January 22, 2019

Today’s digest is packed with interesting reviews from Gut to Rhizosphere microbiomes.

General Microbiome

Short-term consumption of a high-fat diet increases host susceptibility to Listeria monocytogenes infection.Heras VL. Microbiome.

Dietary Fructose and Microbiota-Derived Short-Chain Fatty Acids Promote Bacteriophage Production in the Gut Symbiont Lactobacillus reuteri. Oh JH. Cell Host snd Microbe.

Gut Microbiome

REVIEW: The Gut Microbiome as a Target for IBD Treatment: Are We There Yet?Knox NC. Current Treatment Options in Gastroenterology

Interactions between gut microbiota and non-alcoholic liver disease: the role of microbiota-derived metabolites.Ding Y. Pharmacological Research

Gut bacterial tyrosine decarboxylases restrict levels of levodopa in the treatment of Parkinson’s disease.van Kessel SP. Nature Communications

Lung Microbiome

Multiple respiratory microbiota profiles are associated with lower airway inflammation in children with protracted bacterial bronchitis. Marsh RL. Chest.

Plant, Soil, and Air Microbiome

Resilience and Assemblage of Soil Microbiome in Response to Chemical Contamination Combined with Plant Growth. Jiao S. Applied Environmental Microbiology

Effect of plant growth promoting bacterium; Pseudomonas putida UW4 inoculation on phytoremediation efficacy of monoculture and mixed culture of selected plant species for PAH and lead spiked soils.Afegbua SL. International Journal of Phytoremediation.

REVIEW: Synergistic plant-microbes interactions in the rhizosphere: a potential headway for the remediation of hydrocarbon polluted soils.Asemoloye MD. International Journal of Phytoremediation

Spatial and temporal variation of fungal endophytic richness and diversity associated to the phyllosphere of olive cultivars.Materatski P. Fungal Biology

Rhizosphere fungal community structure succession of Xinjiang continuously cropped cotton.Wei Z. Fungal Biology.

REVIEW: To Fix or Not To Fix: Controls on Free-Living Nitrogen-Fixation in the Rhizosphere.Smercina DN. Applied Environmental Microbiology

An active β-lactamase is a part of an orchestrated cell wall stress resistance network of Bacillus subtilis and related rhizosphere species.Bucher T. Environmental Microbiology

Diversity analysis of the rhizospheric and endophytic bacterial communities of <i>Senecio vulgaris</i> L. (Asteraceae) in an invasive range. Cheng D. PeerJ

Genotype and rhizobium inoculation modulate the assembly of soybean rhizobacterial communities.Zhong Y. Plant, Cell, and Environment

Animal Experiments and Microbiome

Dose-dependent impact of oxytetracycline on the veal calf microbiome and resistome.Keijser BJF. BMC Genomics

Earthworms and cadmium – Heavy metal resistant gut bacteria as indicators for heavy metal pollution in soils?  Šrut M. Ecotoxicology and Environmental

Taxonomic and functional composition of the small intestinal microbiome in neonatal calves provide a framework for understanding early life gut health. Malmuthuge N. Applied Environmental Microbiology

Inland Waters and Marine Microbiomes

High-Throughput Sequencing of the 16S rRNA Gene as a Survey to Analyze the Microbiomes of Free-Living Ciliates Paramecium.Plotnikov AO. Microbial Ecology

Action of oxytetracycline (OTC) degrading bacterium and its application in Moving Bed Biofilm Reactor (MBBR) for aquaculture wastewater pre-treatment.Shao S. Ecotoxicology and Environmental

Metabarcoding and machine learning analysis of environmental DNA in ballast water arriving to hub ports. Gerhard WA. Environment International

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January 14, 2019

Human/General Microbiome

Establishment of vaginal microbiota composition in early pregnancy and its association with subsequent preterm prelabor rupture of the fetal membranes – Richard G. Brown – Translational Research

Sex differences in the gut microbiota as potential determinants of gender predisposition to disease – Jose A. Santos‐Marcos – Molecular Nutrition and Food Research

AllergoOncology: microbiota in allergy and cancer – an EAACI position paper – E Untersmayr – Allergy

Comment: Gut microbiota and hypertension – Jun-ichi Oyama – Hypertension Research

Comment: Host-microbiota interactions: from holobiont theory to analysis – Jean-Christophe Simon – Microbiome

Longitudinal Analyses of Gut-Associated Bacterial Microbiota in Ulcerative Colitis Patients – Luma Al-Bayati – Archives of Iranian Medicine

What is the Healthy Gut Microbiota Composition? A Changing Ecosystem across Age, Environment, Diet, and Diseases – Emanuele Rinninella – Microorganisms

A Prospective Study In Severely Injured Patients Reveals An Altered Gut Microbiome Is Associated With Transfusion Volume – Susannah E. Nicholson – Journal of Trauma and Acute Care Surgery

