May 11, 2019

Have a good weekend! Today, in this MD we recovered some papers released in the previous days. Some highlights: an interesting study about the relationship between Alzheimer’s disease and microbiome, connections between microbial anti-inflammatory pathways and Crohn’s disease exacerbations; the peripartum microbiome on glyphosate, the effect of the microbial metabolite butyrate on sleep and an interesting review about the probiotics concept.

 

Human or General Microbiome

Altered microbiomes distinguish Alzheimer’s disease from amnestic mild cognitive impairment and health in a Chinese cohort – Ping Liu – Brain, Behavior, and Immunity

Anti-inflammatory Gut Microbial Pathways Are Decreased During Crohn’s Disease Exacerbations – Marjolein A Y Klaassen – Journal of Crohn’s and Colitis

Fecal Microbiome, Metabolites, and Stem Cell Transplant Outcomes: A Single-Center Pilot Study – Jessica R Galloway-Peña – Open Forum Infectious Diseases

Dysbiosis of the Gut Microbiome in Lung Cancer – He Zhuang – Frontiers in Celullar and Infection Microbiology

Human gut derived-organoids provide model to study gluten response and effects of microbiota-derived molecules in celiac disease – Rachel Freire – Scientific Reports

Alzheimer’s Disease Microbiome Is Associated with Dysregulation of the Anti-Inflammatory P-Glycoprotein Pathway – John P. Haran – mBio

Modifications in Vaginal Microbiota and Their Influence on Drug Release: Challenges and Opportunities – Gerardo Leyva-Gómez – Pharmaceutics

Strong Multivariate Relations Exist Among Milk, Oral, and Fecal Microbiomes in Mother-Infant Dyads During the First Six Months Postpartum – Janet E Williams – The Journal of Nutrition

Identification of an intestinal microbiota signature associated with hospitalized patients with diarrhea – Mohammadzadeh Nima –  Acta Microbiologica et Immunologica Hungarica

Surface glycan-binding proteins are essential for cereal beta-glucan utilization by the human gut symbiont Bacteroides ovatus – Kazune Tamura – Cellular and Molecular Life Sciences

Humoral response to Clostridium difficile in inflammatory bowel disease, including correlation with immunomodulatory treatment – Gunnel Henriksson – JGH Open

Review: Body site-dependent variations of microbiota in pancreatic cancer pathophysiology – Concetta Panebianco – Critical Reviews in Clinical Laboratory Sciences

Role of Gut Microbiota in Hepatocarcinogenesis – Haripriya Gupta – Microorganisms

 

Animal Microbiome and Experiments

Glyphosate and Glyphosate-based herbicide exposure during the peripartum period affects maternal brain plasticity, maternal behavior and microbiome – Julie Dechartres – Journal of Neuroendocrinology

Invited review: Application of meta-omics to understand the dynamic nature of the rumen microbiome and how it responds to diet in ruminants – R. J. Gruninger – Animal

Comparison of Co-housing and Littermate Methods for Microbiota Standardization in Mouse Models – Susan J. Robertson – Cell Reports

Faecal microbiota changes associated with the moult fast in chinstrap and gentoo penguins – Won Young Lee – PLoS ONE

Intestinal dysbacteriosis mediates the reference memory deficit induced by anaesthesia/surgery in aged mice – Xl Jiang – Brain, Behavior, and Immunity

Oral vitamin B12 supplement is delivered to the distal gut, altering the corrinoid profile and selectively depleting Bacteroides in C57BL/6 mice – Caleb J. Kelly – Gut Microbes

The role of gut microbiota in shaping the relapse-remitting and chronic-progressive forms of multiple sclerosis in mouse models – K. Alexa Orr Gandy – Scientific Reports

Haem iron reshapes colonic luminal environment: impact on mucosal homeostasis and microbiome through aldehyde formation – Océane C. B. Martin – Microbiome

 

Beneficial Microbes and Compounds

Effect of a Multistrain Probiotic on Cognitive Function and Risk of Falls in Patients With Cirrhosis: A Randomized Trial – Eva Román – Hepatology Communications

Perspective: The pros, cons, and many unknowns of probiotics – Jotham Suez – Nature Medicine

Review: Prospecting prebiotics, innovative evaluation methods, and their health applications: a review – Ishu Khangwal – 3 Biotech

Butyrate, a metabolite of intestinal bacteria, enhances sleep – Éva Szentirmai – Scientific Reports

Gut Microbiota-Mediated NLRP12 Expression Drives the Attenuation of Dextran Sulphate Sodium-Induced Ulcerative Colitis by Qingchang Wenzhong Decoction – Zhongmei Sun – Evidence-Based Complementary and Alternative Medicine

Mulberry Leaf Polyphenols and Fiber Induce Synergistic Antiobesity and Display a Modulation Effect on Gut Microbiota and Metabolites – Qian Li – Nutrients

Probiotics mixture increases butyrate, and subsequently rescues the nigral dopaminergic neurons from MPTP and rotenone-induced neurotoxicity – Sunil Srivastav – The Journal of Nutritional Biochemistry

Beneficial effects of tea water extracts on the body weight and gut microbiota in C57BL/6J mice fed with a high-fat diet – Jianhui Liu – Food and Function

 

Extremophiles

Comparative Power Law Analysis for the Spatial Heterogeneity Scaling of the Hot-Spring Microbiomes – Lianwei Li – Molecular Ecology

 

Other

Comparative genomics of Bifidobacterium species isolated from marmosets and humans – Celeste J. Brown – American Journal of Primatology

May 10, 2019

Have a good Friday! Today was published a very interesting article about a longitudinal study using several tools (including microbiome analysis), finding several clinically actionable health discoveries and identified multiple molecular pathways associated with metabolic, cardiovascular and oncologic pathophysiology, in patients with type II diabetes. This article could represent an interesting contribution to precision medicine development.

