August 15, 2019

Have a nice Thursday! Today we have a set of papers showing randomized trials related to antibiotic use and alimentary interventions, metabolic networks associated with C. difficile infection, and analysis of E. coli isolates from human stool. Today, we also include a couple of protocol papers about the use of stable isotope probing in plant microbiome research.

 

Human and General Microbiome

Gut microbiome alteration in MORDOR I: a community-randomized trial of mass azithromycin distribution – T. Doan – Nature Medicine 

Fecal microbiome and metabolome of infants fed bovine MFGM supplemented formula or standard formula with breast-fed infants as reference: a randomized controlled trial – Xuan He – Scientific Reports

Antibiotic Resistance, Virulence Factors, Phenotyping, and Genotyping of E. coli Isolated from the Feces of Healthy Subjects – Stefano Raimondi – Microorganisms

Metabolomic networks connect host-microbiome processes to human Clostridioides difficile infections – John I. Robinson – The Journal of Clinical Investigation

Antibiotic exposure and ‘response failure’ for subsequent respiratory tract infections: an observational cohort study of UK preschool children in primary care – Oliver van Hecke – British Journal of General Practice 

Abnormal vaginal microbiome associated with vaginal mesh complications – Nikolaus Veit‐Rubin – Neurology and Urodynamics

Acceptability, Tolerability and Safety of Faecal Microbiota Transplantation in patients with active Ulcerative Colitis (AT&S Study) – Ajit Sood – Journal of Gastroenterology and Hepatology

The bacteriome of otitis media with effusion: Does it originate from the adenoid? – Oguz Ari – International Journal of Pediatric Otorhinolaryngology 

An Exploratory Analysis of Fecal Immunochemical Test Performance for Colorectal Cancer Screening in Nigeria – Gregory C. Knapp – World Journal of Surgery

Isolates from colonic spirochaetosis in humans show high genomic divergence and potential pathogenic features but are not detected using standard primers for the human microbiota – Kaisa Thorell – Journal of Bacteriology

Microbiota-derived Trimethylamine N-oxide Predicts Cardiovascular Risk After STEMI – Yasushi Matsuzawa – Scientific Reports

Review: Targeting Microbiota: What Do We Know about It at Present? – Aleksejs Derovs – Medicina

Tech News: Reproducibility: the search for microbiome standards – Joseph Martin – BioTechniques

 

Animal Microbiome

Intestinal microbial products from alcohol-fed mice contribute to intestinal permeability and peripheral immune activation – Derrick R. Samuelson – Alcoholism

Comparative metagenomic sequencing analysis of cecum microbiotal diversity and function in broilers and layers – Zhao Qi – 3 Biotech

Oligosaccharides Modulate Rotavirus-Associated Dysbiosis and TLR Gene Expression in Neonatal Rats – Ignasi Azagra-Boronat – Cells

Role of coprophagy in the cecal microbiome development of an herbivorous bird Japanese rock ptarmigan – Atsushi Kobayashi – Journal of Veterinary Medical Science

 

Beneficial compounds and microbes

Review: The role of gut microbiota for the activity of medicinal plants traditionally used in the European Union for gastrointestinal disorders – Timo A. Thumann – Journal of Ethnopharmacology

Commentary: Microbiome, probiotics and dermatology – J.A. Cardenas‐de la Garza – British Journal of Dermatology

Cooked Red Lentils Dose-Dependently Modulate the Colonic Microenvironment in Healthy C57Bl/6 Male Mice – Daniela Graf – Nutrients

Health Benefits of Lactobacillus gasseri CP2305 Tablets in Young Adults Exposed to Chronic Stress: A Randomized, Double-Blind, Placebo-Controlled Study – Kensei Nishida – Nutrients 

Effect of coffee on the compositional shift of oral indigenous microbiota cultured in vitro – 

 

Food Microbiome

Microbial Transformations of Organically Fermented Foods – Ruma Raghuvanshi – Metabolites

 

Plant Microbiome

Protocol: Stable Isotope Probing of Microbiota Structure and Function in the Plant Rhizosphere – Wafa Achouak – Stable Isotope Probing (Methods in Molecular Biology)

Protocol: Targeted Metatranscriptomics of Soil Microbial Communities with Stable Isotope Probing – Ang Hu – Stable Isotope Probing (Methods in Molecular Biology)

