August 24, 2019

This weekend, read about the microbial index of skin health for children with eczema, gut microbiome of koalas, and interactions between the gut bacterial microbiome and virome of rhesus monkey. Happy reading!

General microbiome

Why we need a small data paradigm – Eric B. Hekler – BMC Medicine

Correspondence: The importance of genome sequence quality to microbial comparative genomics – Theo H. M. Smits – BMC Genomics

The applications of Big Data in molecular diagnostics – Yin Kwan Evelyn Wong – Expert Review of Molecular Diagnostics

Tiny Hidden Genes within Our Microbiome – Karin Mittelman & David Burstein – Cell

Skin microbiome

*A Microbiome-Based Index for Assessing Skin Health and Treatment Effects for Atopic Dermatitis in Children – Zheng Sun – mSystems

Gut microbiome

Reproducible changes in the gut microbiome suggest a shift in microbial and host metabolism during spaceflight – Peng Jiang – Microbiome

Review: Gut Microbiota, Dietary Phytochemicals, and Benefits to Human Health – Ran Yin – Current Pharmacology Reports

Mild cognitive impairment has similar alterations as Alzheimer’s disease in gut microbiota – Binyin Li – Alzheimer’s & Dementia

Design of synthetic microbial consortia for gut microbiota modulation – Jorge F. Vázquez-Castellanos – Current Opinion in Pharmacology

Intestinal microbiota and colorectal cancer: changes in the intestinal microenvironment and their relation to the disease – Sandra Aparecida dos Reis – Journal of Medical Microbiology

Review: Celiac disease: a comprehensive current review – Giacomo Caio – BMC Medicine

Pregnancy and early life

Maternal IgA protects against the development of necrotizing enterocolitis in preterm infants – Kathyayini P. Gopalakrishna – Nature Medicine

Oral microbiome

Oral Microbiome and Cancer Therapy-Induced Oral Mucositis – Jean-Luc C Mougeot – JNCI Monographs

Respiratory microbiome

Deciphering the Ecology of Cystic Fibrosis Bacterial Communities: Towards Systems-Level Integration – Annamaria Bevivino – Trends in Molecular Medicine

Water and extremophile microbiome

Effects of water recirculation rate on the microbial community and water quality in relation to the growth and survival of white shrimp (Litopenaeus vannamei) – Zhao Chen – BMC Microbiology

Pseudomethylobacillus aquaticus gen. nov., sp. nov., a new member of the family Methylophilaceae isolated from an artificial reservoir – Ceshing Sheu – International Journal of Systematic and Evolutionary Microbiology

Bacterial Communities from Extreme Environments: Vulcano Island – Camilla Fagorzi – Diversity

Diversity and biogeography of SAR11 bacteria from the Arctic Ocean – Susanne Kraemer – bioRxiv

Review: Metal and organic pollutants bioremediation by extremophile microorganisms – Patricia Giovanella – Journal of Hazardous Material

Animal microbiome

*Faecal inoculations alter the gastrointestinal microbiome and allow dietary expansion in a wild specialist herbivore, the koala – Michaela D. J. Blyton – Animal microbiome

Impact of pine leaf biochar amendment on bacterial dynamics and correlation of environmental factors during pig manure composting – Jiao Li – Bioresource Technology

Animal experiment

Potential roles of gut microbiome and metabolites in modulating ALS in mice – Eran Blacher – Nature

Plant microbiome

Shared mycorrhizae but distinct communities of other root-associated microbes on co-occurring native and invasive maples – Tonia DeBellis – PeerJ

Non-target Effects of Trichoderma on Plants and Soil Microbial Communities – Monika Jangi – Plant Microbe Interface

Inhibitory and nutrient use phenotypes among co‐existing Fusarium and Streptomyces populations suggest local coevolutionary interactions in soil – Adil Essarioui – Environmental Microbiology

Phages and viruses

*The altered gut virome community in rhesus monkeys is correlated with the gut bacterial microbiome and associated metabolites – Heng Li – Virology Journal

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July 9, 2019

Today’s digest features an overview of the “microbiota–nutrient metabolism–epigenetics” axis, a study on the human bile microbiota, an interesting selection of probiotics studies, and more. Check out the new Everything Hertz podcast episode “Improving the scientific poster”. Happy reading/listening!

