Category Archives: Metagenomics & Bioinformatics

July 21, 2018

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Have a good weekend! Today we have a very interesting list of reviews about different aspects of the microbiome. We have also: the effects of edible crickets on microbiota, steatosis in mice induced by obese human microbiota, the effect of probiotics on patients with fibromyalgia, food chemicals and human microbiota and more…  

 

Human and General Microbiome

Review: Host-Gut Microbiota Crosstalk in Intestinal Adaptation – Justine Marchix – CMGH

Review: The Brain-Gut-Microbiome Axis – Clair R. Martin – CMGH

Brief Report: A Gut Feeling: A Hypothesis of the Role of the Microbiome in Attention-Deficit/Hyperactivity Disorders – Xue Ming – Child Neurology Open

Preview: Intestinal Tolerance, with a Little Help from Our Microbial Friends – Hélène Descamps – Immunity

Review: Re-framing the theory of autoimmunity in the era of the microbiome: persistent pathogens, autoantibodies, and molecular mimicry – Amy D Proal – Discovery Medicine

Review: The gut microbiota in neuropsychiatric disorders – Marta Grochowska – Acta Neurobiologiciae Expermentalis

Review: Gut Microbiota and Mucosal Immunity in the Neonate – Majda Dzidic – Medical Sciences

Food Chemicals Disrupt Human Gut Microbiota Activity And Impact Intestinal Homeostasis As Revealed By In Vitro Systems – Clémence Defois – Scientific Reports

Research Highlight: Delivery of the gut microbiome – Ashley York – Nature Reviews Microbiology

Review: Microbiota-Host Crosstalk: A Bridge Between Cardiovascular Risk Factors, Diet, and Cardiovascular Disease – Jacques Amar – American Journal of Hypertension

Metaproteomics reveals associations between microbiome and intestinal extracellular vesicle proteins in pediatric inflammatory bowel disease – Xu Zhang – Nature Communications

 

Animal Microbiome / Animal Experiments

Non-canonicaly recruited TCRαβCD8αα IELs recognize microbial antigens – Lukasz Wojciech – Scientific Reports

Bilophila wadsworthia aggravates high fat diet induced metabolic dysfunctions in mice – Jane M. Natividad – Nature Communications

Beneficial Impact and Molecular Mechanism of Bacillus coagulans on Piglets’ Intestine – Tao Wu – International Journal of Molecular Sciences

Collaborating genomic, transcriptomic and microbiomic alterations lead to canine extreme intestinal polyposis – Jin Wang – Oncotarget

Effects of Intravenous Infusion With Sodium Butyrate on Colonic Microbiota, Intestinal Development- and Mucosal Immune-Related Gene Expression in Normal Growing Pigs – Xue Chen – Frontiers in Microbiology

Microbiome Composition in Both Wild-Type and Disease Model Mice Is Heavily Influenced by Mouse Facility – Kristopher D. Parker – Frontiers in Microbiology

Genetically Obese Human Gut Microbiota Induces Liver Steatosis in Germ-Free Mice Fed on Normal Diet – Ruirui Wang  – Frontiers in Microbiology

Microbial Community Composition Reveals Spatial Variation and Distinctive Core Microbiome of the Weaver Ant Oecophylla smaragdina in Malaysia – Kah-Ooi Chua – Scientific Reports

Antibiotic-induced microbiome depletion alters metabolic homeostasis by affecting gut signaling and colonic metabolism – Amir Zarrinpar –  Nature Communications

 

Food Microbiome

Analysis of microbiota on lettuce (Lactuca sativa) cultivated in South Korea to identify foodborne pathogens – Yeon-Cheol – Journal of Microbiology and Biotechnology

Impact of chlorine dioxide disinfection of irrigation water on the epiphytic bacterial community of baby spinach and underlying soil – Pilar Truchado – PLoS One

 