Environmental pollution effects on plant microbiota: the case study of poplar bacterial-fungal response to silver nanoparticles – Francesco Vitali – Applied Microbiology and Biotechnology

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July 29, 2019

Good Morning! Highlights of today’s digest include a revisited study that showed a significant alterations in the gut microbiome by the consumption of low/no-calorie sweeteners (LNCS), such as Splenda, and raising safety concerns, another work tells us development of Burkholderia-free host plant model to show how Burkholderia helps plant development, and finally a study finds a mechanistic link between the gut microbiome and early childhood asthma as shown with highthened expression of bacterial genes that make 12,13-diHOME which alters immune response.

Human gut microbiome

***Revisited: Assessing the in vivo data on low/no-calorie sweeteners and the gut microbiota – Susan S. Schiffman et al. – Food and Chemical Toxicology

A structured weight loss program increases gut microbiota phylogenetic diversity and reduces levels of Collinsella in obese type 2 diabetics: A pilot study – Fabian Frost et al. – PLOS ONE

Human respiratory microbiome

Chronic obstructive pulmonary disease upper airway microbiome is associated with select clinical characteristics – Alexa A. Pragman et al. – PLOS ONE

Animal experiments

***Elevated faecal 12,13-diHOME concentration in neonates at high risk for asthma is produced by gut bacteria and impedes immune tolerance – Sophia R. Levan et al. – Nature Microbiology

Effect of live yeast Saccharomyces cerevisiae supplementation on the performance and cecum microbial profile of suckling piglets – Tadele G. Kiros et al. – PLOS ONE

Low-dose inoculation of Escherichia coli achieves robust vaginal colonization and results in ascending infection accompanied by severe uterine inflammation in mice – Valerie P. O’Brien – PLOS ONE

Probiotic strains improve high-fat diet-induced hypercholesterolemia through modulating gut microbiota in ways different from atorvastatin – Dun Su et al. – bioRxiv

Host Genotype-shaped Gut Microbiome Modulate Atherosclerosis Development in Mice – Kazuyuki Kasahara et al. – Arteriosclerosis, Thrombosis, and Vascular Biology

Animal microbiome

Fecal microbiota of different reproductive stages of the central population of the lesser-long nosed bat, Leptonycteris yerbabuenae – Osiris Gaona et al. – PLOS ONE

Taxon appearance from extraction and amplification steps demonstrates the value of multiple controls in tick microbiome analysis – Emilie Lejal et al. – bioRxiv

Characterization of the gastrointestinal bacterial microbiome of farmed juvenile and adult white Cachama (Piaractus brachypomus) – Victor Alfonso et al. – Aquaculture

Biosynthesis and Characterization, Antioxidant and Antimicrobial Activities
of Selenium Nanoparticles from Ethanol Extract of Bee Propolis
– Shubharani R. et al. – Journal of Nanomedicine & Nanotechnology

Plant, root and soil microbiome

The role of inoculum dispersal and plant species identity in the assembly of leaf endophytic fungal communities – Kevin D. Ricks et al. – PLOS ONE

***Is the bacterial leaf nodule symbiosis obligate for Psychotria umbellata? The development of a Burkholderia-free host plant – Arne Sinnesael et al. – PLOS ONE

AOA and AOB communities respond differently to changes of soil pH under long-term fertilization – Rubio Sun et al. – Soil Ecology Letters

***Negative plant-microbiome feedback limits productivity in aquaponics – Jessica A. Day et al. – bioRxiv

Do plant–microbe interactions and aluminum tolerance influence
alpine sedge species’ responses to nitrogen deposition?
– Teal S. Potter et al. – Ecosphere

Plant diversity and fertilizer management shape the belowground microbiome of native grass bioenergy feedstocks – Daniel Revillini et al. – Frontiers in Plant Science

Microbial taxonomical composition in spruce phyllosphere, but not community functional structure, varies by geographical location – Yunshi Li et al. – PeerJ

Responses of plant growth, physiological, gas exchange parameters of super and non-super rice to rhizosphere temperature at the tillering stage – Shuying Li at al. – Nature Scientific Reports

Influence of introduced arbuscular mycorrhizal fungi and phosphorus sources on plant traits, soil properties, and rhizosphere microbial communities in organic legume-flax rotation – Yunliang Li et al. – Plant and Soil

