February 13, 2019

Today’s digest features a study on leaf-associated microbiomes of grafted tomato plants, study that reveals the chemical “fingerprint” and contribution of Parasutterella to host health, and Everything Hertz podcast with episode “Promiscuous expertise”. Happy reading/listening!

Gut microbiome

A new genomic blueprint of the human gut microbiota – Alexandre Almeida – Nature

Population structure of human gut bacteria in a diverse cohort from rural Tanzania and Botswana – Matthew E. B. Hansen – Genome Biology

Disturbance of trace element and gut microbiota profiles as indicators of autism spectrum disorder: A pilot study of Chinese children – Qixiao Zhai – Environmental Research

*Defining the role of Parasutterella, a previously uncharacterized member of the core gut microbiota – Tingting Ju – The ISME Journal

Extensive transmission of microbes along the gastrointestinal tract – Thomas Sebastian Benedikt Schmidt – eLife

Bacterial interspecies interactions modulate pH-mediated antibiotic tolerance in a model gut microbiota – Andres Aranda-Diaz – bioRxiv

Skin microbiome

Review: Microbiosis in pathogenesis and intervention of atopic dermatitis – Jianhua Dou – International Immunopharmacology

Plant/root/soil microbiome

*Leaf-associated microbiomes of grafted tomato plants – Hirokazu Toju – Scientific Reports

Fungal Biodiversity of the Most Common Types of Polish Soil in a Long-Term Microplot Experiment – Jarosław Grządziel and Anna Gałązka – Frontiers in Microbiology

Podcast

*Episode 77: Promiscuous expertise – Dan Quintana and James Heathers – Everything Hertz [A great episode about scientists who claim to be a public authority on topics outside their area of expertise!]

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February 1, 2019

Today’s digest is quite diverse: the respiratory microbiome networks in cystic fibrosis patients, ketogenic diet effects on the gut microbiota in children with severe epilepsy, and insect-associated Streptomyces (spoiler: inhibit antimicrobial-resistant pathogens more than soil Streptomyces). Happy reading!

General microbiome

Minireview: The signatures of microorganisms and of human and environmental biomes can now be used to provide evidence in legal cases – A H Bishop – FEMS Microbiology Letters

Transforming medicine with the microbiome – Niv Zmora – Science Translational Medicine

Gut microbiome

Gut intraepithelial T cells calibrate metabolism and accelerate cardiovascular disease – Shun He – Nature

*The ketogenic diet influences taxonomic and functional composition of the gut microbiota in children with severe epilepsy – Marie Lindefeldt – npj Biofilms and Microbiomes

Vaginal microbiome

Association between vaginal washing and vaginal bacterial concentrations – Michelle C. Sabo – PlosOne

Skin microbiome

Investigation of the Skin Microbiome: Swabs vs Biopsies – S. Prast‐Nielsen – British Journal of Dermatology

Oral microbiome

Carbonic Anhydrase 6 Gene Variation influences Oral Microbiota Composition and Caries Risk in Swedish adolescents – A. Esberg – Scientific Reports

Respiratory microbiome

*Microbiome networks and change-point analysis reveal key community changes associated with cystic fibrosis pulmonary exacerbations – Mehdi Layeghifard – npj Biofilms and Microbiomes

Plant/root/soil microbiome

Effects of long-term fertilization on soil organic carbon mineralization and microbial community structure – Zhen Guo – PlosOne

Water microbiome

Functional screening for triclosan resistance in a wastewater metagenome and isolates of Escherichia coli and Enterococcus spp. from a large Canadian healthcare region – Andrew Camero – PlosOne

Animal experiments

Cream Cheese-Derived Lactococcus chungangensis CAU 28 Modulates the Gut Microbiota and Alleviates Atopic Dermatitis in BALB/c Mice – Jong-Hwa Kim – Scientific Reports

Animal Microbiome

*The antimicrobial potential of Streptomyces from insect microbiomes – Marc G. Chevrette – Nature Communications

January 23, 2019

Today’s digest is about the distinct microbial networks within disturbed gut microbiome, multifaceted roles of Staphylococcus epidermidis in skin physiology, and high-throughput cultivation techniques. Happy reading!