Beneficial Microbes and Compounds

Perspective: Green and black tea phenolics – Bioavailability, transformation by colonic microbiota, and modulation of colonic microbiota – Zhibin Liu – Journal of Agricultural and Food Chemistry

Therapeutic effects of probiotics on neurotoxicity induced by clindamycin and propionic acid in juvenile hamsters – Nora Al-Orf – Metabolic Brain Disease

Impact of Edible Cricket Consumption on Gut Microbiota in Healthy Adults, a Double-blind, Randomized Crossover Trial – Valerie J. Stull – Scientific Reports

Nisin, a potent bacteriocin and anti-bacterial peptide, attenuates expression of metastatic genes in colorectal cancer cell lines – Zohreh Norouzi – Microbial Pathogenesis

A Pilot Randomized Controlled Trial to Explore Cognitive and Emotional Effects of Probiotics in Fibromyalgia – Pablo Roman – Scientific Reports

Fiber Supplements Derived From Sugarcane Stem, Wheat Dextrin and Psyllium Husk Have Different In Vitro Effects on the Human Gut Microbiota – Hasinika K. A. H. Gamage –  Frontiers in Microbiology

 

Environmental Microbiology

Effects of Pseudomonas chenduensis and biochar on cadmium availability and microbial community in the paddy soil – Lingjuan Li – Science of The Total Environment

Breeding for soil-borne pathogen resistance impacts active rhizosphere microbiome of common bean – Lucas William Mendes – The ISME Journal

 

Pathogen Research

Exopolysaccharide protects Vibrio cholerae from exogenous attacks by the type 6 secretion system – Jonida Toska – PNAS

The Synergistic Effect of Exogenous Glutamine and Rifampicin Against Mycobacterium Persisters – Xue Huang – Frontiers in Microbiology

 

Bioinformatics

Preprint: MetaMaps – Strain-level metagenomic assignment and compositional estimation for long reads – Alexander Dilthey – BioRxiv

 

July 19, 2018

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An all-around Digest today features newly discovered Wolbachia in Anopheles mosquitoes that can lead to probiotic therapy for malaria, a novel mechanism for the plants to control rhizosphere microbiota, growth and defense, and fascinating art produced entirely by microbes. Enjoy!

General microbiology

Review: Large noncoding RNAs in bacteria – Kimberly A. Harris & Ronald R. Breaker – Microbiology spectrum

Bioremediation and microbial metabolism of benzo(a)pyrene – E M Ostrem Loss & J H Yu – Molecular Microbiology

Changing of the Genomic Pattern of Salmonella Enteritidis Strains Isolated in Brazil Over a 48 year-period revealed by Whole Genome SNP Analyses – Fábio Campioni et al. – Scientific Reports

Preprint: Host adaptation and convergent evolution increases antibiotic resistance without loss of virulence in a major human pathogen – Alicia Fajardo-Lubian et al. – bioRxiv

Pregnancy and early life

Pregestational overweight and obesity are associated with differences in gut microbiota composition and systemic inflammation in the third trimester – María Florencia Zacarías et al. – PLoS One

Mini-Review: Antibiotics and lactation: An overview of relative infant doses and a systematic assessment of clinical studies – J.J. van Wattum et al. – Basic & Clinical Pharmacology & Toxicology

Human respiratory microbiome

Characterisation of the nasal microbiota in granulomatosis with polyangiitis – Rennie L Rhee et al. – Annals of the Rheumatic Diseases

Human skin microbiome

Human skin commensals augment Staphylococcus aureus pathogenesis – Emma Boldock et al. – Nature Microbiology

Human oral microbiome

Unique subgingival microbiota associated with periodontitis in cirrhosis patients – Anders Jensen et al. – Scientific Reports

Human gut microbiome

ACI‐1 beta‐lactamase is widespread across human gut microbiomes in Negativicutes due to transposons harboured by tailed prophages – Chris M Rands et al. – Environmental Microbiology