Effects of arbuscular mycorrhizal fungi on inoculated seedling growth and rhizosphere soil aggregates – Zhongfeng Zhang et al. – Soil and Tillage Research

Properties of bacterial community in the rhizosphere soils of Achyranthes bidentata tolerant to consecutive monoculture – Juanying Wang et al. – Plant Growth Regulation

The role of volatile organic compounds and rhizosphere competence in the mode of action of the non-pathogenic Fusarium oxysporum FO12 towards Verticillium wilt – Mulero-Aparicio et al. – Frontiers in Microbiology

Dynamic changes in soil chemical properties and microbial community structure in response to different nitrogen fertilizers in an acidified celery soil – Yuping Wu et al. – Soil Ecology Letters

Improved rhizoremediation for decabromodiphenyl ether (BDE-209) in E-waste contaminated soils – Jiayin Feng et al. – Soil Ecology Letters

Review: Soil biofilms: microbial interactions, challenges, and advanced techniques for ex-situ characterization – Peng Cai et al. – Soil Ecology Letters

Organic amendment effects on nematode distribution within aggregate fractions in agricultural soils – Xiaoke Zhang et al. – Soil Ecology Letters

Water and extermophile microbiome

Book chapter: New Perspectives on the Distribution and Roles of Thermophilic Fungi – Miriam I. Hutchinson et al. – Fungi in Extreme Environments: Ecological Role and Biotechnological Significance

Diversity and biogeography of eukaryotic microorganism in the deepsea sediment of the Eastern Indian Ocean – Xiaoxia Ma et al. – International Journal of Science

Phages and viruses

Phage composition of a fermented milk and colostrum product assessed by microbiome array; putative role of open reading frames – Stefania Pacini et al. – bioRxiv

Techniques

Modelling approaches for studying the microbiome – Manish Kumar et al. – Nature Microbiology

Guest Editorial: Beyond sequencing: fast and easy microbiome profiling by flow cytometry – Charlotte Esser at al. – Archives of Toxicology

View Point: Opportunities at the Intersection of Synthetic Biology, Machine Learning, and Automation – Pablo Carbonell et al. – ACS Synthetic Biology

Microbes in the News

***Elevated Concentration of Lipid in Neonatal Microbiome Predicts Later Risk for Asthma, Allergy – Allison Inserro – AJMC Newsroom

July 27, 2019

Have a nice weekend! Today, in this Digest, it is worth to remark a study in mice showing the impact of microbiome composition on muscle loss, in addition to a paper presenting the new version of QIIME, one of the most utilized microbiome analysis software available. 

 

Human and General Microbiome

Pearls: Microbiome evolution during host aging – Francisco Daniel Davila Aleman – PLOS Pathogens

Review: The structure and function of the human small intestinal microbiota: Current understanding and future directions – Arthur J. Kastl, Jr – Cellular and Molecular Gastroenterology and Hepatology

Review: The impact of tumor and gut microbiotas on cancer therapy; Beneficial or detrimental? – Yalda Hekmatshoar – Life Sciences 

Review: Gut Microbiota in Phytopharmacology: A Comprehensive Overview Of Concepts, Reciprocal Interactions, Biotransformations And Mode Of Actions – Priyankar Dey – Pharmacological Research

Review: The role of the skin microbiota in acne pathophysiology – S. Ramasamy – British Journal of Dermatology

Review: Study Insights into Gastrointestinal Cancer through the Gut Microbiota – Fanli Kong – BioMed Research International

Review: Contribution of Aging, Obesity, and Microbiota on Tumor Immunotherapy Efficacy and Toxicity – Regina E. M. Baiden-Amissah – International Journal in Molecular Sciences

TARgeting the cutaneous microbiota in atopic dermatitis by coal tar via AHR-dependent induction of antimicrobial peptides – Jos P.H. Smits – Journal of Investigative Dermatology

The Gut Microbiota in Collagenous Colitis Shares Characteristics With Inflammatory Bowel Disease-Associated Dysbiosis – Adam Carstens – Clinical and Translational Gastroenterology

Changes in oral microbial profiles associated with oral squamous cell carcinoma vs leukoplakia – Kengo Hashimoto – Journal of Investigative and Clinical Dentistry

Probiotics modulate the gut microbiota composition and immune responses in patients with atopic dermatitis: a pilot study – Zhifeng Fang – European Journal of Nutrition