Review: Integration of microbiology, molecular pathology, and epidemiology: a new paradigm to explore the pathogenesis of microbiome-driven neoplasms – Tsuyoshi Hamada – The Journal of Pathology

Review: Targeting gut microbiota with dietary components on cancer: Effects and potential mechanisms of action – Jun Tao – Critical Reviews in Food Science and Nutrition

Disorganized Gut Microbiome Contributed to Liver Cirrhosis Progression: A Meta-Omics-Based Study – Li Shao – Frontiers in Microbiology

Review: Leveraging Multilayered “Omics” Data for Atopic Dermatitis: A Road Map to Precision Medicine – Debajyoti Ghosh – Frontiers in Immunology

Systemic instruction of cell-mediated immunity by the intestinal microbiome – John Grainger – F1000Research

Fecal microbiota transplantation in refractory ulcerative colitis – a case report – B. D. Moutinho – Journal of International Medical Research

Current Opinion: Acne, the Skin Microbiome, and Antibiotic Treatment – Haoxiang Xu – American Journal of Clinical Dermatology

Fusobacterium nucleatum promotes chemoresistance to 5-fluorouracil by upregulation of BIRC3 expression in colorectal cancer – Sheng Zhang – Journal of Experimental & Clinical Cancer Research

Enteric dysbiosis and fecal calprotectin expression in premature infants – Thao T. B. Ho – Pediatric Research

 

Animal Models

Obesity Aggravates Acute Pancreatitis via Damaging Intestinal Mucosal Barrier and Changing Microbiota Composition in Rats – Cheng Ye – Scientific Reports

Asperlin Stimulates Energy Expenditure and Modulates Gut Microbiota in HFD-Fed Mice – Chongming Wu – Marine Drugs

Preventive Effect of Spontaneous Physical Activity on the Gut-Adipose Tissue in a Mouse Model That Mimics Crohn’s Disease Susceptibility – Florie Maillard – Cells

Lactobacillus sakei Alleviates High-fat Diet-induced Obesity and Anxiety in Mice by Inducing AMPK Activation and SIRT1 Expression and Inhibiting Gut Microbiota-mediated NF-κB Activation – Hyo‐Min Jang – Molecular Nutrition and Food Research

The Metabolic Response to a Low Amino Acid Diet is Independent of Diet-Induced Shifts in the Composition of the Gut Microbiome – Heidi H. Pak – Scientific Reports

 

More Animal Microbiomes

Generational conservation of composition and diversity of field-acquired midgut microbiota in Anopheles gambiae (sensu lato) during colonization in the laboratory – Jewelna Akorli – Parasites & Vectors

Potential role of host-derived quorum quenching in modulating bacterial colonization in the moon jellyfish Aurelia aurita – Nancy Weiland-Bräuer – Scientific Reports

 

Beneficial Microbes and Compounds

Review: Effect of Food Structure and Processing on (Poly)phenol-Gut Microbiota Interactions and the Effects on Human Health – Francisco A. Tomás-Barberán – Annual Reviews of Food Science and Technology

Dietary Fructooligosaccharide and Glucomannan Alter Gut Microbiota and Improve Bone Metabolism in Senescence-Accelerated Mouse – Kenichi Tanabe – Journal of Agricultural and Food Chemistry

 

Plant Microbiome

Characterizing both bacteria and fungi improves understanding of the Arabidopsis root microbiome – Joy Bergelson – Scientific Reports

 

January 7, 2019

Happy Monday! Today’s digest includes the influence of ant colonies on soil microbes, the assembly of prokaryotic communities in subtropical grasslands, and lactic acid bacteria isolated from sourdough. Have a great week!

Human gut microbiome

Review: The gut microbiome in anorexia nervosa: relevance for nutritional rehabilitation – Ruusunen – Psychopharmacology

Impact of early events and lifestyle on the gut microbiota and metabolic phenotypes in young school-age children – Zhong – Microbiome

Host immunoglobulin G selectively identifies pathobionts in pediatric inflammatory bowel diseases – Armstrong – Microbiome

Animal experiments

Preprint: The gut microbiota is associated with clearance of Clostridium difficile infection independent of adaptive immunity – Leslie – BioRxiv

Animal microbiome

Bioreactivity and Microbiome of Biodeposits from Filter-Feeding Bivalves – Murphy – Microbial Ecology

Modulation of broiler gut microbiota and gene expression of Toll-like receptors and tight junction proteins by diet type and inclusion of phytogenics – Paraskeuas – Poultry Science

Plant, root, and soil microbiome

Responses of soil aggregates and bacterial communities to soil-Pb immobilization induced by biofertilizer – Wang -Chemosphere

Moisture Is More Important than Temperature for Assembly of Both Potentially Active and Whole Prokaryotic Communities in Subtropical Grassland – Lupatini – Microbial Ecology

Ant colonies promote the diversity of soil microbial communities – Delgado-Baquerizo – ISME