Urinary microbiome

Review: The Microbiome and Genitourinary Cancer: A Collaborative Review – Mark C. Markowski – European Urology

Gut microbiome

*Microbial network disturbances in relapsing refractory Crohn’s disease – Bahtiyar Yilmaz – Nature Medicine

Alteration in gut microbiota associated with hepatitis B and non-hepatitis virus related hepatocellular carcinoma – Qisha Liu – Gut Pathogens

Human gut microbes are susceptible to antimicrobial food additives in vitro – Lucia Hrncirova – Folia Microbiologica

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

Skin microbiome

*Microbial guardians of skin health – Apollo Stacy and Yasmine Belkaid – Science

Water microbiome

Comparison of microbial communities in the sediments and water columns of frozen cryoconite holes in the McMurdo Dry Valleys, Antarctica – Pacifica Sommers – Frontiers in Microbiology

Plant/root/soil microbiome

Invasive plant species identity affects soil microbial communities in a mesocosm experiment – Anna M. Stefanowicz – Applied Soil Ecology

Techniques

*High throughput cultivation-based screening on porous aluminum oxide chips allows targeted isolation of antibiotic resistant human gut bacteria – Dennis Versluis – PlosOne

*Cultivation-success of rare soil bacteria is not influenced by incubation time and growth medium – Viola Kurm – PlosOne

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

 

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 17, 2018

Have a good Monday! Today a very brief digest with remarkable articles about: Melanoma-related changes in skin microbiome, the use of microbiome to treat obesity, connections between Parkinson’s disease and microbiome, Asthma and more!

 

Human and General Microbiome

Insular Resting State Functional Connectivity is Associated with Gut Microbiota Diversity – Kaylah Curtis – European Journal of Neuroscience

Mini-Review: Gut microbiome approaches to treat obesity in humans – Fernanda Bianchi – Applied Microbiology and Biotechnology

Melanoma-related changes in skin microbiome – Jakub Mrázek – Folia Microbiologica

Role of TLR4 in the gut-brain axis in Parkinson’s disease: a translational study from men to mice – Paula Perez-Pardo – Gut (BMJ)

Bi-directional drug-microbiome interactions of anti-diabetics – Andrew Whang – EBioMedicine

Gut microbiota-dependent trimethylamine-N-oxide (TMAO) shows a U-shaped association with mortality but not with recurrent venous thromboembolism – Martin F. Reiner – Thrombosis Research

The Microbiome in Asthma: Role in pathogenesis, phenotype, and response to treatment – Ariangela J. Kozik – Annals of Allergy, Asthma & Immunology

Modulating the Microbiome: The Future of Allergy Therapeutics? – Christina E. Ciaccio – Annals of Allergy, Asthma & Immunology

Microbial patterns in patients with histamine intolerance – M. Schink – Journal Of Physiology And Pharmacology

Towards quantitative microbiome community profiling using internal standards – Yajuan Lin – Applied and Environmental Microbiology

Galactose impacts the size and intracellular composition of the asaccharolytic oral pathobiont Porphyromonas gingivalis – Zachary D. Moye – Applied and Environmental Microbiology

 

Functional Compounds

Regulatory Efficacy of Spirulina platensis Protease Hydrolyzate on Lipid Metabolism and Gut Microbiota in High-Fat Diet-Fed Rats – Pengpeng Hua – International Journal of Molecular Sciences

Soluble xyloglucan generates bigger bacterial community shifts than pectic polymers during in vitro fecal fermentation – Thaisa Moro Cantu-Jungles – Carbohydrate Polymers

Dendrobium huoshanense polysaccharide regionally regulates intestinal mucosal barrier function and intestinal microbiota in mice – Song-Zi Xie – Carbohydrate Polymers

Evodiamine prevents dextran sulfate sodium-induced murine experimental colitis via the regulation of NF-κB and NLRP3 inflammasome – Peng Shen – Biomedicine & Pharmacotherapy

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