Review: Recent advances in probiotics as live biotherapeutics against gastrointestinal diseases – Kota RK et al. – Current Pharmaceutical Design

Review: Microbiota–Host Crosstalk: A Bridge Between Cardiovascular Risk Factors, Diet, and Cardiovascular Disease – Jacques Amar – American Journal of Hypertension

Human built environment microbiome

β-Lactam and Fluoroquinolone-Resistant Enterobacteriaceae Recovered from the Environment of Human and Veterinary Tertiary Care Hospitals – Dimitria A. Mathys et al. – Vector-Borne and Zoonotic Diseases

Metabolomics

Quantitative metabolomics comparison of traditional blood draws and TAP capillary blood collection – Alexis Catala et al. – Metabolomics

Functional genetic discovery of enzymes using full-scan mass spectrometry metabolomics – Amy A. Caudy et al. – Biochemistry and Cell Biology

Animal experiments

Dietary L-Arginine Supplementation Alleviates the Intestinal Injury and Modulates the Gut microbiota in Broiler Chickens Challenged by Clostridium perfringens – Beibei Zhang et al. – Frontiers in Microbiology

Dissertation: Recent Evolution of Host Genetic Control of Microbiota in Cichlid Fishes and Humans – Kaitlin Patricia Coyle – North Carolina State University

Mouse: Gut Microbiota-Stimulated Innate Lymphoid Cells Support b-Defensin 14 Expression in Pancreatic Endocrine Cells, Preventing Autoimmune Diabetes – Michela Miani et al. – Cell Metabolism

Mouse: In vitro probiotic properties of vaginal Lactobacillus fermentum MG901 and Lactobacillus plantarum MG989 against Candida albicans – Chang-Ho Kang et al. – European Journal of Obstetrics & Gynecology and Reproductive Biology

Betaine Improves Intestinal Functions by Enhancing Digestive Enzymes, Ameliorating Intestinal Morphology, and Enriching Intestinal Microbiota in High-salt stressed Rats – Haichao Wang et al. – Nutrients

The evolution of ecological facilitation within mixed-species biofilms in the mouse gastrointestinal tract – Xiaoxi B. Lin et al. – The ISME Journal

Differences Between the Intestinal Lumen Microbiota of Aberrant Crypt Foci (ACF)-Bearing and Non-bearing Rats – Xiuli Xiao et al. – Digestive Diseases and Sciences

Mouse: A selective gut bacterial bile salt hydrolase alters host metabolism – Lina Yao et al. – eLife

Diabetes-Associated Alterations in the Cecal Microbiome and Metabolome are Independent of Diet or Environment in the UC Davis Type 2-Diabetes Mellitus Rat Model – Brian D. Piccolo et al. – American Journal of Physiology-Endocrinology and Metabolism

Animal microbiome

Effects of dietary energy levels on rumen bacterial community composition in Holstein heifers under the same forage to concentrate ratio condition – Yanliang Bi et al. – BMC Microbiology

The cecal microbiome of commercial broiler chickens varies significantly by season – Brian B Oakley et al. – Poultry Science

American beaver: Metagenomics reveals functional synergy and novel polysaccharide utilization loci in the Castor canadensis fecal microbiome – Zachary Armstrong et al. – The ISME Journal

High Gut Microbiota Diversity Provides Lower Resistance against Infection by an Intestinal Parasite in Bumblebees – Kathrin Näpflin & Paul Schmid-Hempel – The American Naturalist

Effect of Dietary Fructooligosaccharide (FOS) Supplementation on Ileal Microbiota in Broiler Chickens – Yue Shang et al. – Poultry Science

Arrival date and microorganisms in barn swallows – Z. Al Rubaiee et al. – Journal of Avian Biology

* Preprint: Novel Wolbachia strains in Anopheles malaria vectors from Sub-Saharan Africa – Claire L Jeffries et al. – bioRxiv