In addition, this digest also contains papers about: the role of sphingolipids in symbiosis and gut health, the role of fecal microbiota transplantation in IBS relief, the stability of a probiotic strain in infants, and more…

 

Human/General Microbiome

A longitudinal big data approach for precision health – Sophia Miryam Schüssler-Fiorenza Rose – Nature Medicine

Turning points: Making the microbiome personal – Ami S. Bhatt – Nature Medicine

Bacteroides-Derived Sphingolipids Are Critical for Maintaining Intestinal Homeostasis and Symbiosis – Eric M. Brown – Cell Host & Microbe

Relief of irritable bowel syndrome by fecal microbiota transplantation is associated with changes in diversity and composition of the gut microbiota – Hong Li Huang – Journal of Digestive Diseases

Perspective: Do Interactions Between Environmental Chemicals and the Human Microbiome Need to Be Considered in Risk Assessments? – Joseph Rodricks – Risk Analysis

Association of the oral microbiome with the progression of impaired fasting glucose in a Chinese elderly population – Rui-Rui Wang – Journal of Oral Microbiology

Stroke Dysbiosis Index (SDI) in Gut Microbiome Are Associated With Brain Injury and Prognosis of Stroke – Geng-Hong Xia – Frontiers in Neurology

Review: Alpha-Synuclein Pathology and the Role of the Microbiota in Parkinson’s Disease – Emily Fitzgerald – Frontiers in Neuroscience

Mucosal-associated invariant T cells and oral microbiome in persistent apical periodontitis – Haleh Davanian – International Journal of Oral Science

Obesity, Xenobiotic Intake and Antimicrobial-Resistance Genes in the Human Gastrointestinal Tract: A Comparative Study of Eutrophic, Overweight and Obese Individuals – Marjorie Raquel Anariba Sarmiento – Genes

Effects of Intestinal Microbial⁻Elaborated Butyrate on Oncogenic Signaling Pathways – Jiezhong Chen – Nutrients

Composite Analysis of the Virome and Bacteriome of HIV/HPV Co-Infected Women Reveals Proxies for Immunodeficiency – Juliana D. Siqueira – Viruses

 

Animal Microbiome and Animal Model Experiments

Review: Veterinary ocular microbiome: Lessons learned beyond the culture – Kayla C. Banks – Veterinary Ophthalmology  

Antibiotic-Induced Disruption of Gut Microbiota Alters Local Metabolomes and Immune Responses – Lin Sun – Frontiers in Cellular and Infection Microbiology

Cloacal microbiomes and ecology of individual barn swallows – Roberto Ambrosini – FEMS Microbiology Ecology

Exposure to microplastics lowers arsenic accumulation and alters gut bacterial communities of earthworm Metaphire californica – Hong-Tao Wang – Environmental Pollution

Fermented carrot juice attenuates type 2 diabetes by mediating gut microbiota in rats – Rongkang Hu – Food and Function

Positive effects of a Clostridium butyricum-based compound probiotic on growth performance, immune responses, intestinal morphology, hypothalamic neurotransmitters, and colonic microbiota in weaned piglets – Guangtian Cao – Food and Function

Ripened Pu-erh tea extract protects mice from obesity by modulating gut microbiota composition – Xiaojie Lu – Journal of Agricultural and Food Chemistry

Microbiota alter metabolism and mediate neurodevelopmental toxicity of 17β-estradiol – Tara R. Catron – Scientific Reports

 

Beneficial Microbes and Compounds

Vitamin C and B3 as New Biomaterials to Alter Intestinal Stem Cells – Yijun Qi – Journal of Biomedical Material Research

Bile salt hydrolase can improve Lactobacillus plantarum survival in gastrointestinal tract by enhancing their adhesion ability – Yanrong Liu – FEMS Microbiology Letters

Administration of the Probiotic Escherichia coli Strain A0 34/86 Resulted in a Stable Colonization of the Human Intestine During the First Year of Life – Lenka Micenková – Probiotics and Antimicrobial Proteins

Minireview: Structures and Metabolic Properties of Bovine Milk Oligosaccharides and Their Potential in the Development of Novel Therapeutics – Randall C. Robinson – Frontiers in Nutrition

 

Bioinformatics and Analysis

An Adaptive Multivariate Two-Sample Test With Application to Microbiome Differential Abundance Analysis – Kalins Banerjee – Frontiers in Genetics

Identifying Gut Microbiota Associated With Colorectal Cancer Using a Zero-Inflated Lognormal Model – Dongmei Ai – Frontiers in Microbiology

 

May 4, 2019

Have a good weekend! Today, in this MB, we have interesting papers about different aspects of the microbiome. For example, we have a review overviewing the relationship between epigenetic changes, microbiome and metabolic diseases, as well as a paper focused in the use of a microbial metabolite in the prognosis of coronary issues. We have also the publication of an interesting study authored by the MB founder Elisabeth Bik.

There are also some papers about coral microbiome and an study about the homogenization of the microbiome between both US Air Force cadets and their built environment.

 

Human and General Microbiome

Review: Epigenetic Markers and Microbiota/Metabolite-Induced Epigenetic Modifications in the Pathogenesis of Obesity, Metabolic Syndrome, Type 2 Diabetes, and Non-alcoholic Fatty Liver Disease – Daniela Stols-Gonçalves – Current Diabetes Reports

A novel sequencing-based vaginal health assay combining self-sampling, HPV detection and genotyping, STI detection, and vaginal microbiome analysis – Elisabeth Bik – PLoS ONE

Trimethyllysine, a trimethylamine N-oxide precursor, provides near- and long-term prognostic value in patients presenting with acute coronary syndromes – Xinmin S Li – European Heart Journal

Review: The interaction between Entamoeba histolytica and enterobacteria shed light on an ancient antibacterial response – Nancy Guillén – Cellular Microbiology

PCR Characterization of Microbiota on Contracted and Non-Contracted Breast Capsules – Yara Bachour – Aesthetic Plastic Surgery

Decreased Cephalosporin Susceptibility of Oropharyngeal Neisseria Species in Antibiotic-Using Men-who-have-sex-with-men of Hanoi, Vietnam– Huan V Dong – Clinical Infectious Diseases

Review: Smoking and periodontal microorganisms – Takashi Hanioka – Japanese Dental Science Review

The influence of the vaginal microbiota on preterm birth: A systematic review and recommendations for a minimum dataset for future research – Myrthe JCS. Peelen – Placenta

Gut Microbiome in Health and Disease: Emerging Diagnostic Opportunities – Aonghus Lavelle – Gastroenterology Clinics of North America

Laryngotracheal Microbiota in Adult Laryngotracheal Stenosis – Alexander T. Hillel – mSphere

Antibiotic Resistance Gene Diversity and Virulence Gene Diversity Are Correlated in Human Gut and Environmental Microbiomes – Pedro Escudeiro –  mSphere

 

Beneficial Microbes

Review: Changing our microbiome: Probiotics in dermatology – Y. Yu – British Journal of Dermatology

Amelioration of obesity-related biomarkers by Lactobacillus sakei CJLS03 in a high-fat diet-induced obese murine model – Josep Ji – Scientific Reports

 

Animal Models / Animal Microbiome

Age-related analysis of the gut microbiome in a purebred dog colony – Keijiro Mizukami – FEMS Microbiology Letters

Addition of plant dietary fibre to a raw red meat high protein, high fat diet, alters the faecal bacteriome and organic acid profiles of the domestic cat (Felis catus) – Christina F. Butowski – PLoS ONE

Effects of diet on gut microbiota of soil collembolans – Qian Xiang – Science of The Total Environment

Multiple stressors interact primarily through antagonism to drive changes in the coral microbiome – Rebecca L. Maher – Scientific Reports

Structure and stability of the coral microbiome in space and time – Courtney M. Dunphy – Scientific Reports

