May 4th, 2017

Lots of papers on gut microbiota in today’s digest!


Multi-site human microbiome

The Female Urinary Microbiota/Microbiome: Clinical and Research Implications.

Brubaker L et al – Rambam Maimonides Med J

A case controlled study examining the bladder microbiome in women with Overactive Bladder (OAB) and healthy controls.
Curtiss N et al. – Eur J Obstet Gynecol Reprod Biol

Human respiratory microbiome

Illumina MiSeq 16S amplicon sequence analysis of bovine respiratory disease associated bacteria in lung and mediastinal lymph node tissue.
Johnston D et al. – BMC Vet Res.


Human gut microbiome

The Gut Microbiota and the Hepatologist: Will Our Bugs Prove to be the Missing Link?

Pallen MJ and Quraishi MN – Digestive Diseases

A Specific Gut Microbiota Dysbiosis of Type 2 Diabetic Mice Induces GLP-1 Resistance through an Enteric NO-Dependent and Gut-Brain Axis Mechanism.

Grasset E et al – Cell Metab

Gut Microbiome-Based Metagenomic Signature for Non-invasive Detection of Advanced Fibrosis in Human Nonalcoholic Fatty Liver Disease.

Loomba R et al  –  Cell Metab

16S rRNA gene sequencing and healthy reference ranges for 28 clinically relevant microbial taxa from the human gut microbiome.

Almonacid DE – PLoS One

Autophagy Genes of Host Responds to Disruption of Gut Microbial Community by Antibiotics.

Singh SB – Dig Dis Sci

Interaction between the gut microbiome and mucosal immune system.

Shi N

Saccharomyces boulardii Administration Changes Gut Microbiota and Attenuates D-Galactosamine-Induced Liver Injury.
Yu L et al. – Sci Rep

Faecal microbiota transplantation for ulcerative colitis.
Drug Ther Bull.

Microbiome and colorectal cancer: Unraveling host-microbiota interactions in colitis-associated colorectal cancer development.
Kang M et al. Semin Immunol

Alpha-ketoglutarate (AKG) lowers body weight and affects intestinal innate immunity through influencing intestinal microbiota.
Chen S et al. – Oncotarget

The composition of gut microbiota in infant and its influencing factors
Liu W et al – Zhonghua Yu Fang Yi Xue Za Zhi

Occurrence of antibiotic resistance genes in the Faecal DNA of healthy omnivores, Ovo-Lacto vegetarians and vegans.
Milanović V et al. Mol Nutr Food Res

Seasonal variation in the copepod gut microbiome in the subtropical North Atlantic Ocean.
Shoemaker KM et al. Environ Microbiol

Models of antimicrobial pressure on intestinal bacteria of the treated host populations.
Volkova VV et al. – Epidemiol Infect

The food-gut human axis: the effects of diet on gut microbiota and metabolome.
De Angelis M et al.

The chicken or the egg dilemma: intestinal dysbiosis in multiple sclerosis.
Ochoa-Repáraz J, et al. – Ann Transl Med.

Impact of faecal microbiota transplantation on mouse digestive colonization with two extensively resistant bacteria.
Mahieu R et al – J Infect.


Plant, root, and soil microbiome

Lactic acid bacteria population dynamics during spontaneous fermentation of radish (Raphanus sativus L.) roots in brine.

Pardali E – World J Microbiol Biotechnol
Water and extremophile microbiome (sea, rivers, lakes, glaciers, permafrost, high-salt)

Intraspecific Variation in the Skin-Associated Microbiome of a Terrestrial Salamander.

Prado-Irwin SR – Microb Ecol

Analysis of biofilm bacterial communities under different shear stresses using size-fractionated sediment.

Unraveling microbial structure and diversity of activated sludge in a full-scale simultaneous nitrogen and phosphorus removal plant using metagenomic sequencing.
Guo J et al – Enzyme Microb Technol.

The interacting roles of climate, soils, and plant production on soil microbial communities at a continental scale.
Waldrop MP et al. – Ecology

Correspondence of coral holobiont metabolome with symbiotic bacteria, archaea and Symbiodinium communities.
Sogin EM et al. – Environ Microbiol Rep
Fang H et al. Sci Rep.

Influence of root components of celery on pyrene bioaccessibility, soil enzymes and microbial communities in pyrene and pyrene-diesel spiked soils.
Wei J et al. – Sci Total Environ


ICoVeR – an interactive visualization tool for verification and refinement of metagenomic bins.
Broeksema B et al. – BMC Bioinformatics

May 3, 2017

Pregnancy and early life

Development of the cutaneous microbiome in the preterm infant: A prospective longitudinal study
Mohan Pammi et al. PLoS One

Human respiratory microbiome

The presence of bacterial microcolonies on the maxillary sinus ciliary epithelium in healthy young individuals
Monika Morawska-Kochman et al. PLoS One

Human gut microbiome

Review of mechanisms of deoxynivalenol-induced anorexia: The role of gut microbiota

Probiotics are a good choice in remission of inflammatory bowel diseases: A meta analysis and systematic review
Mahboube Ganji-Arjenaki et al – JOURNAL OF CELLULAR PHYSIOLOGY

Differences in gut microbial composition correlate with regional brain volumes in irritable bowel syndrome.
Labus JS et al – Microbiome

The shrinking human gut microbiome.
Moeller AH. – Curr Opin Microbio

Animal experiments

Maternal obese-type gut microbiota differentially impact cognition, anxiety and compulsive behavior in male and female offspring in mice

Jing Chen et al. PLoS One


Dysbiosis of intestinal microbiota and decrease in paneth cell antimicrobial peptide level during acute necrotizing pancreatitis in rats
Annadora J. et al . PLoS One

Animal microbiome

Bacterial microbiome of the nose of healthy dogs and dogs with nasal disease
Barbara Tress, et al . PLoS One
Characterization of the fecal microbiome during neonatal and early pediatric development in puppies
Blake C. Guard et al. PLoS One

Effects of Saccharomyces cerevisiae fermentation products on dairy calves: Ruminal fermentation, gastrointestinal morphology, and microbial community.
Xiao JX et al – J Diary Sci

Studies on bacterial community composition are affected by the time and storage method of the rumen content
Yury Tatiana Granja-Salcedo et al. PLoS One

Competition drives the response of soil microbial diversity to increased grazing by vertebrate herbivores.
Eldridge DJ et al – Ecology

Diversity of culturable bacterial communities in the intestinal tracts of goldfish (Carassius auratus) and their ability to produce N-acyl homoserine lactone.
Sugita H et al – Folia Microbiol


Water and extremophile microbiome (sea, rivers, lakes, glaciers, permafrost, high-salt)

Crude oil impairs immune function and increases susceptibility to pathogenic bacteria in southern flounder
Keith M. Bayha et al. PLoS One

Pyrosequencing reveals microbial community dynamics in integrated simultaneous desulfurization and denitrification process at different influent nitrate concentrations.
Chen C et al – Chemosphere



Abundance profiling of specific gene groups using precomputed gut metagenomes yields novel biological hypotheses
Konstantin Yarygin et al. PLoS One

Evaluation of the reproducibility of amplicon sequencing with Illumina MiSeq platform
Chongqing Wen et al. PLoS One

February 12, 2017

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


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

February 7, 2017

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



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



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)