Plant, root and soil microbiome

Metabolomics analysis of Cajanus cajan L. seedlings unravelled amelioration of stress induced responses to salinity after halopriming of seeds – Sabarni Biswas, Asok K. Biswas & Bratati De – Plant Signaling & Behavior

* Root exudate metabolites drive plant-soil feedbacks on growth and defense by shaping the rhizosphere microbiota – Lingfei Hu et al. – Nature Communications

Water and extremophile microbiome

Abstract: Exploring the relative importance of surficial cyanobacteria communities versus physical, chemical and bioloigical processes at depth on sulfur cycling in two microbial mat environments – Maya Gomes et al. – Caltech Authors

Temperature driven changes in benthic microbial diversity influences biogeochemical cycling in coastal sediments – Natalie Hicks et al. – Frontiers in Microbiology

Resistance and Recovery of Methane-Oxidizing Communities depends on Stress Regime and History; a Microcosm Study – Henri van Kruistum et al. – Frontiers in Microbiology

Enterococci Concentrations in a Coastal Ecosystem are a Function of Fecal Source Input, Environmental Conditions, and Environmental Sources – Derek Rothenheber & Stephen Jones – Applied and Environmental Microbiology

Agulhas Current properties shape microbial community diversity and potential functionality – Sandra Phoma et al. – Scientific Reports

Microscale ecology regulates particulate organic matter turnover in model marine microbial communities – Tim N. Enke et al. – Nature Communications

Abundance and diversity of prokaryotes in ephemeral hypersaline lake Chott El Jerid using Illumina Miseq sequencing, DGGE and qPCR assays – Manel Ben Abdallah et al. – Extremophiles

Microplastic bacterial communities in the Bay of Brest: Influence of polymer type and size – Laura Frère et al. – Environmental Pollution

Systematic, continental scale temporal monitoring of marine pelagic microbiota by the Australian Marine Microbial Biodiversity Initiative – Mark V. Brown et al. – Scientific Data

Microbes in space

The influence of bioregenerative life‐support system (BLSS) dietary structure and lifestyle on the gut microbiota: A 105‐day ground‐based space simulation in Lunar Palace 1 – Zikai Hao et al. – Environmental Microbiology

Probiotics, Prebiotics and Synbiotics

Harms Reporting in Randomized Controlled Trials of Interventions Aimed at Modifying Microbiota: A Systematic Review – Aïda Bafeta et al. – Annals of Internal Medicine

Lactobacillus acidophilus and Clostridium butyricum ameliorate colitis in murine by strengthening the gut barrier function and decreasing inflammatory factors – Y. Wang et al. – Beneficial Microbes

Technology

Review: Interkingdom microbial consortia mechanisms to guide biotechnological applications – Shu Zhang et al. – Microbial Biotechnology

Establishing a mucosal gut microbial community in vitro using an artificial simulator – LinShu Liu et al. – PLoS One

Bioinformatics

Minimizing confounders and increasing data quality in murine models for studies of the gut microbiome – Jun Miyoshi et al. – PeerJ

Preprint: Macroecological relationships in the dynamics of gut microbiota – Brian W. Ji et al. – bioRxiv

Microbes in the news

Designer microbiomes – Alfie Gleeson & Abigail Sawyer – BioTechniques

* You need to see this award-winning artwork made entirely from microbes – Irish News

Disgusting Things You Never Knew Your Pets Are Bringing Into Your Home – Amanda Harding – Cheat Sheet

Scientific education

Preprint: Long term impact of intensive post graduate laboratory training at the Cold Spring Harbor Neurobiology of Drosophila summer course – Sarah Ly et al. – bioRxiv

July 13, 2018

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Comparing affects of host physiology and diet on primate gut microbiomes, oral bacterial and fungal dysbiosis in people with HIV, contribution of non-fermentable dietary fiber to prevention of autoimmune neurological disease via the gut microbiota.