The effect of dissolved nickel and copper on the adult coral Acropora muricata and its microbiome – Francesca Gissi – Environmental Pollution

 

Food Microbiome

Microbiota and Chemical Compounds in Fermented Pinelliae Rhizoma (Banxiaqu) from Different Areas in the Sichuan Province, China – Bo Shu – Polish Journal of Microbiology

 

Built Environment

Longitudinal homogenization of the microbiome between both occupants and the built environment in a cohort of United States Air Force Cadets –  Anukriti Sharma – Microbiome

 

Environmental Microbiome

The Influence of Temperature and Nitrogen Source on Cellulolytic Potential of Microbiota Isolated from Natural Environment –  Agnieszka Wita  – Polish Journal of Microbiology

 

Techniques

The potential of nanoflow liquid chromatography-nano electrospray ionisation-mass spectrometry for global profiling the faecal metabolome – Andrew J. Chetwynd – Journal of Chromatography A

May 2, 2019

In today’s digest read about variations in milk and infant fecal microbiome (Ethiopia, Gambia, USA, Ghana, Kenya, Peru, Spain, and Sweden), the microbiome, metabolome, and lipidome of obese and non-obese horses (USA), and Bacteroides fragilis adaptive evolution (Western countries and China). Happy reading!

Pregnancy and birth

*What’s normal? Microbiomes in human milk and infant feces are related to each other but vary geographically: the INSPIRE study – Kimberly A. Lackey – Frontiers in Nutrition

Progesterone Increases Bifidobacterium Relative Abundance during Late Pregnancy – Meital Nuriel-Ohayon – Cell Reports

Gut microbiome

Neonatal Vitamin A Supplementation and Vitamin A Status Are Associated with Gut Microbiome Composition in Bangladeshi Infants in Early Infancy and at 2 Years of Age – M Nazmul Huda – The Journal of nutrition

Fungi form interkingdom microbial communities in the primordial human gut that develop with gestational age – Kent A. Willis – bioRxiv

*Adaptive Evolution within Gut Microbiomes of Healthy People – Shijie Zhao – Cell Host & Microbe

Small intestinal microbial dysbiosis underlies symptoms associated with functional gastrointestinal disorders – George B. Saffouri – Nature Communications

Oral microbiome

Review: The Role of Exopolysaccharides in Oral Biofilms – C. Cugini – Journal of Dental Research

Human Salivary Amylase Gene Copy Number Impacts Oral and Gut Microbiomes – Angela C. Poole – Cell Host & Microbe

Animal microbiome

*Comparison of the microbiome, metabolome, and lipidome of obese and non-obese horses – Michelle C. Coleman – PlosOne

Utilizing the fecal microbiota to understand foal gut transitions from birth to weaning – Ubaldo De La Torre – PlosOne

Microbiome characterization of poultry products based on the poultry part and production label – Sang In Lee – FEMS Microbiology Letters

Metagenomic analysis of isolation methods of a targeted microbe, Campylobacter jejuni, from chicken feces with high microbial contamination – Junhyung Kim – Microbiome

Invited review: Advances and challenges in application of feedomics to improve dairy cow production and health – H.Z.Sun – Journal of Dairy Science

Characterization of pig saliva as the major natural habitat of Streptococcus suis by analyzing oral, fecal, vaginal, and environmental microbiota – Kazunori Murase – PlosOne

Insight into the microbial world of Bemisia tabaci cryptic species complex and its relationships with its host – Hua-Ling Wang – Scientific Reports

Water and extremophile microbiome

The Plastisphere – Uncovering tightly attached plastic “specific” microorganisms – Inga Vanessa Kirstein – PlosOne

The cooling tower water microbiota: Seasonal dynamics and co-occurrence of bacterial and protist phylotypes – Han-Fei Tsao – Water Research

Modular Assembly of Polysaccharide-Degrading Marine Microbial Communities – Tim N.Enke – Current Biology

Impact of a river flood on marine water quality and planktonic microbial communities – Annamaria Zoppini – Estuarine, Coastal and Shelf Science

Microbial ecological processes in MBBR biofilms for biological phosphorus removal from wastewater – Knut Rudi – Water Science & Technology

Highly diverse fungal communities in carbon-rich aquifers of two contrasting lakes in Northeast Germany – Anita Perkins – bioRxiv

Plant/root/soil microbiome

The rice leaf microbiome has a conserved community structure controlled by complex host-microbe interactions – Veronica Roman-Reyna – bioRxiv

Spatial vs. temporal controls over soil fungal community similarity at continental and global scales – Colin Averil – The ISME Journal

Metabolomics Reveal that Engineered Nanomaterial Exposure in Soil Alters Both Soil Rhizosphere Metabolite Profiles and Maize Metabolic Pathways – Lijuan Zhao – Environmental Science: Nano

High-throughput sequencing reveals the diversity and community structure of rhizosphere fungi of Ferula Sinkiangensis at different soil depths – Tao Zhang – Scientific Reports

Microplastics can change soil properties and affect plant performance – Anderson Abel de Souza Machado – Environmental Science and Technology

April 29, 2019

Today’s Monday morning digest is about correlations of human gut microbiome with circulating metabolites, coronary artery disease severity; microbial communities in biogas plants, and proteomic profiling of gut microbiota-associated bile salt hydrolase activity.

Human gut microbiome

Correlation of Gut Microbiome Between ASD Children and Mothers and Potential Biomarkers for Risk Assessment – Ning Li – Genomics, Proteomics & Bioinformatics

Neonatal Vitamin A Supplementation and Vitamin A Status Are Associated with Gut Microbiome Composition in Bangladeshi Infants in Early Infancy and at 2 Years of Age – M Nazmul Huda – Journal of Nutrition

Diversification and evolution of vancomycin-resistant Enterococcus faecium during intestinal domination – Krista A. Dubin – Infection and Immunity

Microbiota as a cornerstone in the development of primary sclerosing cholangitis: paving the path for translational diagnostic and therapeutic approaches – Catherine Mooser – Gut

Alterations in the gut microbiome and metabolism with coronary artery disease severity – Honghong Liu – Microbiome

Deciphering the complex interplay between microbiota, HPV, inflammation and cancer through cervicovaginal metabolic profiling – Zehra Esra Ilhan – EBio Medicine

Relationship between gut microbiota and circulating metabolites in population-based cohorts – Dina Vojinovic – BioRxiv

Animal experiments

Antibiotics-induced perturbations in gut microbial diversity influence metabolic phenotypes in a murine model of high-fat diet-induced obesity – Dongmin Liu – Applied Microbiology and Biotechnology

Composition, diversity and function of gastrointestinal microbiota in wild red-billed choughs (Pyrrhocorax pyrrhocorax) – Wen Wang – International Microbiology

