDF. – Cong Y – Front Microbiol

Techniques

A quantitative SMRT cell sequencing method for ribosomal amplicons. – Jones BM – J Microbiol Methods

RiboTagger: fast and unbiased 16S/18S profiling using whole community shotgun metagenomic or metatranscriptome surveys. – Xie C – BMC Bioinformatics

Survey of (Meta)genomic Approaches for Understanding Microbial Community Dynamics. – Sharma A – Indian J Microbiol

Microbe in the news

Malin takes 33% Stake in Start-Up Microbiome Targeting Firm Artizan – Genetic Engineering & Biotechnology News (blog)

A Pilot Study Assessing Intestinal Microbiota Diversification and Changes After Travel to South(East) Asia From the US – Satellite PR News (press release)