Role of Bile Acids in Dysbiosis and Treatment of Nonalcoholic Fatty Liver Disease –  – Caihua Wang – Mediators of Inflammation

Rectal Swabs from Critically Ill Patients Provide Discordant Representations of the Gut  Microbiome Compared to Stool Samples – Katherine Fair – mSphere 

Measurement of gut microbial metabolites in cardiometabolic health and translational research – Wei‐Kai Wu – Rapid Communications in Mass Spectrometry

 

Animal Microbiome and Animal Experiments

The gut microbiota influences skeletal muscle mass and function in mice – Shawon Lahiri – Science Translational Science

Intestinal Clostridium species lower host susceptibility to enterohemorrhagic Escherichia coli O157:H7 infection – Yukako Koyanagi – Pathogens and Disease

Preparation and characterization of selenium enriched-Bifidobacterium longum DD98, and its repairing effects on antibiotic-induced intestinal dysbacteriosis in mice – Hui Zhu – Food and Function 

The Ruminal Microbiome and Metabolome Alterations Associated with Diet-Induced Milk Fat Depression in Dairy Cows – Hongbo Zeng – Metabolites

 

Water Microbiome

Insights into the antibiotic resistance dissemination in a wastewater effluent microbiome:  bacteria, viruses and vesicles matter – Lucia Maestre‐Carballa – Environmental Microbiology

 

Built Environment Microbiome

Identification of city specific important bacterial signature for the MetaSUB CAMDA challenge microbiome data – Alejandro R. Walker – Biology Direct 

 

Plant Microbiome

Genome Evolution and Host Microbiome Shifts Correspond with Intraspecific Niche Divergence within Harmful Algal Bloom-Forming Microcystis aeruginosa – Sara L. Jackrel – Molecular Ecology

Novel insights into plant-associated archaea and their functioning in arugula (Eruca sativa Mill.) – Julian Taffner – Journal of Advanced Research

Seeds of native alpine plants host unique microbial communities embedded in cross-kingdom networks – Birgit Wassermann – Microbiome

 

Bioinformatics

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2 – Evan Bolyen – Nature Biotechnology

Friday, July 19th

Happy Friday! Today’s digest includes the microbiome of plankton, viral diversity of ticks, and a review of microbiome engineering. Enjoy!

General microbiome

Homeorhesis and ecological succession quantified in synthetic microbial ecosystems – Chuang – PNAS

Human nearly-sterile sites

Insights into the Microbiome of Breast Implants and Periprosthetic Tissue in Breast Implant-Associated Anaplastic Large Cell Lymphoma – Walker – Scientific Reports

Human gut microbiome

Review: Precision Medicine Goes Microscopic: Engineering the Microbiome to Improve Drug Outcomes – Lam – Cell Host & Microbe

A structured weight loss program increases gut microbiota phylogenetic diversity and reduces levels of Collinsella in obese type 2 diabetics: A pilot study – Frost – PLoS One

Animal experiments

Changes in cecal microbiota community of suckling piglets infected with porcine epidemic diarrhea virus – Tan – PLoS One

Animal microbiome

Cicadae pupa promotes metabolites synthesis of Isaria cicadae, a dominant species in cicada flowers microbiota – Chunyu – Journal of Agricultural and Food Chemistry

Experimental Evidence for Adaptation to Species-Specific Gut Microbiota in House Mice – Moeller – mSphere

Fecal microbiota of different reproductive stages of the central population of the lesser-long nosed bat, Leptonycteris yerbabuenae – Gaona – PLoS One

Diel transcriptional response of a California Current plankton microbiome to light, low iron, and enduring viral infection – Kolody – ISME

Plant, root, and soil microbiome

Preprint: Maize residues changes soil fungal composition and decrease soil microbial co-ocurrence networks complexity – Cobo-Diaz – BioRxiv

Water and extremophile microbiome

Impacts of continuous inflow of low concentrations of silver nanoparticles on biological performance and microbial communities of aerobic heterotrophic wastewater biofilm – Alizadeh – Journal of Agricultural and Food Chemistry

Phages and viruses

Preprint: Metagenomic exploration of viral diversity and virus-host interactions in a deep freshwater lake – Okazaki – BioRxiv

Preprint: Identification and evolution of avian endogenous foamy viruses – Chen – BioRxiv