Plant, root, soil microbiome

Antioxidant activity changes of exopolysaccharides with different carbon sources from Lactobacillus plantarum LPC-1 and its metabolomic analysis – Xin Cheng – World Journal of Microbiology and Biotechnology

Effects of grassland afforestation on structure and function of soil bacterial and fungal communities – Kaibo Wang – Science of the Total Environment

Water microbiome and extremophiles

Effect of applied voltage and temperature on methane production and microbial community in microbial electrochemical anaerobic digestion systems treating swine manure – Jaecheul Yu – Journal of Industrial Microbiology & Biotechnology

Metaproteome analysis reveals that syntrophy, competition, and phage-host interaction shape microbial communities in biogas plants – R. Heyer – Microbiome

Techniques

Improving Assignment of Microbial Genetic Polymorphisms Assignments in Complex Samples by Bayesian Estimation – Jiarui Li – Genomics, Proteomics & Bioinformatics

Accounting for Biological Variation With Linear Mixed-effects Modelling Improves the Quality of Clinical Metabolomics Data – Kwanjeera Wanichthanarak – Computational and Structural Biotechnology Journal

Chemoproteomic Profiling of Gut Microbiota-Associated Bile Salt Hydrolase Activity – Bibudha Parasar – ACS Central Science

Microbiome in news

Human Microbiome Therapeutics Market Research Methodology- Prominent Players Enterome Bioscience, Yakult Honsha Co. Ltd., DuPont – The Market Bureau

The Week That Wasn’t: See-Through Skulls, Fecal Soup, Microbiome Pill – Medscape

Non-Microbiology Picks

The incretin system in healthy humans: the role of GIP and GLP-1 – Jens Juul Holst – Metabolism

April 28, 2019

Human Gut and General Microbiome

Review: Stereotypes About Enterotype: the Old and New Ideas – Mingyue Cheng – Genomics, Proteomics & Bioinformatics

Review: Gut Microbiota Regulation of T Cells During Inflammation and Autoimmunity – Eric M. Brown –  Annual Review of Immunology

Review: The Microbiome and Food Allergy – Onyinye I. Iweala – Annual Review of Immunology

Review: An Updated Review of Clostridium difficile Treatment in Pediatrics – Christopher T. Campbel –  The Journal of Pediatric Pharmacology and Therapeutics

Review: Pediatric inflammatory bowel disease: continuous lessons for adult inflammatory bowel disease – Shahzad Ahmed – Current Opinion in Gastroenterology

Review: Intestinal Microbiota in Cardiovascular Health and Disease: JACC State-of-the-Art Review – W.H. Wilson Tang – Journal of the American College of Cardiology

Review: The role of the gut microbiome in sex differences in arterial pressure – Anna L. Beale – Biology of Sex Differences

Review: Precision Nutrition and the Microbiome, Part I: Current State of the Science – Susan Mills – Nutrients

Review: Impact of bariatric surgery on type 2 diabetes: contribution of inflammation and gut microbiome? – Jean Debédat – Seminars in Immunopathology

Review: The Gut Microbiota-Host Partnership as a Potential Driver of Kawasaki Syndrome – Susanna Esposito – Frontiers in Pediatrics

Review: A Review of Mixed Strain Clostridium difficile Colonization and Infection – Pete Dayananda – Frontiers in Microbiology

Review: Small Intestinal Bacterial Overgrowth in Patients With Cirrhosis – Gaurav Ghosh – Journal of Clinical and Experimental Hepatology

Perspective: Effect of Metformin on Antipsychotic-Induced Metabolic Dysfunction: The Potential Role of Gut-Brain Axis – Chao Luo –  Frontiers in Pharmacology

Antibiotic Treatment Drives the Diversification of the Human Gut Resistome – Jun Li – Genomics, Proteomics & Bioinformatics

Contribution of Non-immune Cells to Activation and Modulation of the Intestinal Inflammation – Renata Curciarello – Frontiers in Immunology

Environmental DNA metabarcoding to detect pathogenic Leptospira and associated organisms in leptospirosis-endemic areas of Japan – Yukuto Sato – Scientific Reports

The short-chain fatty acid propionate increases glucagon and FABP4 production, impairing insulin action in mice and humans – Amir Tirosh – Science Translational Medicine

 

Cancer and Microbiome

The diversity of gut microbiome is associated with favorable responses to anti-PD-1 immunotherapy in Chinese non-small cell lung cancer patients – Yueping Jin – Journal of Thoracic Oncology

Gut Microbiota as a Positive Potential Therapeutic Factor in Carcinogenesis: an Overview of Microbiota-Targeted Therapy – Farahnaz Joukar – Journal of Gastrointestinal Cancer

Detection of Fusobacterium nucleatum in stool and colonic tissues from Norwegian colorectal cancer patients – Hege Smith Tunsjø – European Journal of Clinical Microbiology & Infectious Diseases

 

Oral Microbiome

Gender-Specific Associations Between Saliva Microbiota and Body Size  – Sajan C. Raju – Frontiers in Microbiology

Chemotherapy-induced oral mucositis is associated with detrimental bacterial dysbiosis – Bo-Young Hong – Microbiome

 

Respiratory Tract Microbiome

The airway microbiota in children newly diagnosed with bronchiectasis largely retains its diversity – Naveen Pillarisetti – European Respiratory Journal

Performance of the Biomark HD real-time qPCR System (Fluidigm) for the detection of nasopharyngeal bacterial pathogens and Streptococcus pneumoniae typing – Courtney P. Olwagen – Scientific Reports

 

Mother and Child Microbiome

Systematic Review: Repertoire of human breast and milk microbiota: a systematic review – Amadou Togo – Future Medicine

Variation of cultured skin microbiota in mothers and their infants during the first year postpartum – Georgios Gaitanis – Pediatric Dermatology

 

Correlation of Gut Microbiome Between ASD Children and Mothers and Potential Biomarkers for Risk Assessment – Ning Li – Genomics, Proteomics & Bioinformatics

 

Reproductive tract Microbiome

Impact of reproductive aging on the vaginal microbiome and soluble immune mediators in women living with and at-risk for HIV infection – Kerry Murphy – PLoS ONE

The Vaginal and Urinary Microbiomes in Premenopausal Women With Interstitial Cystitis/Bladder Pain Syndrome as Compared to Unaffected Controls: A Pilot Cross-Sectional Study – Kate V. Meriwether – Frontiers in Cellular and Infection Microbiology

Microorganisms in the healthy upper reproductive tract: from denial to beneficial assignments for reproductive biology – Rebekka Einenkel – Reproductive Biology

 

Animal Microbiome

Structural shifts in the intestinal microbiota of rats treated with cyclosporine A after orthotropic liver transplantation – Junjun Jia – Frontiers of Medicine

Composition, diversity and function of gastrointestinal microbiota in wild red-billed choughs (Pyrrhocorax pyrrhocorax) – Wen Wang – International Microbiology