General microbiome

Tools for engineering coordinated system behaviour in synthetic microbial consortia – Nicolas Kylilis – Nature Communications

Human oral microbiome

Dysbiosis in the oral bacterial and fungal microbiome of HIV-infected subjects is associated with clinical and immunologic variables of HIV infection – Pranab K Mukherjee – PLOS ONE

Human gut microbiome

Dietary non-fermentable fiber prevents autoimmune neurological disease by changing gut metabolic and immune status – Kerstin Berer – Scientific Reports

Physiology and central carbon metabolism of the gut bacterium Prevotella copri – Thomas Franke – Molecular Microbiology

Chemotaxis of Escherichia coli to major hormones and polyamines present in human gut – Joana G Lopes – The ISME Journal

Stool Microbiota Composition Differs in Patients with Stomach, Colon, and Rectal Neoplasms – Omar Youssef – Digestive Diseases and Sciences

Animal experiments

Of Mice and Men . . . and Microbes: Conclusions and Cautions from a Murine Study of the Lung Microbiome and Microbiome-Immune Interactions – John E McGinniss – American Journal of Respiratory and Critical Care Medicine

Modulation of gut microbiota by mulberry fruit polysaccharide treatment of obese diabetic db/db mice – Chun Chen – Food & Function

Evidence for the Role of the Cecal Microbiome in Maintenance of Immune Regulation and Homeostasis – Preeti Chhabra – Annals of Surgery

Human Milk Fortification with Bovine Colostrum Is Superior to Formula‐Based Fortifiers to Prevent Gut Dysfunction, Necrotizing Enterocolitis, and Systemic Infection in Preterm Pigs – Jing Sun – Journal of Parenteral & Enteral Nutrition

Fecal Microbiota Transplantation Is Effective in Relieving Visceral Hypersensitivity in a Postinfectious Model – Tao Bai – BioMed Research International

Animal microbiome

First report of foregut microbial community in proboscis monkeys: Are diverse forests a reservoir for diverse microbiomes? – Takashi Hayakawa – Environmental Microbiology Reports

Evolutionary trends in host physiology outweigh dietary niche in structuring primate gut microbiomes – Katherine R Amato – The ISME Journal

The composition of the perinatal intestinal microbiota in cattle – Mohammad Jaber Alipour – Scientific Reports

Metagenomic evaluation of the effects of storage conditions on the bacterial microbiota of oysters Crassostrea gasar (Adanson, 1757) – Antonio Ostrensky – Journal of Applied Microbiology

16S rRNA sequencing reveals likely beneficial core microbes within faecal samples of the EU protected slug Geomalacus maculosus – Inga Reich – Scientific Reports

A Robust Noninvasive Approach to Study Gut Microbiota Structure of Amphibian Tadpoles by Feces – Xiaowei Song – Herpetology Research

Plant, root, and soil microbiome

Isolation and characterization of two phosphate-solubilizing fungi from rhizosphere soil of moso bamboo and their functional capacities when exposed to different phosphorus sources and pH environments – Yang Zhang – PLOS ONE

Water and extremophile microbiome

Hydrothermal chimneys host habitat-specific microbial communities: analogues for studying the possible impact of mining seafloor massive sulfide deposits – Yuchen Han – Scientific Reports

Food microbiology

Changes in Quality and Microbial Succession of Lightly Salted and Sugar-Salted Blunt Snout Bream (Megalobrama amblycephala) Fillets Stored at 4°C – Yan Li – Journal of Food Protection

Review: Novel approaches for Chemical and Microbiological shelf life extension of cereal crops – Marcus Schmidt – Critical Reviews in Food Science and Nutrition

Probiotics/prebiotics

The short-term impact of probiotic consumption on the oral cavity microbiome – Erik Dassi – Scientific Reports

Bioinformatics

The evolutionary signal in metagenome phyletic profiles predicts many gene functions – Vedrana Vidulin – Microbiome

More microbes

Pre-print: Listeria monocytogenes cell-to-cell spread in epithelia is heterogeneous and dominated by rare pioneer bacteria – Fabian E Ortega – bioRxiv

Microbes in the news

Gut microbiota: a new way to take your vitamins – João Carlos Gomes-Neto – Nature Reviews Gastroenterology & Hepatology

11 July, 2018

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Today’s digest is short but full of exciting research. Firstly, a look at how maternal diet can influence infant microbiome and a brilliant preprint highlighting the role women have played in science

General Microbiome

Maternal diet during pregnancy is related with the infant stool microbiome in a delivery mode-dependent manner. Lundgren SN. Microbiome.

