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

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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

March 28, 2019

Today’s digest covers interesting reviews on different aspects of host-microbiome interactions, research articles about how structural variation in gut microbiome affects host health, characterization of a simplified microbial community to study microbial interaction with diet in mice and viral diversity in soil metagenomes. Happy reading!

General microbiome

Review – Microbiome: Our opponents or allies in healthcare and medicine – Horst A von Recum – Experimental Biology and Medicine

Review –  To B12 or not to B12: Five questions on the role of cobalamin in host-microbial interactions – Carol A. Rowley – Plos Pathogens

Review – Can oral bacteria affect the microbiome of the gut? – Ingar Olsen – Journal of Oral Microbiology

Review –  Inter-kingdom signaling between gut microbiota and their host – Qing Li – Cellular and Molecular Life Sciences

Human gut microbiome

Structural variation in the gut microbiome associates with host health – David Zeevi – Nature

Effects of fermentable high fiber diet supplementation on gut derived and conventional nitrogenous product in patients on maintenance hemodialysis: a randomized controlled trial – Hamid Tayebi Khosroshahi – Nutrition and Metabolism

Identification of the microbial diversity after fecal microbiota transplantation therapy for chronic intractable constipation using 16s rRNA amplicon sequencing – Tadashi Ohara – PlosOne

The microbiome and tuberculosis: state of the art, potential applications, and defining the clinical research agenda – Charissa C Naidoo – Lancet Respiratory medicine

Fecal Microbiota Transplantation: An Update on Clinical Practice – Kyeong Ok Kim – Clinical Endoscopy

Aryl hydrocarbon receptor and uremic toxins from gut microbiota in chronic kidney disease patients: Is there a relationship? – Jessyca Brito – Biochemistry

Animal experiments

Bacterial AB5 toxins inhibit the growth of gut bacteria by targeting ganglioside-like glycoconjugates – Robert T. Patry – Nature Communications

Simplified Intestinal Microbiota to Study Microbe-Diet-Host Interactions in a Mouse Model – Petia Kovatcheva-Datchary – Cell Reports

Pomegranate ellagitannin-gut microbial-derived metabolites, urolithins, inhibit neuroinflammation in vitro – Nicholas A. DaSilva – Nutritional Neuroscience

Endogenous Enterobacteriaceae underlie variation in susceptibility to Salmonella infection – Eric M. Velazquez – Nature Microbiology

Plant, root, soil microbiome

Thickness determines microbial community structure and function in nitrifying biofilms via deterministic assembly – Carolina Suarez – Scientific Reports

Untapped viral diversity in global soil metagenomes – Emily B. Graham – BioRxiv

Water microbiome and extremophiles

Fate of antibiotic resistance genes in two Arctic tundra wetlands impacted by municipal wastewater – Jennifer L. Hayward – Science of the Total Environment

Probiotics

Importance of probiotics in the prevention and treatment of colorectal cancer – Majid Eslami – Journal of Cellular Physiology

Non-microbiology picks

Artificial womb technology breaks its four minute mile – Science Daily

March 14, 2019

Today’s digest covers interesting reviews on microbiota for immunotherapies, non-digestible carbohydrates for infant microbiota and contribution of marine microbiota in reactive oxygen species; research articles on how gluten sensitivity is affected by duodenal microbiota and how ginger intake affects mouse microbiota.

General microbiome

Review: Mining the microbiota for microbial and metabolite-based immunotherapies – Ashwin N. Skelly – Nature Reviews Immunology

Pregnancy and early life microbiome

Relationship between vitamin D status and the vaginal microbiome during pregnancy – Kimberly K. Jefferson – Journal of Perinatology

Review: Shaping the Infant Microbiome With Non-Digestible Carbohydrates – Stella A. Verkhnyatskaya – Frontiers in Microbiology

Variations in early gut microbiome are associated with childhood eczema – Yu Zhang – FEMS Microbiology Letters

Human gut microbiome

Gut microbiota in HIV–pneumonia patients is related to peripheral CD4 counts, lung microbiota, and in vitro macrophage dysfunction – Meera K. Shenoy – Microbiome

Effects of bowel preparation on the human gut microbiome and metabolome – Naoyoshi Nagata – Scientific Reports

Human colon mucosal biofilms from healthy or colon cancer hosts are carcinogenic – Sarah Tomkovich – The Journal of Clinical Investigation

Animal experiments

Host NLRP6 exacerbates graft-versus-host disease independent of gut microbial composition – Tomomi Toubai – Nature Microbiology

Duodenal bacterial proteolytic activity determines sensitivity to dietary antigen through protease-activated receptor-2 – Alberto Caminero – Nature Communications

The dynamics of the antibiotic resistome in the feces of freshly weaned pigs following therapeutic administration of oxytetracycline – Mahdi Ghanbari – Scientific Reports

Beneficial effects of ginger on prevention of obesity through modulation of gut microbiota in mice – Jing Wang – European Journal of Nutrition