Viral Diversity of Tick Species Parasitizing Cattle and Dogs in Trinidad and Tobago – Sameroff – Scientific Reports

Bioinformatics

Predictive metabolomic profiling of microbial communities using amplicon or metagenomic sequences – Mallick – Nature Communications

Heterogeneity spacers in 16S rDNA primers improve analysis of mouse gut microbiomes via greater nucleotide diversity – Jensen – BioTechniques

July 2, 2019

This Tuesday, read about the fecal microbial transplantation for cardiometabolic syndrome treatment, oral microbiome of early stage Parkinson’s disease, Finnish Health and Early Life Microbiota (HELMi) project, and more. Happy reading!

General microbiome

Review: Defining Division of Labour in Microbial Communities – Samir Giri – JMB

Review: Selective pressures during chronic infection drive microbial competition and cooperation – Jiwasmika Baishya & Catherine A. Wakeman – Biofilms and Microbiomes

Gut microbiome

*Review: Fecal Microbial Transplantation and Its Potential Application in Cardiometabolic Syndrome – Avner Leshem – Frontiers in Immunology

Review: The Microbiome and Irritable Bowel Syndrome – A Review on the Pathophysiology, Current Research and Future Therapy – Pei Pei Chong – Frontiers in Microbiology

Alterations of the bile microbiome in primary sclerosing cholangitis – Timur Liwinski – BMJ Gut Microbiota

Selective and suppressive effects of antibiotics on donor and recipient bacterial strains in gut microbiota determine transmission efficiency of blaNDM-1-bearing plasmids – Lianwei Ye – Journal of Antimicrobial Chemotherapy

Pregnancy and early life

Contributions to human breast milk microbiome and enteromammary transfer of Bifidobacterium breve – Kattayoun Kordy – bioRxiv

Experimental support for multidrug resistance transfer potential in the preterm infant gut microbiota – Mari Hagbø – Paediatric research

*Cohort profile: Finnish Health and Early Life Microbiota (HELMi) longitudinal birth cohort – Katri Korpela – BMJ Paediatrics

Oral microbiome

*The oral microbiome of early stage Parkinson’s disease and its relationship with functional measures of motor and non-motor function – Dragos Mihaila – PlosOne

Phages and viruses

What is (not) known about the dynamics of the human gut virome in health and disease – Leen Beller Jelle Matthijnssens – Current Opinion in Virology

Water and extremophile microbiome

Characterization of indigenous bacteria from radon-rich groundwater and their tolerance to physicochemical stress – T. Nayak – International Journal of Environmental Science and Technology

Sewage effluent from an Indian hospital harbors novel carbapenemases and integron-borne antibiotic resistance genes – Nachiket P. Marathe – Microbiome

Techniques

Primer-free FISH probes from metagenomics/metatranscriptomics data permit the study of uncharacterised taxa in complex microbial communities – Shi Ming Tan – Biofilms and microbiomes

Bioinformatics

Use and abuse of correlation analyses in microbial ecology – Alex Carr – ISME Journal

Education

From trainees to trainers to instructors: Sustainably building a national capacity in bioinformatics training – Annette McGrath – Plos Computational Biology

Ten quick tips for effective dimensionality reduction – Lan Huong Nguyen and Susan Holmes – Plos Computational Biology

July 1, 2019

Today’s Monday digest is about microbiome changes in diseases such as Parkinson’s disease, schizophrenia, colorectal cancer and inflammatory bowel disease; review on importance of pig microbiota and impact of fecal storage protocols on microbial diversity and composition.

General microbiome

The pig microbiota and the potential for harnessing the power of the microbiome to improve growth and health – Nirosh D Aluthge – Journal of Animal Science

Microbial genes and pathways in inflammatory bowel disease – Melanie Schirmer – Nature Reviews Microbiology

Human microbiome

Changes in Gut Microbiome after Bariatric Surgery Versus Medical Weight Loss in a Pilot Randomized Trial – Clare J. Lee – Obesity Surgery

Microbiome Signatures Associated with Steatohepatitis and Moderate to Severe Fibrosis in Children With Nonalcoholic Fatty Liver Disease – Jeffrey B. Schwimmer – Gastroenterology

Altered gut microbiota and mucosal immunity in patients with schizophrenia – Ruihuan Xu – Brain Behavior and Immunity