Gut microbiome

*Epigenetic Regulation at the Interplay Between Gut Microbiota and Host Metabolism – Joan Miro-Blanch and Oscar Yanes – Frontiers in Genetics

Microbiome and type 1 diabetes – Heli Siljander – EBioMedicine

Framework for rational donor selection in fecal microbiota transplant clinical trials – Claire Duvallet – medRxiv

A calcium-rich multi-mineral intervention to modulate colonic microbial communities and metabolic profiles in humans: Results from a 90-day trial – Muhammad N. Aslam – medRxiv

*The human gallbladder microbiome is related to the physiological state and the biliary metabolic profile – Natalia Molinero – Microbiome

Oral microbiome

Microbial differences between dental plaque and historic dental calculus are related to oral biofilm maturation stage – Irina M. Velsko – Microbiome

Respiratory microbiome

Microbial Composition of the Human Nasopharynx Varies According to Influenza Virus Type and Vaccination Status – Tao Ding – mBio

Skin microbiome

Trait-based analysis of the human skin microbiome – Sharon Bewick – Microbiome

Probiotics

Intermittent Lactobacilli-containing Vaginal Probiotic or Metronidazole Use to Prevent Bacterial Vaginosis Recurrence: Safety and Preliminary Efficacy by Microscopy and Sequencing – Janneke H.H.M. van de Wijgert – medRxiv

Impact of spray‐drying on the pili of Lactobacillus rhamnosus GG – Shari Kiekens – Microbial Biotechnology

The Probiotic Mixture VSL#3 Reverses Olanzapine-Induced Metabolic Dysfunction in Mice – Navneet Dhaliwal – Psychiatric Disorders

Prophylactic Effects of Bifidobacterium adolescentis on Anxiety and Depression-Like Phenotypes After Chronic Stress: A Role of the Gut Microbiota-Inflammation Axis – Ying Guo – Frontiers in Behavioral Neuroscience

Water microbiome

Active eukaryotes in drinking water distribution systems of ground and surface waterworks – Jenni Inkinen – Microbiome

Detection of introduced and resident marine species using environmental DNA metabarcoding of sediment and water – Luke E. Holman – bioRxiv

Plant/root/soil microbiome

Microscale interactions between immigrant bacteria and plant leaf microbiota as revealed by live imaging – Shifra Steinberg – bioRxiv

Soil bacterial populations are shaped by recombination and gene-specific selection across a meadow – Alexander Crits-Christoph – bioRxiv

Bioinformatics

DeepMicrobes: taxonomic classification for metagenomics with deep learning – Qiaoxing Liang – bioRxiv

Misclassification of a whole genome sequence reference defined by the Human Microbiome – DJ Darwin R. Bandoy – medRxiv

CarboLogR: a Shiny/R application for statistical analysis of bacterial utilisation of carbon sources – Kevin Vervier – bioRxiv

Using collaboration networks to identify authorship bias in meta-analyses – Thiago C. Moulin and Olavo B. Amaral – medRxiv

Podcast

*Episode 87: Improving the scientific poster (with Mike Morrison) – Dan Quintana and James Heathers – Everything Hertz

A terrific interview with @mikemorrison about the Better Poster format and UX design principles in science.

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

June 22, 2019

Have a nice Saturday! Today, in this Digest: A set of reviews about the relationship between the microbiome and autism-related complications, Helicobacter infection, non-alcoholic fatty liver disease and hypertension; a study about potential microbiome changes on fibromyalgia, the microbiota of milk in primates, the relationship between genomic and microbiome content in pigs and an interesting report about the effect of microbiota on cirrhosis-associated neuroinflammation.

 

Human and General Microbiome

Review: Can we reduce autism-related gastrointestinal and behavior problems by gut microbiota based dietary modulation? A review – Nalan Hakime Nogay – Nutritional Neuroscience

Review: A Novel View of Human Helicobacter pylori Infections: Interplay between Microbiota and Beta-Defensins – Raffaela Pero – Biomolecules

Review: Fecal Microbial Transplantation For Diseases Beyond Recurrent Clostridium Difficile Infection – Geert R. D’Haens – Gastroenterology

Review: Microbiota and nonalcoholic fatty liver disease: promising prospects for clinical interventions? – Christelle Knudsen – Current Opinion in Clinical Nutrition and Metabolic Care

Review: Impaired Autonomic Nervous System-Microbiome Circuit in Hypertension – Jasenka Zubcevic – Circulation Research

Altered microbiome composition in individuals with fibromyalgia – Amir Minerbi – Pain