Oral Microbiome

Dysbiosis of oral microbiota and its association with salivary immunological biomarkers in autoimmune liver disease.Kazumichi Abe. PLos ONE

Gut Microbiome

Gut microbiota-immune-brain interactions in chemotherapy-associated behavioral comorbidities.Jordan KR Cancer

Analysis of the Gut Microbiome of Rural and Urban Healthy Indians Living in Sea Level and High Altitude Areas. Das B. Scientific Reports

Commentary:Reducing Viability Bias in Analysis of Gut Microbiota in Preterm Infants at Risk of NEC and Sepsis.Agustí G. Frontier in Cellular and Infection Microbiology .

Animal Experiments and Microbiome

Non-nutritive sweeteners possess a bacteriostatic effect and alter gut microbiota in mice.Wang. PLoS One

The spleen microbiota of small wild mammals reveals distinct patterns with tick-borne bacteria. Ge Y. PLoS Neglected Tropical Diseases

Drosophila melanogaster establishes a species-specific mutualistic interaction with stable gut-colonizing bacteria.Pais IS. PLoS Biology

Plant, Soil, and Water Microbiome

Microbial community of tannery wastewater involved in nitrification revealed by Illumina MiSeq sequencing.Ma X. Journal of Microbiology and Biotechnology

Rhizosphere fungal community dynamics associated with Rehmannia glutinosa replant disease in a consecutive monoculture regime. Wu L Phytopathology.

Effects of soil erosion on agro-ecosystem services and soil functions: A multidisciplinary study in nineteen organically farmed European and Turkish vineyards. Costantini EAC. Journal of Environmental Management

Virome

Temporal dynamics of the lung and plasma viromes in lung transplant recipients Maia Segura-Wang. PLos ONE

Techniques

Mining Novel Constitutive Promoter Elements in Soil Metagenomic Libraries in <i>Escherichia coli</i>.Westmann CA. Frontier in Microbiology.

Taxonomic and Functional Compositions Impacted by the Quality of Metatranscriptomic Assemblies.Lau MCY. Frontiers in Microbiology.

Preprint

Illuminating women’s hidden contribution to the foundation of theoretical population genetics. Samantha Dung. bioRxiv

July 9, 2018

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Today’s Digest features new insights into the microbial communities associated with shisha (water pipe), microbial mats, and tropical marine ecosystems. In addition, there are some new techniques and benchmarks to read about, including domain intelligible models for mining ‘omics data and the potential of giant viruses to introduce errors into metagenomic binning. I also highlighted some non-microbiology picks about the potential role for robots in autism therapies and photographs of a brand new planet taken at the Max Planck Institute for Astronomy!

Human gut microbiome
Faecal microbiota transplantation alters gut microbiota in patients with irritable bowel syndrome: results from a randomised, double-blind placebo-controlled study – Sofie Ingdam Halkjær – Gut

Animal experiments
Early-life sickness may predispose Siberian hamsters to behavioral changes following alterations of the gut microbiome in adulthood – Kristyn E. Sylvia – Brain, Behavior, and Immunity

Deficiency in class III PI3-kinase confers postnatal lethality with IBD-like features in zebrafish – Shaoyang Zhao – Nature Communications

Plant, root, and soil microbiome
Shisha microbiota: the good, the bad and the not so ugly – Julia Hani – BMC Research Notes