Water and extemophile microbiome

Morphological response to salinity, temperature, and pH changes by marine fungus Epicoccum nigrum – Ahumada-Rudolph – Environmental Monitoring and Assessment

Thermoplasmatales and sulfur-oxidizing bacteria dominate the microbial community at the surface water of a CO2-rich hydrothermal spring located in Tenorio Volcano National Park, Costa Rica – Arce-Rodríguez – Extremophiles

Metagenomic, phylogenetic, and functional characterization of predominant endolithic green sulfur bacteria in the coral Isopora palifera – Yang – Microbiome

Water pollution and observation of acquired antibiotic resistance in Bayou Lafourche, a major drinking water source in Southeast Louisiana, USA – Bird – Environmental Science and Pollution Research

Metagenomic Analysis of Zinc Surface–Associated Marine Biofilms – Ding – Microbial Ecology

Evolutionary constraints on species diversity in marine bacterioplankton communities – Lu – ISME

Built environment

Wastewater treatment and microbial community dynamics in a sequencing batch reactor operating under photosynthetic aeration – Parakh – Chemosphere

Novel ecological insights and functional roles during anaerobic digestion of saccharides unveiled by genome-centric metagenomics – Zhu – Water Research

Food microbiology

Effect of in vitro digestion-fermentation on green and roasted coffee bioactivity: The role of the gut microbiota – Pérez-Burillo – Food Chemistry

In vitro and in vivo investigations of probiotic properties of lactic acid bacteria isolated from Chinese traditional sourdough – Li – Applied Microbiology and Biotechnology

Bacterial community dynamics and physical–chemical characteristics in natural fermentation of jiang‐shui, a traditional food made in Northwest China – Liu – Science of Food and Agriculture

Science, publishing, and career

Here’s what scientists searched for in 2018: AI is up, stress is down – Kelly Oakes – Nature News

January 4, 2019

Highlights of today’s Digest include: animal microbiomes from snakes to bald eagles to porcupines, studies of bacteria promoting plant growth, and a nice review of ‘omics in fermented foods. Happy reading!

Human oral microbiome
Microcosm biofilms cultured from different oral niches in periodontitis patients – Fabian Cieplik – Journal of Oral Microbiology

Xylitol and sorbitol effects on the microbiome of saliva and plaque – Reisha Rafeek – Journal of Oral Microbiology

Human vaginal microbiome
Vaginal microbiome variances in sample groups categorized by clinical criteria of bacterial vaginosis – Hui-Mei Chen – BMC Genomics

Human gut microbiome
Five years of fecal microbiota transplantation – an update of the Israeli experience – Sharon A Greenberg – World Journal of Gastroenterology

Review: Association between the intestinal microbiota and allergic sensitization, eczema, and asthma: A systematic review – Petra Zimmermann – Journal of Allergy and Clinical Immunology

Interplay between food and gut microbiota in health and disease – Niels Banhos Danneskiold-Samsøe – Food Research International

Gut microbiome changes in overweight male adults following bowel preparation – Hui-Mei Chen – BMC Genomics

Animal Microbiome
Preprint: Bacterial Diversity in Feces of Wild Bald Eagles, Turkey Vultures and Common Ravens from the Pacific Northwest Coast, U.S.A. – Rocio Crespo – bioRxiv

Next-generation sequencing analysis reveals high bacterial diversity in wild venomous and non-venomous snakes from India – Sajesh Puthenpurackal Krishnankutty – Journal of Venomous Animals and Toxins including Tropical Diseases

Understanding the roles of surface proteins in regulation of Lactobacillus pentosus HC-2 to immune response and bacterial diversity in midgut of Litopenaeus vannamei – Yang Du – Fish & Shellfish Immunology

Characterization of novel lignocellulose-degrading enzymes from the porcupine microbiome using synthetic metagenomics – Mackenzie Thornbury – PLOS One

Plant, root, and soil microbiome
Review: Planting the Microbiome – Jennifer K. Spinler – Trends in Microbiology

Arabidopsis thaliana responds to colonisation of Piriformospora indica by secretion of symbiosis-specific proteins – Johannes Thürich – PLOS One

Screening of plant growth promotion ability among bacteria isolated from field-grown sorghum under different managements in Brazilian drylands – Jéssica Fernanda da Silva – World Journal of Microbiology and Biotechnology

Streptomyces: implications and interactions in plant growth promotion – Oluwaseyi Samuel Olanrewaju – Applied Microbiology and Biotechnology

Mycorrhizal features and leaf traits covary at the community level during primary succession – J. Rasmus P. Jespersen – Fungal Ecology

Microbial communities controlling methane and nutrient cycling in leach field soils – Cristina P.Fernandez-Baca – Water Research

Gradients of three coastal environments off the South China Sea and their impacts on the dynamics of heterotrophic microbial communities – Xianhua Liu – Science of the Total Environment

New insights into the impact of nZVI on soil microbial biodiversity and functionality – Carmen Fajardo – Journal of Environmental Science and Health, Part A