Six‐Week High‐Fat Diet Alters the Gut Microbiome and Promotes Cecal Inflammation, Endotoxin Production, and Simple Steatosis without Obesity in Male Rats – Melisa Crawford – Lipids

Gut microbiome structure and adrenocortical activity in dogs with aggressive and phobic behavioral disorders – Elisabetta Mondo – BioRxiv

The gut microbiota regulates mouse biliary regenerative responses – Wenli Liu – BioRxiv

Plant, root, soil microbiome

Consistent bacterial selection by date palm root system across heterogeneous desert oasis agroecosystems – Maria J. Mosqueira – Scientific Reports

Bacterial fermentation and respiration processes are uncoupled in anoxic permeable sediments – Adam J. Kessler – Nature Microbiology

Effects of graphene oxide and graphite on soil bacterial and fungal diversity – Christian Forstner – BioRxiv

Water microbiome and extremophiles

Review: The microbial contribution to reactive oxygen species dynamics in marine ecosystems – Erik R. Zinser – Environmental Microbiology Reports

Non-microbiology picks

Nano-bot can probe inside human cells – Science Daily

February 27, 2019

Today’s short digest covers articles on bacterial interaction with intestinal cells, semen microbiome and how microbiota affects insulin reactive immune cells.

General microbiome

The founder hypothesis: A basis for microbiota resistance, diversity in taxa carriage, and colonization resistance against pathogens – Yael Litvak -Plos Pathogens

Review : Impact of the gut microbiome on the genome and epigenome of colon epithelial cells: contributions to colorectal cancer development – Jawara Allen – Genome Medicine

Paneth cell granule dynamics on secretory responses to bacterial stimuli in enteroids – Yuki Yokoi – Scientific Reports

Human gut microbiome

Altered immunity and microbial dysbiosis in aged individuals with long-term controlled HIV infection – Nicholas S. Rhoades – Frontiers in Immunology

Bacterial viability in faecal transplants: Which bacteria survive? – Lito E. Papanicolas – EbioMedicine

Semen Microbiome Biogeography: An Analysis Based on a Chinese Population Study – Zhanshan Ma – Frontiers in Microbiology

Animal experiments

The effects of unfermented and fermented cow and sheep milk on the gut microbiota – Elizabeth Rettedal – Frontiers in Microbiology

Altered Gut Microbiota Activate and Expand Insulin B15-23-Reactive CD8+ T-Cells – James A. Pearson – Diabetes

Lactobacillus plantarum PFM 105 Promotes Intestinal Development Through Modulation of Gut Microbiota in Weaning Piglets – Tianwei Wang – Frontiers in Microbiology

Water microbiome and extremophiles

Microbial residence time is a controlling parameter of the taxonomic composition and functional profile of microbial communities – Cresten Mansfeldt – ISME Journal

Microbial community structure and functionality in the deep sea floor: evaluating the causes of spatial heterogeneity in a submarine canyon system (NW Mediterranean, Spain) – Sara Román – Frontiers in Marine Science

Non-microbiology picks

Dual AAV-mediated gene therapy restores hearing in a DFNB9 mouse model – Omar Akil – PNAS

 

January 31, 2019

Today’s digest covers articles describing sphingolipids in host-microbiome interaction, unique microbiome and metabolome of Indian population, selection and stabilization of soil microbiome and effect of probiotics on early sepsis in patients and immune response in childrenEnjoy reading!

General microbiome

Metabolic Modeling of Human Gut Microbiota on a Genome Scale: An Overview – Partho Sen – Metabolites

Altered composition and function of intestinal microbiota in autism spectrum disorders: a systematic review – Feitong Liu – Translational Psychiatry

Sphingolipids in host–microbial interactions – Stacey L. Heaver – Current Opinion in Microbiology

Pregnancy and early life

Mixed Viral-Bacterial Infections and Their Effects on Gut Microbiota and Clinical Illnesses in Children – Shilu Mathew – Scientific Reports

Pathways linking caesarean delivery to early health in a dual burden context: Immune development and the gut microbiome in infants and children from Galápagos, Ecuador – Amanda L. Thompson – American Journal of Human Biology

Human gut microbiome

The vagino-cervical microbiome as a woman’s life history – Zhuye Jie – BioRxiv

Dynamics of Human Gut Microbiota and Short-Chain Fatty Acids in Response to Dietary Interventions with Three Fermentable Fibers – Nielson T. Baxter – mBio

The unique composition of Indian gut microbiome, gene catalogue and associated faecal metabolome deciphered using multi-omics approaches – D.B. Dhakan – Gigascience

Animal experiments

Oral neonatal antibiotic treatment perturbs gut microbiota and aggravates central nervous system autoimmunity in Dark Agouti rats – Suzana Stanisavljević – Scientific Reports

Intestinal epithelial N-acylphosphatidylethanolamine phospholipase D links dietary fat to metabolic adaptations in obesity and steatosis – Amandine Everard – Nature Communications

Mutual interplay between IL-17–producing γδT cells and microbiota orchestrates oral mucosal homeostasis – Anneke Wilharm – PNAS