Disentangling the drivers of functional complexity at the metagenomic level in Shark Bay microbial mat microbiomes – Hon Lun Wong – The ISME Journal

Water and extremophile microbiome
A long-standing complex tropical dipole shapes marine microbial biogeography – Wei Yan – Applied and Environmental Microbiology

Probiotics / prebiotics
Probiotic Lactobacillus paracasei HII01 protects rats against obese-insulin resistance-induced kidney injury and impaired renal organic anion transporter 3 (Oat3) function – Keerati Wanchai – Clinical Science

Bioinformatics
Domain Intelligible Models – Sultan Imangaliyev – Methods

Techniques
Metagenomic binning reconstruction coupled with automatic pipeline annotation and giant viruses: a potential source of mistake in annotations – Julien Andreani – Virus Research

Does universal 16S rRNA gene amplicon sequencing of environmental communities provide an accurate description of nitrifying guilds? – Vaibhav Diwan – Journal of Microbiological Methods

Linking uncultivated microbial populations with benthic carbon turnover using quantitative stable isotope probing – Ömer K. Coskun – Applied and Environmental Microbiology

Determining lineage-specific bacterial growth curves with a novel approach based on amplicon reads normalization using internal standard (ARNIS) – Kasia Piwosz – The ISME Journal

Alyson’s non-microbiology picks
Personalized machine learning for robot perception of affect and engagement in autism therapy – Ognjen Rudovic – Science Robotics

Scientists Capture First Birth Of A Planet – M. Keppler – via NPR

July 8, 2018

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Today’s Microbiome Digest blog comes up with the current research articles on the microbiome of GIT, Respiratory, UT, Vagina, Infant, Oral, Marine, Plant-Soil and Animal- Bird. It also features the articles on the bioremediation, pre/pro-biotics, nutrient and dietary effects on microbiome, the potential prognosis, biofilm reduction and multi-omics study of pregnancy cohort, role of Environmental Contaminants(ECs), spore-forming bacteria, attenuation of colitis score, systematic repercussions by antibiotics, glucocorticoid signaling, TMAO, drug-induced liver injury (DILI), neurotransmitter interactions, effect of glycation of fish proteins, NOD2-IBD, Carbapenemase-producing Enterobacteriaceae (CPE).

Have a look and enjoy SUNDAY!

EVENTS, JOBS, PhD POSITIONS:

EVENT – Third Annual Microbiome Symposium on September 24 , 8:00AM – 7:00PM at the Stanford Faculty Club

 

GASTRO-INTESTINAL MICROBIOME: 

Analysis of the Gut Microbiome of Rural and Urban Healthy Indians Living in Sea Level and High Altitude Areas – Bhabatosh Das – Scientific Reports 

Review – The Mammalian Intestinal Microbiome: Composition, Interaction with the Immune System, Significance for Vaccine Efficacy, and Potential for Disease Therapy – Desselberger U – Pathogens

The presence of genetic risk variants within PTPN2 and PTPN22 is associated with intestinal microbiota alterations in Swiss IBD cohort patients – Bahtiyar Yilmaz – PLoS One

Absence of NOD2 receptor predisposes to intestinal inflammation by a deregulation in the immune response in hosts that are unable to control gut dysbiosis – Patrícia Reisde Souza – Immunobiology

Review – Outside the liver box: The gut microbiota as pivotal modulator of liver diseases – Annika Wahlström – Biochimica et Biophysica Acta (BBA) – Molecular Basis of Disease

 

RESPIRATORY MICROBIOME:

Review – Microbiome in the primary prevention of allergic diseases and bronchial asthma – B.Sozańska – Allergologia et Immunopathologia

Severe Obstructive Sleep Apnea is Associated with Alterations in the Nasal Microbiome and Increase in Inflammation – Benjamin G Wu – American Journal of Respiratory and Critical Care Medicine

URINARY TRACT MICROBIOME:

Review – Infections – The Urinary Tract Microbiome: The Answer to All Our Open Questions? – Giuseppe Magistro – European Urology focus