Syntrophic effect of indigenous and inoculated microorganisms in the leaching of rare earth elements from Western Australian monazite – Melissa K.Corbett – Research in Microbiology

Removal of veterinary antibiotics in constructed wetland microcosms – Response of bacterial communities – Filipa Santos – Ecotoxicology and Environmental Safety

Water and extremophile microbiome
Bacterial diversity in the water column of meromictic Lake Cadagno and evidence for seasonal dynamics – Francesco Danza – PLOS One

Microbial community succession and pollutants removal of a novel carriers enhanced duckweed treatment system for rural wastewater in Dianchi Lake basin – Guoke Chen – Bioresource Technology

Food Microbiology
Omics in traditional vegetable fermented foods and beverages – Jocelin Rizo – Critical Reviews in Food Science and Nutrition

Preprint: Construction of synthetic microbiota for reproducible flavor metabolism in Chinese light aroma type liquor produced by solid-state fermentation – Qun Wu – bioRxiv

Bioinformatics
A latent allocation model for the analysis of microbial composition and disease – Ko Abe – BMC Bioinformatics

Techniques
Metatranscriptomic and thermodynamic insights into medium-chain fatty acid production using an anaerobic microbiome – Matthew J. Scarborough – mSystems

December 30, 2018

In the midst of the festive season have a fiesta with the recent articles on Microbiome. Todays MicroBiome Digest covers the Techniques and Treatments, Drugs, Immunostimulatory Diet and Nutrition, Multivariate Count Data Model, Antimicrobials, Pre/Pro-biotcs, Host-Microbe Interactions, Genes, Genomics and Pathways of Microbiota, Infant Microbiome, Animal Models, Animal Microbiome, Microbial Ecology of plant and soil. Happy Reading!!! 

TECHNIQUES & TREATMENTS:

LEMMI: A Live Evaluation of Computational Methods for Metagenome Investigation – Mathieu Seppey – bioRxiv

Single-cell virus sequencing of influenza infections that trigger innate immunity – Alistair B Russell – bioRxiv

METHODS TO IMPROVE INDUCTION OF IGG AND IGA ANTIBODIES BY VACCINES – Boyaka, Prosper -United States Patent Application 20180360953 -PATENT

Are the Statins promising antifungal agents against invasive candidiasis? – William GustavoLima -Biomedicine & Pharmacotherapy

Bayesian variable selection for multivariate zero-inflated models: Application to microbiome count data – Lee KH – Biostatistics

Metatranscriptomic and comparative genomic insights into resuscitation mechanisms during enrichment culturing – Mu DS – Microbiome

Prognostic Impact of Fusobacterium nucleatum Depends on Combined Tumor Location and Microsatellite Instability Status in Stage II/III Colorectal Cancers Treated with Adjuvant Chemotherapy – Oh HJ – J Pathol Transl Med.

Loss of Gut Microbiota Alters Immune System Composition and Cripples Post-Infarction Cardiac Repair – Tang TW – Circulation

DRUG, DIET and NUTRITION:

Review article: implementation of a diet low in FODMAPs for patients with irritable bowel syndrome-directions for future research – Mitchell Hrticle – Aliment Pharmacol Ther.

Compound polysaccharides ameliorate experimental colitis by modulating gut microbiota composition and function – Cai Y – J Gastroenterol Hepatol.

Rifaximin Altered Gut Microbiota Components Associated with Liver/Neuropsychological Functions in Patients with Hepatic Encephalopathy: An Exploratory Data Analysis of a Phase II/III Clinical Trials – Kawaguchi T – Hepatol Res.

Inulin ameliorates alcoholic liver disease via suppressing LPS-TLR4-Mψ axis and modulating gut microbiota in mice – Yang X – Alcohol Clin Exp Res.

Effect of Resistant Starch on the Gut Microbiota and Its Metabolites in Patients with Coronary Artery Disease – Yoshida N – J Atheroscler Thromb.

Late gestation diet supplementation of resin acid-enriched composition increases sow colostrum immunoglobulin G content, piglet colostrum intake and improve sow gut microbiota – Hasan S – Animal

PRE/PRO- BIOTICS and ANTIMICROBIAL:

The human skin microbiota is a rich source of bacteriocin producing staphylococci which kill human pathogens – O’Sullivan JN – FEMS Microbiol Ecol.

Comparative immunostimulatory effect of probiotics and prebiotics in Channa punctatus against Aphanomyces invadans – Devi G – Fish Shellfish Immunol

GENES, GENOMICS & PATHWAYS:

Detection of a novel mutation G511T in the 530 loop in 16S rRNA in multi drugs resistant Mycobacterium tuberculosis isolated from Sudanese patients – Yousif Mohammed Alfatih – bioRxiv

Review: Interactions Between Autophagy and the Unfolded Protein Response: Implications for Inflammatory Bowel Disease – Hooper KM – Inflamm Bowel Dis.