Plant, root and soil microbiome

Selection, succession and stabilization of soil microbial consortia – Elias K. Zegeye – BioRxiv

Comparison of the bacterial and methanotrophic diversities between an Italian paddy field and its neighboring meadow – Mohammad Ghashghavi – BioRxiv

Quality of Irrigation Water Affects Soil Functionality and Bacterial Community Stability in Response to Heat Disturbance – Sammy Frenk – Applied and Environmental Microbiology

Water and extremophiles microbiome

Archaea dominate the microbial community in an ecosystem with low-to-moderate temperature and extreme acidity – Aleksei A. Korzhenkov – Microbiome

Antibiotic disturbance affects aquatic microbial community composition and foodweb interactions but not community resilience – Ester M. Eckert – Molecular Ecology

 Phages and viruses

Megaphages infect Prevotella and variants are widespread in gut microbiomes – Audra E. Devoto – Nature Microbiology

Probiotics / prebiotics

Dysbiosis in early sepsis can be modulated by a multispecies probiotic: a randomised controlled pilot trial – V. Stadlbauer – Beneficial Microbes

Lactobacillus plantarum IS-10506 supplementation increases faecal sIgA and immune response in children younger than two years – P.D. Kusumo – Beneficial Microbes

Supplementation with Lactobacillus kefiranofaciens ZW3 from Tibetan Kefir improves depression-like behavior in stressed mice by modulating the gut microbiota – Ye Sun – Food and Function

Non-microbiology picks

Identification of Enteroendocrine Regulators by Real-Time Single-Cell Differentiation Mapping – Helmuth Gehart – Cell

January 24, 2019

Today’s digest covers interesting reviews on microbiome and microbial metabolites, and research articles showing bacteria in meconium, how host and microbial factors affect host physiology and mechanistic insight into role of microbiota in alleviation of intestinal inflammation.

General microbiome

Review: Role of the microbiome in human development – Maria Gloria Dominguez-Bello – Gut

Review: The role of the intestinal microbiota in uremic solute accumulation: a focus on sulfur compounds – Alessandra F. Perna – Journal of Nephrology

Review: Gut microbial metabolites in obesity, NAFLD and T2DM – Emanuel E. Canfora – Nature Reviews Endocrinology

Pregnancy and early life

Characterisation of the bacterial microbiome in first‐pass meconium using propidium monoazide (PMA) to exclude non‐viable bacterial DNA – Lisa F. Stinson – Letters in Applied Microbiology

Perinatal antibiotics alter preterm infant EEG and neurobehavior in the Family Nurture Intervention trial – Morgan R. Firestein – Developmental Psychobiology

Altered gut microbiota and short chain fatty acids in Chinese children with autism spectrum disorder – Simeng Liu – Scientific Reports

Human gut microbiome

Gut microbiota density influences host physiology and is shaped by host and microbial factors – Eduardo J. Contijoch – Elife

The Crohn’s disease polymorphism, ATG16L1 T300A, alters the gut microbiota and enhances the local Th1/Th17 response – Sydney Lavoie – Elife

Alterations in the intestinal microbiota of patients with severe and active Graves’ orbitopathy: a cross-sectional study – T. T. Shi – Journal of Endocrinological Investigation

Fecal microbiota transplantation for treatment of recurrent C. difficile infection: An updated randomized controlled trial meta-analysis – Wenjia Hui – PlosOne

Evolutionary dynamics of bacteria in the gut microbiome within and across hosts – Nandita R. Garud – PlosBiology

MicroRNA-Mediated Tumor–Microbiota Metabolic Interactions in Colorectal Cancer – Ce Yuan – DNA and Cell Biology

Modulation of the Gut Microbiota by Resistant Starch as a Treatment of Chronic Kidney Diseases: Evidence of Efficacy and Mechanistic Insights – Matthew Snelson – Advances in Nutrition

Animal experiments

Microbiota fermentation-NLRP3 axis shapes the impact of dietary fibres on intestinal inflammation Vishal Singh – Gut

A high linoleic acid diet exacerbates metabolic responses and gut microbiota dysbiosis in obese rats with diabetes mellitus – Hsiu-Chuan Lee – Food and Function

Gut microbiota profiling with differential tolerance against the reduced dietary fibre level in rabbit – Shi-Yi Chen – Scientific Reports

Novel strains of Bacteroides fragilis and Bacteroides ovatus alleviate the LPS-induced inflammation in mice – Huizi Tan – Applied Microbiology and Biotechnology

Water and extremophile microbiome

Consistency in microbiomes in cultures of Alexandrium species isolated from brackish and marine waters – Eva Sörenson – Environmental Microbiology Reports

Probiotics / prebiotics

Review: Beneficial Effects of Probiotic Consumption on the Immune System – C. Maldonado Galdeano – Annals of Nutrition and Metabolism

Microbes on the market

Ferring, Rebiotix and Karolinska Institutet Extend Collaboration to Research Next Generation of Microbiome Treatments – Microbiome Times

Non-microbiology picks

Those with inadequate access to food likely to suffer from obesity – Science Daily