Controlling intestinal colonization of high-risk haematology patients with ESBL-producing Enterobacteriaceae: a randomized, placebo-controlled, multicentre, Phase II trial (CLEAR) – Vassiliki Dimitriou – The Journal of Antimicrobial Chemotherapy

Editorial: Microbiota and the clock: sexual dimorphism matters! – Benjamin D. Weger – Aging

Microbiomes, Community Ecology, and the Comparative Method – Sarah M. Hird – mSystems

Technology Feature: Engineers embrace microbiome messiness – Vivien Marx – Nature Methods

Urolithin B suppresses tumor growth in hepatocellular carcinoma through inducing the inactivation of Wnt/β-catenin signaling – Min‐yi Lv – Journal of Cellular Biochemistry

 

Animal Microbiome / Animal Experiments

Diversity and temporal dynamics of primate milk microbiomes – Carly R. Muletz‐Wolz – American Journal of Primatology

Association between the pig genome and its gut microbiota composition – Daniel Crespo-Piazuelo – Scientific Reports

Misoprostol protects mice against severe Clostridium difficile infection and promotes recovery of the gut microbiota after antibiotic perturbation – Joseph P. Zackular – Anaerobe

Neuroinflammation in Murine Cirrhosis is Dependent on the Gut Microbiome and is Attenuated by Fecal Transplant – Runping Liu – Hepatology

Modulation of Lactobacillus acidophilus KLDS 1.0738 on intestinal SCFAs metabolism and GPR41/43 expression in β-lactoglobulin-sensitized mice – Jun‐juan Wang – Microbiology and Immunology

Effect of a proanthocyanidin-rich polyphenol extract from avocado on the production of amino acid-derived bacterial metabolites and the microbiota composition in rats fed a high-protein diet – María José Cires – Food & Nutrition

Environmental microcystin targets the microbiome and increases the risk of intestinal inflammatory pathology via NOX2 in underlying murine model of Nonalcoholic Fatty Liver Disease – Sutapa Sarkar – Scientific Reports

Probiotic supplementation improves the cognitive function and the anxiety-like behaviors in the stressed rats Mahsa Hadizadeh – Iranian Journal of Basic Medical Sciences

 

Bioinformatics

MetaNN: accurate classification of host phenotypes from metagenomic data using neural networks – Chieh Lo – BMC Bioinformatics

Screening methods for detection of ancient Mycobacterium tuberculosis complex fingerprints in next-generation sequencing data derived from skeletal samples – Paulina Borówka – Gigascience

May 28, 2019

Today’s digest is about metaproteomics in microbial communities, infant and child microbiome and association with diseases, coral ecosphere, microbial biospherics and updates on new techniques to analyze microbiome sequencing data.

General microbiome

Metaproteomics: Much More than Measuring Gene Expression in Microbial Communities – Manuel Kleiner – mSystems

Associational effects in the microbial neighborhood – Anja Worrich – ISME Journal

Uncovering complex molecular networks in host–pathogen interactions using systems biology – Joshua M. Peters – Emerging Topics in Life Sciences

Human microbiome

The skin microbiome of vertebrates – Ashley A. Ross – Microbiome

Patterns in the longitudinal oropharyngeal microbiome evolution related to ventilator-associated pneumonia – Rami Sommerstein – Antimicrobial Resistance & Infection Control

Microbial composition of the human nasopharynx varies according to influenza virus type and vaccination status – Tao Ding -BioRxiv

Cytometric fingerprints of gut microbiota predict Crohn’s disease state – Peter Rubbens – BioRxiv

Dynamic colonization of microbes and their functions after fecal microbiota transplantation for inflammatory bowel disease – Nathaniel D. Chu – BioRxiv

Pregnancy and infant microbiome

Paediatrician’s perspective of infant gut microbiome research: current status and challenges – Paul MacDaragh Ryan – Archives of Disease in Childhood

The Salivary Microbiome Is Altered in Children With Eosinophilic Esophagitis and Correlates With Disease Activity – Hiremath Girish – Clinical and Translational Gastroenterology

Influence of own mother’s milk and different proportions of formula on intestinal microbiota of very preterm newborns – Adriana Zanella – PlosOne

Influence of a Serratia marcescens outbreak on the gut microbiota establishment process in low-weight preterm neonates – Esperanza Escribano – PlosOne