Antibiotics-induced perturbations in gut microbial diversity influence metabolic phenotypes in a murine model of high-fat diet-induced obesity – Dongmin Liu – Applied Microbiology and Biotechnology

Rumen fermentation, intramuscular fat fatty acid profiles and related rumen bacterial populations of Holstein bulls fed diets with different energy levels – Haibo Wang – Applied Microbiology and Biotechnology

The Gut Microbiome on a Periodized Low-Protein Diet Is Associated With Improved Metabolic Health – Zhencheng Li – Frontiers in Microbiology

Human activity can influence the gut microbiota of Darwin’s finches in the Galapagos Islands – Sarah A. Knutie – Molecular Ecology

Diversity and composition of the gut microbiota of Atlantic salmon (Salmo salar) farmed in Irish waters – Colin Fogarty – Journal of Applied Microbiology

Metagenomic analysis revealed beneficial effects of probiotics in improving the composition and function of the gut microbiota in dogs with diarrhoea – Haiyan Xu – Food & Nutrition

Microbiome analysis of Ixodes scapularis ticks from New York and Connecticut – Rafal Tokarz – Ticks and Tick-borne Diseases

Human gut microbiota transferred to germ-free NOD mice modulate the progression towards type 1 diabetes regardless of the pace of beta cell function loss in the donor – Vit Neuman – Diabetologia

Gut microbiome composition of wild western lowland gorillas is associated with individual age and sex factors – Barbora Pafčo – American Journal of Physical Anthropology

The bumble bee microbiome increases survival of bees exposed to selenate toxicity – Jason A. Rothman – Environmental Microbiology

Effect of probiotic supplementation on seizure activity and cognitive performance in PTZ-induced chemical kindling – Samaneh Bagheri – Epilepsy and Behavior

Inulin Can Alleviate Metabolism Disorders in ob/ob Mice by Partially Restoring Leptin-Related Pathways Mediated by Gut Microbiota – Xiaofeng Song – Genomics, Proteomics & Bioinformatics

Supplementation with compound polysaccharides contributes to the development and metabolic activity of young rat intestinal microbiota – Mengxia Wang – Food & Nutrition

A Risky Business? Habitat and Social Behavior Impact Skin and Gut Microbiomes in Caribbean Cleaning Gobies – Raquel Xavier – Frontiers in Microbiology

Ovarian progesterone suppresses depression and anxiety-like behaviors by increasing the Lactobacillus population of gut microbiota in ovariectomized mice – Watcharin N.Sovijit – Neuroscience Research

 

Beneficial Microbes and Compounds

Meta-analysis: Probiotics improve glucose and lipid metabolism in pregnant women: a meta-analysis – Man-Man Han – Annals of Translational Medicine

Probiotic Bifidobacterium lactis V9 Regulates the Secretion of Sex Hormones in Polycystic Ovary Syndrome Patients through the Gut-Brain Axis – Jiachao Zhang – mSystem

Major Traditional Probiotics: Comparative Genomic Analyses and Roles in Gut Microbiome of Eight Cohorts – Guangwen Luo – Frontiers in Microbiology

The beneficial effects of purple yam (Dioscorea alata L.) resistant starch on hyperlipidemia in high-fat-fed hamsters – Tao Li – Food & Nutrition

Restoration of Bacterial Microbiome Composition and Diversity Among Treatment Responders in a Phase 2 Trial of RBX2660: An Investigational Microbiome Restoration Therapeutic – Ken F Blount – Open Forum Infectious Diseases

Lactobacillus reuteri DSM 17938 – A comparative study on the effect of probiotics and lysates on human skin – I. Khmaladze – Experimental Dermatology

 

Plant and Soil Microbiome

Nodulation induces systemic resistance of Medicago truncatula and Pisum sativum against Erysiphe pisi and primes for powdery mildew-triggered salicylic acid accumulation – Lara Smigielski – IS-MPMI

Land Use and Seasonal Effects on the Soil Microbiome of a Brazilian Dry Forest – Gileno V. Lacerda-Júnior – Frontiers in Microbiology

Microbial Diversity in the Edible Gall on White Bamboo Formed by the Interaction between Ustilago esculenta and Zizania latifolia – Zhihao Tu – Current Microbiology

Species-specific response of the soil collembolan gut microbiome and resistome to soil oxytetracycline pollution – Qi Zhang – Science of The Total Environment

 

Food Microbiome

Gamma Irradiation Influences the Survival and Regrowth of Antibiotic-Resistant Bacteria and Antibiotic-Resistance Genes on Romaine Lettuce – Vaishali Dharmarha – Frontiers in Microbiology

 

Bioinformatics

How Microbes Shape Their Communities? A Microbial Community Model Based on Functional Genes – Xiaoqing Jiang – Genomics, Proteomics & Bioinformatics

Phy-PMRFI: Phylogeny-aware Prediction of Metagenomic Functions using Random Forest Feature Importance – Jyotsna Talreja Wassan – IEEE Transactions on NanoBioscience

 

Other

Flood Season Microbiota from the Amazon Basin Lakes: Analysis with Metagenome Sequencing – Célio Dias Santos Júnior – Microbiology Resource Announcements

Genome-resolved metagenomics of an autotrophic thiocyanate-remediating microbial bioreactor consortium – Mathew P. Watts – Water Research

April 24, 2019

Today’s rich Digest features a report on how an invasive fungus restructures bat skin microbiome and a review on how plant-based culture media might come about. How is authorship determined? Enjoy reading!

Human gut microbiome

Review: Gut Microbiota in Alzheimer’s Disease, Depression, and Type 2 Diabetes Mellitus: The Role of Oxidative Stress – Maria Luca et al. – Oxidative Medicine and Cellular Longevity

Cancer microbiome

Review: Exploring the emerging role of the microbiome in cancer immunotherapy – Jessica Fessler & Vyara Matson et al. – Journal for ImmunoTherapy of Cancer

Salivary Microbial Dysbiosis is Associated with Systemic Inflammatory Markers and Predicted Oral Metabolites in Non-Small Cell Lung Cancer Patients – Weiquan Zhang et al. – Journal of Cancer

Metabolomics

Review: Systems Biology and Multi-Omics Integration: Viewpoints from the Metabolomics Research Community – Farhana R. Pinu et al. – Metabolites

BLANKA: an Algorithm for Blank Subtraction in Mass Spectrometry of Complex Biological Samples – Jessica L. Cleary et al. – Journal of The American Society for Mass Spectrometry

Review: Comparative genomics and metagenomics of the metallomes – Yan Zhang et al. – Metallomics

Animal experiments

Analysis of the In Vivo Transcriptome of Bordetella pertussis during Infection of Mice – Ting Y. Wong et al. – mSphere