In vitro and in vivo characterization of Clostridium scindens bile acid transformations – Marion S- Gut Microbes

Bioinformatic, phylogenetic, and chemical analysis of the UV-absorbing compounds scytonemin and mycosporine-like amino acids from the microbial mat communities of Shark Bay, Australia – D’Agostino PM – Environ Microbiol

Genetic diversity of Escherichia coli in gut microbiota of patients with Crohn’s disease discovered using metagenomic and genomic analyses – Tyakht AV – BMC Genomics

Complete Genome Sequence of a blaKPC-2-Positive Klebsiella pneumoniae Strain Isolated from the Effluent of an Urban Sewage Treatment Plant in Japan Complete Genome Sequence of a blaKPC-2-Positive Klebsiella pneumoniae Strain Isolated from the Effluent of an Urban Sewage Treatment Plant in Japan – Sekizuka T – mSphere

HOST-MICROBE INTERACTION:

Nitrogen- and phosphorus-starved Triticum aestivum show distinct belowground microbiome profiles – Antoine P Pagé -bioRxiv

Bacterial secretion of histamine within the gut influences immune responses within the lung – Barcik W – Allergy

GUT MICROBIOME:

Extensive Transmission of Microbes along the Gastrointestinal Tract – Thomas SB Schmidt – bioRxiv

VAGINAL MICROBIOME:

Human β-defensin-2 as a biochemical indicator of vaginal environment in pregnant women – Hideko Kotani – Hypertension Research In Pregnancy

PREGNANCY AND EARLY LIFE:

Physiology of Stress and Use of Skin-to-Skin Care as a Stress-Reducing Intervention in the NICU – Britt Frisk Pados – Nursing for Women’s Health

Longitudinal analysis of infant stool bacteria communities before and after acute febrile malaria and artemether/lumefantrine treatment – Mandal RK – J Infect Dis.

Haemophilus-dominant nasopharyngeal microbiota is associated with delayed clearance of respiratory syncytial virus in infants hospitalized for bronchiolitis – Mansbach JM – J Infect Dis

ANIMAL MODEL EXPERIMENTS:

Dietary nucleotides can directly stimulate the immunity of zebrafish independent of the intestinal microbiota – Guo X – Fish Shellfish Immunol.

Antimicrobial assessment of phage therapy using a porcine model of biofilm infection – Milho C – Int J Pharm

ANIMAL MICROBIOME:

Effect of different levels of tryptophan on productive performance, egg quality, blood biochemistry, and caecal microbiota of hens housed in enriched colony cages under commercial stocking density – Khattak F -Poult Sci.

Exogenous carbohydrases added to a starter diet reduced markers of systemic immune activation and decreased Lactobacillus in weaned pigs – Li Q – J Anim Sci.

Gut microbiota dynamics and functionality in Reticulitermes grassei after a 7-day dietary shift and ciprofloxacin treatment – Berlanga M – PLoS One

MICROBIAL ECOLOGY:

Culturomics-Based Taxonomic Diversity of Bacterial Communities in the Hot Springs of Saudi Arabia – Yasir M – OMICS

Rhizosphere microorganisms can influence the timing of plant flowering – Lut T – Microbiome

December 16, 2018

A Happy Weekend to one and all. 

Today’s Microbiome Digest features the recent articles covering the techniques and treatments, microbiome of infants, gut, oral, eye and vaginal microbiome, host-microbe interactions, diet and probiotic supplementations, co-culture models and its impact on biofilm reduction, soil microbiome and microbial ecology, comparative study of microbiome in various diseases, role of microbiome on various cancers, metabolomics, animal and insect microbiome, myco and yeast biome, genes and genomics of good and bad bacteria.  ENJOY READING.

TECHNIQUES:

Rapid Determination of Antibiotic Susceptibility by Stimulated Raman Scattering Imaging of D2O Metabolism – Weili Hong – bioRxiv

CaptureSeq: Capture-based enrichment of cpn60 gene fragments empowers pan-Domain profiling of microbial communities without universal PCR – Matthew G Links – bioRxiv

Characterization of Hydrocarbon-Degrading Bacteria in Constructed Wetland Microcosms Used to Treat Crude Oil Polluted Water– Amer Jamal Hashmat- Bulletin of Environmental Contamination and Toxicology

A Probe-Enabled Approach for the Selective Isolation and Characterization of Functionally Active Subpopulations in the Gut Microbiome – Whidbey C – J Am Chem Soc.

Combined extraction method for metabolomic and PLFA analysis of soil – Jeffrey S.Buyer – Applied Soil Ecology

CLAME: a new alignment-based binning algorithm allows the genomic description of a novel Xanthomonadaceae from the Colombian Andes – Andres Benavides – BMC Genomics

Harnessing CRISPR-Cas systems for precision engineering of designer probiotic lactobacilli – Yong JunGoh – Current Opinion in Biotechnology

Evaluating the Efficiency of Primer Extension Capture as a Method to Enrich DNA Extractions – Winters M – J Forensic Sci

TREATMENTS:

Intestinal Anti-Inflammatory Activity of the Aqueous Extract from Ipomoea asarifolia in DNBS-Induced Colitis in Rats – da Silva VC – Int J Mol Sci.