Patients Eligible for Trials of Microbe-based Therapeutics do not Represent the Population With Recurrent Clostridioides difficile Infection – Colleen R. Kelly – Clinical Gastoenterology and Hepatology

A role for the mammalian female reproductive tract microbiome in pregnancy outcomes – Babiche A. Heil – Physiological Genomics

Altered intestinal microbiota associated with colorectal cancer – Hong Zhang – Frontiers of Medicine

Gut microbiota is associated with adiposity markers and probiotics may impact specific genera – Aline Corado Gomes – European Journal of Nutrition

Consistent alterations in faecal microbiomes of patients with primary sclerosing cholangitis independent of associated colitis – Malte Ruhlemann – Alimentary Pharmacology and Therapeutics

Altered gut microbiota and inflammatory cytokine responses in patients with Parkinson’s disease – Chin-Hsien Lin – Journal of Neuroinflammation

Animal experiments

Hypergravity disrupts murine intestinal microbiota – Corentine Alauzet – Scientific Reports

Dietary fructose-induced gut dysbiosis promotes mouse hippocampal neuroinflammation: a benefit of short-chain fatty acids – Jian-Mei Li – Microbiome

Gut microbiota depletion from early adolescence alters adult immunological and neurobehavioral responses in a mouse model of multiple sclerosis – Maryam Zeraati – Neuropharmacology

Enrichment of intestinal Lactobacillus by enhanced secretory IgA coating alters glucose homeostasis in P2rx7−/− mice – Lisa Perruzza – Scientific Reports

Plant, root, soil microbiome

Higher stochasticity of microbiota composition in seedlings of domesticated wheat compared to wild wheat – Ezgi Özkurt – BioRxiv

Emphasis on the deep or shallow parts of the tree provides a new characterization of phylogenetic distances – Julia Fukuyama – Genome Biology

Techniques

Assessment of the impact of different fecal storage protocols on the microbiota diversity and composition: a pilot study – Shirin Moossavi – BMC Mirobiology

Microbes and the market

Microbiome Sequencing Market players include: Biolog Inc., CosmosID Inc., Illumina Inc., Metabiomics and Oxford Nanopore Technologies Ltd – News Exterior

Global Microbiome Drugs Market NEWS 2019 By Types Probiotics, Prebiotics, Small Molecules, Biological Drugs – Market Reports

 

June 29, 2019

Happy Saturday! Today, in this Digest: a review about the relationship between hypertension and the gut (including the microbiome as a key player) and a systematic review of the associations between vaginal microbiota, HPV and cervical dysplasia. Today we have also several papers about bioinformatic tools, methods, and techniques associated with microbiome research, including the analysis of well-to-well contamination during microbiome research. And of course, many more papers!

 

Human or General Microbiome

Review: Hypertension as a Metabolic Disorder and the Novel Role of the Gut – Masami Tanaka – Current Hypertension Reports

Minireview: Antibiotics and immunotherapy in gastrointestinal tumors: Friend or foe? – Cong Yan – World Journal of Clinical Cases

Review: Proton pump inhibitors and dysbiosis: Current knowledge and aspects to be clarified – Giovanni Bruno – World Journal of Gastroenterology

Systematic Review: The vaginal microbiota, HPV and cervical dysplasia: a systematic review and network meta-analysis – Johanna Norenhag – BJOG

Microbiota therapy acts via a regulatory T cell MyD88/RORγt pathway to suppress food allergy – Azza Abdel-Gadir – Nature Medicine

Exploration of the Vaginal and Gut Microbiome in African American Women by Body Mass Index, Class of Obesity, and Gestational Weight Gain: A Pilot Study – Mary Ann Faucher - American Journal of Perinatology

Banking feces: a new frontier for public blood banks? – Simon Mark Dahl Jørgensen – Transfusion

Diet-microbiota-metabolite interaction networks reveal key players in inflammatory bowel disease – Yijie Weng – Journal of Digestive Diseases

The microbiome of calcium-based urinary stones – Ryan A. Dornbier – Urolithiasis

Scientometric analysis of the term “microbiota” in research publications (1999-2017): A second youth of a century-old concept – Lesya Baudoin – FEMS Microbiology Letters

Microbiome analysis as a platform R&D tool for parasitic nematode disease management – Glenn Hogan – The ISME Journal