Structural modulation of gut microbiota reveals Coix seed contributes to weight loss in mice – Sheng Liu et al. – Applied Microbiology and Biotechnology

Supplementation with compound polysaccharides contributes to the development and metabolic activity of young rat intestinal microbiota – Mengxia Wang et al. – Food & Function

Animal microbiome

Closely-related Photobacterium strains comprise the majority of bacteria in the gut of migrating Atlantic cod (Gadus morhua) – Typhaine Le Doujet et al. – Microbiome

Comparative analysis of intestinal bacteria among venom secretion and non-secrection snakes – Zuodong Qin et al. – Scientific Reports

Parallel sequencing of porA reveals a complex pattern of Campylobacter genotypes that differs between broiler and broiler breeder chickens – Frances. M. Colles et al. – Scientific Reports

** Preprint: White-nose syndrome restructures bat skin microbiomes – Meghan A. Ange-Stark et al. – bioRxiv

Food microbiome

Establishment limitation constrains the abundance of lactic acid bacteria in the Napa cabbage phyllosphere – Esther R. Miller et al. – Applied and Environmental Microbiology

Plant, root and soil microbiome

Unprecedented bacterial community richness in soybean nodules vary with cultivar and water status – Hazem Sharaf et al. – Microbiome

Fungi Originating From Tree Leaves Contribute to Fungal Diversity of Litter in Streams – Pirjo Koivusaari et al. – Frontiers in Microbiology

Successional trajectories of soil bacterial communities in mine tailings: The role of plant functional traits – Yannick Colin et al. – Journal of Environmental Management

Elevated CO2, chlorpyrifos and biochar influence nitrification and microbial abundance in the rhizosphere of wheat cultivated in a tropical vertisol – Bharati Kollah et al. – Rhizosphere

Increasing livestock wastewater application in alternate-furrow irrigation reduces nitrification gene abundance but not nitrification rate in rhizosphere – Yuan Liu et al. – Biology and Fertility of Soils

** Review: Culturomics of the plant prokaryotic microbiome and the dawn of plant-based culture media – A review – Mohamed S. Sarhan et al. – Journal of Advanced Research

Water and extremophile microbiome

Coupling growth kinetics modeling with machine learning reveals microbial immigration impacts and identifies key environmental parameters in a biological wastewater treatment process – Ran Mei et al. – Microbiome

Fungal Community Composition and Potential Depth-Related Driving Factors Impacting Distribution Pattern and Trophic Modes from Epi- to Abyssopelagic Zones of the Western Pacific Ocean – Wei Li et al. – Microbial Ecology

Different response of bacteria, archaea and fungi to process parameters in nine full-scale anaerobic digesters – Susanne G. Langer et al. – Microbial Biotechnology

Increasing livestock wastewater application in alternate-furrow irrigation reduces nitrification gene abundance but not nitrification rate in rhizosphere – Yuan Liu et al. – Biology and Fertility of Soils

Oil Hydrocarbon Degradation by Caspian Sea Microbial Communities – John I. Miller et al. – Frontiers in Microbiology

Bacterial Community 16S rRNA Gene Sequencing Characterizes Riverine Microbial Impact on Lake Michigan – Cindy H. Nakatsu et al. – Frontiers in Microbiology

Patterns of bacterial and archaeal communities in sediments in response to dam construction and sewage discharge in Lhasa River – Ke Tao et al. – Ecotoxicology and Environmental Safety

Potentially toxic metal contamination and microbial community analysis in an abandoned Pb and Zn mining waste deposit – M.C. Kasemodel et al. – Science of The Total Environment

Structure and function of microbial community associated with phenol co-substrate in degradation of benzo[a]pyrene in coking wastewater – Haizhen Wu et al. – Chemosphere

Phages and viruses

Distribution and Phylogeny of Erythrocytic Necrosis Virus (ENV) in Salmon Suggests Marine Origin – Veronica A. Pagowski et al. – Viruses

Interaction of RNA viruses of the natural virome with the African malaria vector, Anopheles coluzzii – Ferdinand Nanfack-Minkeu et al. – Scientific Reports

Technology

Active harvesting enhances energy recovery and function of electroactive microbiomes in microbial fuel cells – Lu Lu et al. – Applied Energy

Bioinformatics

Letter to Editor: Towards precision quantification of contamination in metagenomic sequencing experiments – M. S. Zinter et al. – Microbiome

Annotated bacterial chromosomes from frame-shift-corrected long-read metagenomic data – Krithika Arumugam et al. – Microbiome

Review: Evolution of biosequence search algorithms: a brief survey – Gregory Kucherov – Bioinformatics

Microbes in the news

Two new studies reveal universal gut microbiome signatures in colorectal cancer – Andreu Prados – Gut Microbiota for Health

Prime the Pump – Robert B Corbett – Bovine Vet Online

Germ-Killing Brands Now Want to Sell You Germs – Caroline Winter – Bloomberg

Podcast: What is Functional Medicine’s Role In Gut Healing? – The Microbiome Report

Microbes on the market

Viome Raised $25M for its Microbiome-based Dietary Guide Platform – Chris Albrecht – The Spoon

Non-microbiology pick

** Preprint: A qualitative study exploring researchers’ perspectives on authorship decision-making – Lauren A Maggio et al. – bioRxiv

April 17, 2019

Today’s Digest contains quite a few news articles. Features for today include a review on the importance of proper controls in microbiome studies, a patent for one method of analyzing microbiome dynamics (really?), and the NASA Twins Study, how can one year in space change your gut microbiota and much more? Enjoy reading!

General microbiology

Guideline: Microbiology Investigation Criteria for Reporting Objectively (MICRO): a framework for the reporting and interpretation of clinical microbiology data – Paul Turner & Andrew Fox-Lewis et al. – BMC Medicine

** Patent: Method of analyzing microbiome – E Segal & E Elinav

Combined deterministic and stochastic processes control microbial succession in replicate granular biofilm reactors – R Liébana et al. – Environmental Science & Technology

** Uncorrected proof: Issues and current standards of controls in microbiome research – Bastian V.H. Hornung et al. – FEMS Microbiology Ecology

Pregnancy and early life

Review: Intestinal Microbiota in Early Life and Its Implications on Childhood Health – Lu Zhuang et al. – Genomics, Proteomics & Bioinformatics

Cancer microbiome

PDF: Gastric Microbiota in Helicobacter pylori-Negative and -Positive Gastritis Among High Incidence of Gastric Cancer Area – Boldbaatar Gantuya et al. – Cancers

Human respiratory microbiome

Review: Microbes, metabolites, and the gut–lung axis – Anh Thu Dang & Benjamin J. Marsland – Mucosal Immunology

Microbial contributions to bronchial asthma occurrence in children: A metagenomic study – Man Tian et al. – Journal of Cellular Biochemistry