Effect of Marine Microalga Chlorella pyrenoidosa Ethanol Extract on Lipid Metabolism and Gut Microbiota Composition in High-Fat Diet-Fed Rats – Wan X – Mar Drugs

Flavonoids and Colorectal Cancer Prevention – Li Y – Antioxidants (Basel)

Effects of Rich-Polyphenols Extract of Dendrobium loddigesii on Anti-Diabetic, Anti-Inflammatory, Anti-Oxidant, and Gut Microbiota Modulation in db/db Mice – Li XW – Molecules

Evidence-based mixture containing Lactobacillus strains and lactoferrin to prevent recurrent bacterial vaginosis: a double blind, placebo controlled, randomised clinical trial – R. Russo – Beneficial Microbes

ORAL MICROBIOME:

Bacterial profile of the supragingival dental biofilm in children with deciduous and early mixed dentition using next generation sequencing (HOMINGS) technique – Harris-Ricardo J – Enferm Infecc Microbiol Clin.

Oral Dysbiosis in Pancreatic Cancer and Liver Cirrhosis: A Review of the Literature – Mohammed H – Biomedicines

Subgingival lipid A profile and endotoxin activity in periodontal health and disease – Strachan A – Clin Oral Investig

GENOME AND GENOMICS:
Iron-associated protein interaction networks reveal the key functional modules related to survival and virulence of Pasteurella multocida – Theeraphol Jatuponwiphat – Microbial Pathogenesis

Identification of putative non-host essential genes and novel drug targets against Acinetobacter baumannii by in silico comparative genome analysis – Reaz Uddin – Microbial pathogenesis

Epilithic Biofilms in Lake Baikal: Screening and Diversity of PKS and NRPS Genes in the Genomes of Heterotrophic Bacteria – Sukhanova E – Pol J Microbiol.

Comparative analysis of Faecalibacterium prausnitzii genomes shows a high level of genome plasticity and warrants separation into new species-level taxa – Fitzgerald CB – BMC Genomics

INSECT MICROBIOME:

Metagenomic 16S rRNA gene sequencing survey of Borrelia species in Irish samples of Ixodes ricinus ticks – John S Lambert – bioRxiv

MARINE MICROBIOME:

Uncultured marine cyanophages encode for active NblA, phycobilisome proteolysis adaptor protein – Omer Nadal – bioRxiv

A fundamental difference between macrobiota and microbial eukaryotes: Protistan plankton has a species maximum in the freshwater-marine transition zone of the Baltic Sea – Filker S – Environ Microbiol

ANTIBIOTIC RESISTANCE:

Antibiotic usage promotes the evolution of resistance against gepotidacin, a novel multi-targeting drug – Petra Szili – bioRxiv

Role of Bentonite on the Mobility of Antibiotic Resistance Genes, and Microbial Community in Oxytetracycline and Cadmium Contaminated Soil – Guo H – Front Microbiol

HflXr, a homolog of a ribosome-splitting factor, mediates antibiotic resistance – Duval M – Proc Natl Acad Sci U S A.

Antibiotics may increase triazine herbicide exposure risk via disturbing gut microbiota – Zhan J – Microbiome

SOIL MICROBIOME:

REVIEW: The rhizosphere microbiome: A key component of sustainable cork oak forests in trouble – Fatima Zahra Maghnia – Forest Ecology and Management

VIROME:

The intestinal virome of malabsorption syndrome-affected and unaffected broilers through shotgun metagenomics – Diane A.Lima – Virus Research

MYCO and YEAST-BIOME:

Snf2 controls pulcherriminic acid biosynthesis and connects pigmentation and antifungal activity of the yeast Metschnikowia pulcherrima – Deborah Gore-Lloyd – bioRxiv

Nitrogen deprivation in Fusarium oxysporum promotes mycotoxin production via intermediates in the Krebs cycle and unreported methylmalonyl-CoA mutase activity – A. V. Karpe – Metabolomics

METABOLOMICS:

Gut microbiome structure and metabolic activity in inflammatory bowel disease – Eric A. Franzosa – Nature Microbiology

Active Acupoints Differ from Inactive Acupoints in Modulating Key Plasmatic Metabolites of Hypertension: A Targeted Metabolomics Study – Yang M – Sci Rep

Isobaric Labeling Quantitative Metaproteomics for the Study of Gut Microbiome Response to Arsenic – Liu CW – J Proteome Res.

GENERAL MICROBIOME:

The Human Microbiome in Health and Disease – Wyatt M. Arnold – Genomic Applications in Pathology

Microbes: possible link between modern lifestyle transition and the rise of metabolic syndrome – Moossavi S – Obes Rev.