Is the Oral Microbiome Associated with Blood Pressure in Older Women? – Joshua H. Gordon – High Blood Pressure & Cardiovascular Prevention

An untargeted fecal and urine metabolomics analysis of the interplay between the gut microbiome, diet and human metabolism in Indian and Chinese adults – Abhishek Jain – Scientific Reports

Gut Microbiota Alteration is Characterized by a Proteobacteria and Fusobacteria Bloom in Kwashiorkor and a Bacteroidetes Paucity in Marasmus – Thi-Phuong-Thao Pham – Scientific Reports

The effects of perineal disinfection on infant’s oral microflora after transvaginal examination during delivery – Hongping Li – BMC Pregnancy and Childbirth

Metagenomic analysis of bile salt biotransformation in the human gut microbiome – Promi Das – BMC Genomics

 

Animal Microbiome / Animal Experiments

Metagenomic assessment of the Cebus apella gut microbiota – Jenni Firrman – American Journal of Primatology

Multipartner Symbiosis across Biological Domains: Looking at the Eukaryotic Associations from a Microbial Perspective – Marta Turon – mSystems

Arthropod-bacteria interactions influence assembly of aquatic host microbiome and pathogen defense – Sasha E. Greenspan – Proceedings of the Royal Society B

Intestinal microbiota contributes to altered glucose metabolism in simulated microgravity mouse model – Yifan Wang – The FASEB Journal

Impact of Low-dose Ionising Radiation on the Composition of the Gut Microbiota of Mice – Xiaodan Liu – Toxicological Sciences

Habitat fragmentation is associated with dietary shifts and microbiota variability in common vampire bats – Melissa R. Ingala – Ecology and Evolution

 

Microbiome and Therapeutics (Compounds, Microbes or Procedures)

Review: Effects of Fish n-3 PUFAs on Intestinal Microbiota and Immune System – Cinzia Parolini – Marine Drugs

Review: Updates in Treatment of Recurrent Clostridium difficile Infection – Tanveer Singh – Journal of Clinical Medicine Research

Synbiotics suppress colitis-induced tumorigenesis in a colon-specific cancer mouse model – Yasufumi Saito – PLOS One

Roles of Chinese Medicine and Gut Microbiota in Chronic Constipation – Zhenyuan Xu – Evidence-Based Complementary and Alternative Medicine

Increasing the Dose and/or Repeating Faecal Microbiota Transplantation (FMT) Increases the Response in Patients with Irritable Bowel Syndrome (IBS) – Magdy El-Salhy – Nutrients

Interleukin-37 sensitize the elderly type 2 diabetic patients to insulin therapy through suppressing the gut microbiota dysbiosis – Tianyi Li – Molecular Immunology

Skin microbiome modulation induced by probiotic solutions – Bernhard Paetzold – Microbiome

Evaluation of Predation Capability of Periodontopathogens Bacteria by Bdellovibrio Bacteriovorus HD100. An in Vitro Study – Romeo Patini – Materials

 

Bioinformatics, Methods and Techniques

Quantifying and Understanding Well-to-Well Contamination in Microbiome Research – Jeremiah J. Minich – mSystems

Associated commentary: A Lot on Your Plate? Well-to-Well Contamination as an Additional Confounder in Microbiome Sequence Analyses – Alan W. Walker – mSystems

redbiom: a Rapid Sample Discovery and Feature Characterization System – Daniel McDonald – mSystems

Review: Methods and basic concepts for microbiota assessment – Marcio Costa – The Veterinary Journal

Long-read based de novo assembly of low-complexity metagenome samples results in finished genomes and reveals insights into strain diversity and an active phage system – Vincent Somerville – BMC Microbiology

Robust biomarker discovery for microbiome-wide association studies – Qiang Zhu – Methods

A Method for Comprehensive Proteomic Analysis of Human Faecal Samples to Investigate Gut Dysbiosis in Patients with Cystic Fibrosis – Griet Debyser – Emerging Sample Treatments in Proteomics

metaQuantome: An integrated, quantitative metaproteomics approach reveals connections between taxonomy and protein function in complex microbiomes – Caleb W. Easterly – Molecular & Cellular Proteomics

Review: The dark side of technological advances in analysis of microbial ecosystems – Mick Bailey – Journal of Animal Science and Biotechnology