Human gut microbiome

Review: A Review on Bile Acids: Effects of the Gut Microbiome, Interactions with Dietary Fiber, and Alterations in the Bioaccessibility of Bioactive Compounds – Jashbir Singh et al. – Journal of Agricultural and Food Chemistry

Increased mucosal neutrophil survival is associated with altered microbiota in HIV infection – Tiffany Hensley-McBain et al. – PLoS Pathogens

Review: Thinking bigger: How early life environmental exposures shape the gut microbiome and influence the development of asthma and allergic disease – Hind Sbihi et al. – Allergy

** The NASA Twins Study: A multidimensional analysis of a year-long human spaceflight – Francine E. Garrett-Bakelman et al. – Science

Metabolomics

Review: Changes in the Human Metabolome Associated With Alcohol Use: A Review – Taija Voutilainen & Olli Kärkkäinen – Alcohol and Alcoholism

Animal microbiome

Dynamic changes in rumen fermentation and bacterial community following rumen fluid transplantation in a sheep model of rumen acidosis: implications for rumen health in ruminants – Junhua Liu et al. – The FASEB Journal

Rainbow trout (Oncorhynchus mykiss) gut microbiota is modulated by insect meal from Hermetia illucens prepupae in the diet – Genciana Terova et al. – Reviews in Fish Biology and Fisheries

Plant, root and soil microbiome

Effects of mycorrhizae and water conditions on perennial ryegrass growth in rare earth tailings – Qiao Yang et al. – RSC Advance

Niche separation of species of entomopathogenic fungi within the genera Metarhizium and Beauveria in different cropping systems in Mexico – J.A. Cabrera-Mora et al. – Fungal Ecology

Soil abiotic properties and plant functional traits mediate associations between soil microbial and plant communities during a secondary forest succession on the Loess Plateau – Yongfu Chai et al. – Frontiers in Microbiology

Microbial Diversity and Antimicrobial Resistance Profile in Microbiota from Soils of Conventional and Organic Farming Systems – Julija Armalytė et al. – Frontiers in Microbiology

Effects of elevated temperature and elevated CO2 on soil nitrification and ammonia-oxidizing microbial communities in field-grown crop – Linh T.T. Nguyen et al. – Science of The Total Environment

Tropical forest conversion to rubber plantation affects soil micro- & mesofaunal community & diversity – Dharmesh Singh et al. – Scientific Reports

Water and extremophile microbiome

Sulfate reduction by a haloalkaliphilic bench-scale sulfate-reducing bioreactor and its bacterial communities at different depths – Tingzhen Mu et al. – Biochemical Engineering Journal

Extremely acidic environment: Biogeochemical effects on algal biofilms – Ana Teresa Luís et al. – Ecotoxicology and Environmental Safety

Proliferation of hydrocarbon-degrading microbes at the bottom of the Mariana Trench – Jiwen Liu & Yanfen Zheng et al. – Microbiome

Metagenomic insights to understand transient influence of Yamuna River on taxonomic and functional aspects of bacterial and archaeal communities of River Ganges – Rachel Samson et al. – Science of The Total Environment

Distribution of microbial communities in metal-contaminated nearshore sediment from Eastern Guangdong, China – Mei Zhuang et al. – Environmental Pollution

Phages and viruses

Diversities and potential biogeochemical impacts of mangrove soil viruses – Min Jin et al. – Microbiome

Technology

Explore mediated co-varying dynamics in microbial community using integrated local similarity and liquid association analysis – Dongmei Ai et al. – BMC Genomics

Microbes in the news

Can changing the microbiome reverse lactose intolerance? – PATRICIA L. FOSTER – PhillyVoice

A Look at the Trillions of Microorganisms That Live in and on You – Shayla Love – Vice

Mode of delivery alters infants’ gut microbiota and this may impact respiratory health in first year of life – EurekAlert!

Fecal Transplant Reduces Nearly 50 Percent Of Autism Symptoms In Children – Allan Adamson – Tech Times

Edinburgh Science Festival: from gut bacteria and depression to how rice is risking the planet – Helen McArdle – The Herald

Gut microbiome changes emerge as a potential modulator of age-associated cardiovascular disease risk – Andreu Prados – Gut Microbiota for Health

The Gut Microbiome & Cancer Immunotherapy – Osman, Afaf E. G. & Luke, Jason J. – Oncology Times

April 15, 2019

Today’s Monday morning digest covers reviews on different aspects of human microbiome, interesting articles about effects of early life treatments in rodents and news updates on market prediction of microbiome sequencing and therapeutics.

General microbiome

Current understanding of the human microbiome – Jack A Gilbert – Nature Communications

The Importance of the Microbiome in Bariatric Surgery: a Systematic Review – Josianne C. H. B. M. Luijten – Obesity surgery

A potential role for the gut microbiome in substance use disorders – Katherine R. Meckel – Psychopharmacology

The power of small changes: Comprehensive analyses of microbial dysbiosis in breast cancer – Sheetal Parida -Biochimica et Biophysica Acta

The lung microbiome and transplantation –  Alicia B. Mitchell – Current Opinion in Organ Transplantation

Human gut microbiome

Encrustations on ureteral stents from patients without urinary tract infection reveal distinct urotypes and a low bacterial load – Matthias T. Buhmann – Microbiome

Overuse of anti‐anaerobic drug is associated with poor post‐chemotherapy prognosis of patients with hepatocellular carcinoma – Noriho Lida – International Journal of Cancer

Antibiotic-induced shifts in fecal microbiota density and composition during hematopoietic stem cell transplantation – Sejal Morjaria – BioRxiv

Surveillance-embedded genomic outbreak resolution of methicillin-susceptible Staphylococcus aureus in a neonatal intensive care unit – AJH Cremers – BioRxiv

Animal experiments

Antidepressants affect gut microbiota and Ruminococcus flavefaciens is able to abolish their effects on depressive-like behavior – Iva Lukić – Translational Psychiatry

Early life stress induces type 2 diabetes-like features in ageing mice – Hanna Ilchmann-Diounou – Brain, Behavior and Immunity

Early-life vancomycin treatment promotes airway inflammation and impairs microbiome homeostasis – Xin Yang – Aging

Early-life stress, microbiota, and brain development: probiotics reverse the effects of maternal separation on neural circuits underpinning fear expression and extinction in infant rats – Caitlin S.M. Cowan – Developmental Cognitive Neuroscience

Commensal Escherichia coli aggravates acute necrotizing pancreatitis through targeting intestinal epithelial cells – Junyuan Zheng – Applied and Environmental Microbiology

Host-Microbiome Synergistic Control on Sphingolipid Metabolism by Mechanotransduction in Model Arthritis – Xiaoyuan Zhou – Biomolecules

Plant, root, soil microbiome

Bacterial community diversity associated with the severity of bacterial wilt disease in tomato fields in south-east China – Xuefang Zheng – Canadian Journal of Microbiology