CANCER and MICROBIOTA:

Microbiota in cancer development and treatment – Muhammad Hassan Raza – Journal of Cancer Research and Clinical Oncology

Alcohol and gastrointestinal cancers – Vanella G – Curr Opin Gastroenterol.

Gut microbiota in patients after surgical treatment for colorectal cancer – Jin Y – Environ Microbiol

The Microbiome in Bipolar Depression: A Longitudinal Study of One Pair of Monozygotic Twins – Jiang HY – Bipolar Disord.

Gut Microbiota, Fusobacteria, and Colorectal Cancer – Kelly D – Diseases

PRENATAL AND INFANT MICROBIOME:

The Prenatal Microbiome: A New Player for Human Health – D’Argenio V – High Throughput

Enteric dysbiosis and fecal calprotectin expression in premature infants – Thao T. B. Ho – Pediatric Research

Long-term colonization exceeding six years from early infancy of Bifidobacterium longum subsp. longum in human gut. – Oki K – BMC Microbiol.

EYE MICROBIOME:

Alterations in gut bacterial and fungal microbiomes are associated with bacterial Keratitis, an inflammatory disease of the human eye – Jayasudha R – J Biosci.

GUT MICROBIOME:

Gut microbiota dysbiosis in male patients with chronic traumatic complete spinal cord injury – Zhang C – J Transl Med.

Traumatic Brain Injury in Mice Induces Acute Bacterial Dysbiosis Within the Fecal Microbiome – Treangen TJ – Front Immunol.

A comparative study of the gut microbiota in immune-mediated inflammatory diseases-does a common dysbiosis exist – Forbes JD – Microbiome.

Microbiome-The Missing Link in the Gut-Brain Axis: Focus on Its Role in Gastrointestinal and Mental Health – Skonieczna-Żydecka K – J Clin Med.

ANIMAL MICROBIOME:

The valproic acid rat model of autism presents with gut bacterial dysbiosis similar to that in human autism – Fang Liu – Molecular Aurtism

Effects of smoking on the lower respiratory tract microbiome in mice – Zhang R – Respir Res

Evaluating the profound effect of gut microbiome on host appetite in pigs – Yang H – BMC Microbiol.

Comparative analysis of the intestinal bacterial community and expression of gut immunity genes in the Chinese Mitten Crab (Eriocheir sinensis) – Dong J – AMB Express.

Rumen methanogen and protozoal communities of Tibetan sheep and Gansu Alpine Finewool sheep grazing on the Qinghai-Tibetan Plateau, China – Huang J – BMC Microbiol.

PSXIV-15 The Effect Of Intravaginal Progesterone Implant In The Vaginal Microbiota Of Holstein Cows – E Zanella – Journal of Animal Science

The role of the bovine respiratory microbiota in health and disease – T Alexander – Journal of Animal Science

MICROBIAL ECOLOGY:

Polychaete mucopolysaccharide alters sediment microbial diversity and stimulates ammonia-oxidising functional groups – Dale H – FEMS Microbiol Ecol.

Profiling grapevine trunk pathogens in planta: a case for community-targeted DNA metabarcoding – Morales-Cruz A – BMC Microbiol.

The bacterial community significantly promotes cast iron corrosion in reclaimed wastewater distribution systems – Zhang G – Microbiome

Long-term soil metal exposure impaired temporal variation in microbial metatranscriptomes and enriched active phages – Jacquiod S – Microbiome

Shotgun Metagenomics Reveals Taxonomic and Functional Shifts in Hot Water Microbiome Due to Temperature Setting and Stagnation – Dai D – Front Microbiol

HOST-MICROBE CROSSTALK:

Neutrophils Restrict Tumor-Associated Microbiota to Reduce Growth and Invasion of Colon Tumors in Mice – Triner D – Gastroenterology

Impact of CFTR modulation with Ivacaftor on Gut Microbiota and Intestinal Inflammation– Ooi CY – Sci Rep

Using Enteric Pathogens to Probe the Gut Microbiota – Spiga L – Trends Microbiol.

DIET, NUTRITION AND PROBIOTICS:

Treatment of Active Crohn’s Disease With an Ordinary Food-based Diet That Replicates Exclusive Enteral Nutrition – Svolos V – Gastroenterology

The Dietary Intervention of Transgenic Low-Gliadin Wheat Bread in Patients with Non-Celiac Gluten Sensitivity (NCGS) Showed No Differences with Gluten Free Diet (GFD) but Provides Better Gut Microbiota Profile – Haro C – Nutrients.

SIRT3 Deficiency Promotes High-Fat Diet-Induced Non-Alcoholic Fatty Liver Disease In Correlation With Impaired Intestinal Permeability Through Gut Microbial Dysbiosis – Chen M – Mol Nutr Food Res

Maternal probiotic supplementation for prevention of morbidity and mortality in preterm infants – Grev J – Cochrane Database Syst Rev

Role of prebiotics and probiotics in the functionality of the microbiota in the patients receiving enteral nutrition – Ballesteros Pomar – Nutr Hosp.