Reviewing the evidence on breast milk composition and immunological outcomes – Alba Boix-Amorós – Nutrition Reviews

Characterization of Stool Virome in Children Newly Diagnosed With Moderate to Severe Ulcerative Colitis – Rafal Tokarz – Inflammatory Bowel Diseases

Animal experiments

Effect of intestinal tapeworms on the gut microbiota of the common carp, Cyprinus carpio – Pei P. Fu – Parasites and Vectors

Comparison of Bacterial Populations in the Ceca of Swine at Two Different Stages and their Functional Annotations – Himanshu Kumar – Genes

Toll‐like receptor 2 and toll‐like receptor 4 responses regulate neutrophil infiltration into the junctional epithelium and significantly contribute to the composition of the oral microbiota – Ana M. Chang – Journal of Periodontology

Plant, root, soil microbiome

Mediterranean grassland soil C–N compound turnover is dependent on rainfall and depth, and is mediated by genomically divergent microorganisms – Spencer Diamond – Nature Microbiology

Rhizosphere microbiomes diverge among Populus trichocarpa plant-host genotypes and chemotypes, but it depends on soil origin – Allison M. Veach – Microbiome

Microbial community drivers of PK/NRP gene diversity in selected global soils – Chiara Borsetto – Microbiome

Decreased temporary turnover of bacterial communities along soil depth gradient during a 35-year grazing exclusion period in a semiarid grassland – Chao Zhang – Geoderma

Soil bacterial community dynamics following surfactant addition and bioaugmentation in pyrene-contaminated soils – D.C.Wolf – Chemosphere

Structural and Functional Responses of Soil Microbial Communities to Biodegradable Plastic Film Mulching in Two Agroecosystems – Sreejata Bandopadhyay – BioRxiv

Ecological and genomic attributes of novel bacterial taxa that thrive in subsurface soil horizons – Tess E. Brewer – BioRxiv

Water microbiome and extremophiles

The coral ecosphere: A unique coral reef habitat that fosters coral–microbial interactions – Laura Weber – Limnology and Oceanography

Tide driven microbial dynamics through virus-host interactions in the estuarine ecosystem – Xiaowei Chen – Water Research

Microbial biofilm formation and community structure on low-density polyethylene microparticles in lake water microcosms – Mengting Gong – Environmental Pollution

Diversity and relative abundance of ammonia- and nitrite-oxidizing microorganisms in the offshore Namibian hypoxic zone – Evan Lau – PlosOne

Consistent metagenome-derived metrics verify and define bacterial species boundaries – Matthew R. Olm – BioRxiv

Techniques

Competitive interaction with keystone taxa induced negative priming under biochar amendments – Lijun Chen – Microbiome

Strengthening Insights in Microbial Ecological Networks from Theory to Applications – Xiaofei Lv – mSystems

Microbial biospherics: The experimental study of ecosystem function and evolution Matthias C. Rillig – PNAS

NUFEB: A Massively Parallel Simulator for Individual-based Modelling of Microbial Communities – Bowen Li – BioRxiv

Detecting interaction networks in the human microbiome with conditional Granger causality – Kumar Mainali – Plos Computational Biology

M1CR0B1AL1Z3R—a user-friendly web server for the analysis of large-scale microbial genomics data – Oren Avram – Nucleic Acids Research

End-to-end assessment of fecal bacteriome analysis: from sample processing to DNA sequencing and bioinformatics results – Ana Paula Christoff – BioRxiv

Microbiome in news

Antibiotics may help curb Alzheimer’s symptoms – Medical News Today

SANISCALP®, to preserve the Microbiome for a soothed and healthy scalp! – Cosmetics desgin.com – Mamamia

Mother Dirt Expands Biome-Friendly Skincare Range With New Body Care Line – Mid Daily News

Microbes and the market

Global Microbiome Drugs Market Forecast 2019-2025: MaaT Pharma, Pfizer, Second Genome, Seres Therapeutics – Technology Market

Microbiome Therapeutics Market 2019 – By Future Growth, Trends Plans, Top Key Players, Business Opportunities, Region, Pricing Analysis, Opportunities and Forecast to 2024 – Norwalk Daily

Global Human Microbiome Modulators Market Report 2019: Trends and Opportunities for the Business Prediction over 2024 – Current News Magazine

Microbiome Sequencing Services Market 2019 Report Shows the Competitive Situation Among the Top Manufacturers, With Sales, Revenue and Share – Augusta Observer

 

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