Bacterial disease induced changes in fungal communities of olive tree twigs depend on host genotype – Teresa Gomes – Scientific Reports

Co‐inoculation of Bacillus spp. and Pseudomonas putida at different development stages acts as a biostimulant to promote growth, yield and nutrient uptake of tomato – Yanhui He – Journal of Applied Microbiology

Water microbiome and extremophiles

Extant microbial communities in the partially desiccated Rincon de Parangueo maar crater lake in Mexico – Janet Sánchez-Sánchez – Fems Microbiology Ecology

Novosphingobium meiothermophilum sp. nov., isolated from a hot spring – Wen-Dong Xian – International Journal of Systematic and Evolutionary Microbiology

Built Environment

Impacts of Indoor Surface Finishes on Bacterial Viability – Jinglin Hu – Indoor air

Probiotics

Probiotics: If It Does Not Help It Does Not Do Any Harm. Really? – Aaron Lerner – Microorganisms

Effects of Lactobacillus plantarum PS128 on Children with Autism Spectrum Disorder in Taiwan: A Randomized, Double-Blind, Placebo-Controlled Trial – Yen-Wenn Liu – Nutrients

Microbes in the news

Global Human Microbiome Therapeutics Market Outlook 2019-2024: ENTEROME Bioscience, Rebiotix, Seres Therapeutics – NewsPrimo

Caesarean babies slower to acquire ‘good’ gut bacteria: study – PanArmenian Net

Mode of delivery has substantial impact on infants’ health – Business Standard

Newborn’s ‘Microbiome’ Could Give Clues to Weight Later – Doctors Lounge

Microbiome Sequencing Services Market is expected to grow at a CAGR of 18% during the forecast period of (2018 – 2023) – Redfield Report

Human Microbiome Market boosting the growth Worldwide – Business Herald

April 13, 2019

In today’s digest read about diverse population of bacteria and fungi on the International Space Station, how antidepressants affect gut microbiota, and check out a new framework for comparing and assessing taxonomic profilers (OPAL). Happy weekend!

Vaginal microbiome

Defining characteristics of genital health in South African adolescent girls and young women at high risk for HIV infection – Smritee Dabee – PlosOne

Detection of ureaplasmas and bacterial vaginosis associated bacteria and their association with non-gonococcal urethritis in men – Maria Frølund – PlosOne

Group B streptococcal screening, intrapartum antibiotic prophylaxis, and neonatal early-onset infection rates in an Australian local health district: 2006-2016 – Kathryn Braye – PlosOne

Gut microbiome

Long-term benefit of Microbiota Transfer Therapy on autism symptoms and gut microbiota – Dae-Wook Kang – Scientific Reports

The Prevotella copri complex comprises four distinct clades that are underrepresented in Westernised populations – Adrian Tett – bioRxiv

Fecal short-chain fatty acids are not predictive of colonic tumor status and cannot be predicted based on bacterial community structure – Marc A. Sze – bioRxiv

Evidence for a multi-level trophic organization of the human gut microbiome – Tong Wang – bioRxiv

Animal microbiome

Comparative analysis of amplicon and metagenomic sequencing methods reveals key features in the evolution of animal metaorganisms – Philipp Rausch – bioRxiv

Metagenomic Analysis of the Whole Gut Microbiota in Brazilian Termitidae Termites Cornitermes cumulans, Cyrilliotermes strictinasus, Syntermes dirus, Nasutitermes jaraguae, Nasutitermes aquilinus, Grigiotermes bequaerti, and Orthognathotermes mirim – Maria B. Grieco – Current Microbiolgy

The sponge microbiome within the greater coral reef microbial metacommunity – Daniel F. R. Cleary – Nature Communications

Insights into the intestinal microbiota of several aquatic organisms and association with the surrounding environment – Fulin Sun – Aquaculture

Animal experiments

*Antidepressants affect gut microbiota and Ruminococcus flavefaciens is able to abolish their effects on depressive-like behavior – Iva Lukić – Translational Psychiatry

Chronic paradoxical sleep deprivation-induced depression­like behavior, energy metabolism and microbial changes in rats – Weini Ma – Life Sciences

Ability of bifidobacteria to metabolize chitin-glucan and its impact on the gut microbiota – Giulia Alessandri – Scientific Reports

Probiotics

Fasting breath H2 and gut microbiota metabolic potential are associated with the response to a fermented milk product in irritable bowel syndrome – Boris Le Nevé – PlosOne

Lactobacillus fermentum and Lactobacillus plantarum increased gut microbiota diversity and functionality, and mitigated Enterobacteriaceae, in a mouse model – C. Linninge – Beneficial Microbes

Complex responses to inflammatory oxidants by the probiotic bacterium Lactobacillus reuteri – Poulami Basu Thaku – bioRxiv

Plant/root/soil microbiome

Urban traffic changes the biodiversity, abundance, and activity of phyllospheric nitrogen-fixing bacteria – Yang Li – Environmental Science and Pollution Research

Comparative analysis of the rhizomicrobiome of the wild versus cultivated crop: insights from rice and soybean – Shaohua Shi – Archives of Microbiology

Copper and zinc in rhizospheric soil of wild plants growing in long-term acid vineyard soils – C.Campillo-Cora – Science of The Total Environment

Review: Soil microbiome: a key player for conservation of soil health under changing climate – Anamika Dubey – Biodiversity and Conservation

Rhizosphere microbiota compositional changes reflect potato blackleg disease – Lutian Mao – Applied Soil Ecology

Pseudomonas urumqiensis sp. nov., isolated from rhizosphere soil of Alhagi sparsifolia – Yuanyuan Zou – International Journal of Systematic and Evolutionary Microbiology

Insights gained from metagenomic shotgun sequencing of apple fruit epiphytic microbiota – Dario Angeli – Postharvest Biology and Technology

Extremophile microbiome

*Characterization of the total and viable bacterial and fungal communities associated with the International Space Station surfaces – Aleksandra Checinska Sielaff – Microbiome

Techniques

Review: Untargeted LC/MS-based metabolic phenotyping (metabonomics/metabolomics): The state of the art – Helen Gika – Journal of Chromatography B

Bioinformatics

*Assessing taxonomic metagenome profilers with OPAL – Fernando Meyer – Genome Biology

Analysis of error profiles in deep next-generation sequencing data – Xiaotu Ma – Genome Biology

clonealign: statistical integration of independent single-cell RNA and DNA sequencing data from human cancers – Kieran R. Campbell – Genome Biology

RnBeads 2.0: comprehensive analysis of DNA methylation data – Fabian Müller – Genome Biology

Review: Big data analytics for personalized medicine – Davide Cirillo and Alfonso Valencia – Current Opinion in Biotechnology

Meta-network: optimized species-species network analysis for microbial communities – Pengshuo Yang – BMC Genomics