Probiotics Streptococcus salivarius 24SMB and Streptococcus oralis 89a interfere with biofilm formation of pathogens of the upper respiratory tract – Bidossi A – BMC Infect Dis

VAGINAL MICROBIOME:

Vaginal dysbiosis, and the risk of human papillomavirus and cervical cancer: systematic review and meta-analysis – Brusselaers N – Am J Obstet Gynecol.

Microbiota dysbiosis is associated with HPV-induced cervical carcinogenesis – Kwasniewski W – Oncol Lett.

CO-CULTURE MODEL and EFFECTS:

Dynamics of Biofilm Formation by Salmonella Typhimurium and Beef Processing Plant Bacteria in Mono- and Dual-Species Cultures – Visvalingam J – Microb Ecol

Anaerobic Degradation of the Plant Sugar Sulfoquinovose Concomitant With H2S Production: Escherichia coli K-12 and Desulfovibrio sp. Strain DF1 as Co-culture Model – Burrichter A – Front Microbiol.

December 15, 2018

Colonizing FMT patients with donor bacteriophages, the microbial communities of tigers, fruit bats, hemlocks, and rainbow trout, a review on the advances in urinary microbiome research.

Multi-site human microbiome

Review: The role of the microbiota in infectious diseases – Josie Libertucci – Nature Microbiology

Human skin microbiome

Ultraviolet radiation, both UVA and UVB, influences the composition of the skin microbiome – Erin M Burns – Experimental Dermatology

Human urinary microbiome

Review: Urobiome updates: advances in urinary microbiome research – Alan J Wolfe – nature Reviews Urology

Human gut microbiome

Pre-print: Gut microbiome response to a modern Paleolithic diet in a Western lifestyle context – Monica Barone – bioRxiv

Difference in Pathomechanism Between Crohn’s Disease and Ulcerative Colitis Revealed by Colon Transcriptome – Lili Yang – Inflammatory Bowel Diseases

GABA-modulating bacteria of the human gut microbiota – Philip Strandwitz – Nature Microbiology

Impact of Individual Traits, Saturated Fat, and Protein Source on the Gut Microbiome – Jennifer M Lang – mBio

Animal experiments

Microbiome interactions shape host fitness – Alison L Gould – PNAS

Gut microbiota dysbiosis worsens the severity of acute pancreatitis in patients and mice – Yin Zhu – Journal of Gastroenterology

Microbiota-Derived Lactate Accelerates Intestinal Stem-Cell-Mediated Epithelial Development – Yong-Soo Lee – Cell Host & Microbe

A Microbiota-Derived Bacteriocin Targets the Host to Confer Diarrhea Resistance in Early-Weaned Piglets – Jun Hu – Cell Host & Microbe

Animal microbiome

Exploring variation in phyllosphere microbial communities across four hemlock species – Timothy J Rogers – Ecosphere

Analysis of the gut and gill microbiome of resistant and susceptible lines of rainbow trout (Oncorhynchus mykiss) – Ryan M Brown – Fish & Shellfish Immunology

Metagenomic analysis of captive Amur tiger faecal microbiome – Fengping He – BMC Veterinary Research

Coordinated change at the colony level in fruit bat fur microbiomes through time – Oren Kolodny – Nature Ecology & Evolution

Plant, root, and soil microbiome

Remediation of deterioration in microbial structure in continuous Pinellia ternata cropping soil by crop rotation – Zhigui He – Candadian Journal of Microbiology

Plant compartment and genetic variation drive microbiome composition in switchgrass roots – Esther Singer – Environmental Microbiology Reports

Desert plant bacteria reveal host influence and beneficial plant growth properties – Abdul Aziz Eida – PLOS ONE

Water and extremophile microbiome

Marine probiotics: increasing coral resistance to bleaching through microbiome manipulation – Phillipe M Rosado – The ISME Journal

Microbes in space

International Space Station conditions alter genomics, proteomics, and metabolomics in Aspergillus nidulans – Jillian Romsdahl – Applied Microbiology and Biotechnology

Phages and viruses

Long-term colonisation with donor bacteriophages following successful faecal microbial transplantation – L A Draper – Microbiome

Metatranscriptomic Analysis and In Silico Approach Identified Mycoviruses in the Arbuscular Mycorrhizal Fungus Rhizophagus spp. – Achal Neupane – Viruses

The intestinal virome of malabsorption syndrome-affected and unaffected broilers through shotgun metagenomics – Diane A Lima – Virus Research

Techniques

Detection of Bacteriophages: Sequence-Based Systems – Siân V Owen – Bacteriophages

More microbes

Pseudomonas aeruginosa quorum-sensing metabolite induces host immune cell death through cell surface lipid domain dissolution – Dingka Song – Nature Microbiology