VAGINAL MICROBIOME:

Anti-HIV-1 Activity of Lactic Acid in Human Cervicovaginal Fluid – Tyssen D – mSphere

INFANT MICROBIOME:

Bifidobacterium longum subsp. infantis EVC001 stably restores the infant gut microbiome over the first year of life in breastfed infants – Jennifer Smilowitz – Pediatrics

Review – Does antibiotic choice for the treatment of suspected late-onset sepsis in premature infants determine the risk of developing necrotising enterocolitis? A systematic review – Josephine V.Seale – Early Human Developmment

ORAL MICROBIOME: 

Review – Cariogenic microbiome and microbiota of the early primary dentition: a contemporary overview – Fakhruddin KS – Oral Diseases

Differential preservation of endogenous human and microbial DNA in dental calculus and dentin – Mann AE – Scientific Reports

Distinctions and associations between the microbiota of saliva and supragingival plaque of permanent and deciduous teeth – Shi W – PLoS One

Dysbiosis of oral microbiota and its association with salivary immunological biomarkers in autoimmune liver disease – Kazumichi Abe – PLoS One

GENERAL HUMAN MICROBIOME:

Human-associated microbial populations as evidence in forensic casework – Frederike C.A – Forensic Science International: Genetics

Book chapter – Genomics and Drug-Metabolizing Enzymes and Its Application in Drug Delivery: Evaluating the Influence of the Microbiome – Sheeba Varghese Gupta

Effects of Substance Use and Sex Practices on the Intestinal Microbiome During HIV-1 Infection – Jennifer A Fulcher –The Journal of Infectious Diseases

Preview – Interactions between Clostridioides difficile and fecal microbiota in in vitro batch model: growth, sporulation and microbiota changes – Sabina Horvat – Frontiers in Microbiology

Review – Metagenomic and clinical microbiology – Sophie Amrane – Human Microbiome

Implants induce a new niche for microbiomes – Tim H. Jakobsen – Wiley Online Library

Short Communication Transmission of IMI-2 carbapenemase-producing Enterobacteriaceae from river water to human – Chrislène Laurens – Journal of Global Antimicrobial Resistance

Review – The hygiene hypothesis: immunological mechanisms of airway tolerance – Eline Haspeslagh – Current Opinion in Immunology

Microbiota affects the expression of genes involved in HPA axis regulation and local metabolism of glucocorticoids in chronic psychosocial stress – M. Vodička – Brain, Behavior, and Immunity

Review – The Role of Microbiota in Cardiovascular Risk: Focus on Trimethylamine Oxide – HusseinAl-Rubaye – Current Problems in Cardiology

 

HUMAN-MICROBE CROSS-TALK:

Gut Microbiota-Dependent Trimethylamine N-Oxide Predicts Risk of Cardiovascular Events in Patients With Stroke and Is Related to Proinflammatory Monocytes – Haghikia A – Arterioscler Thromb Vasc Biol.

Cutting Edge: Critical Roles for Microbiota-Mediated Regulation of the Immune System in a Prenatal Immune Activation Model of Autism – Catherine R. Lammert – J Immunol

Critical Role for the Microbiota in CX3CR1+ Intestinal Mononuclear Phagocyte Regulation of Intestinal T Cell Responses – Myunghoo Kim – Immunity

 

MARINE/WATER MICROBIAL ECOLOGY:

Review – Ecology and evolution of seafloor and subseafloor microbial communities – WD Orsi – Nature Reviews Microbiology

Metabolic potential of microbial communities from ferruginous sediments – Aurèle Vuillemin – Environmental Microbiology

Metagenomic analysis of basal ice from an Alaskan glacier – Kayani MUR – Microbiome

Patterns of Change in Metabolic Capabilities of Sediment Microbial Communities in River and Lake Ecosystems – Oest A1 – Int J Microbiol

Succession of toxicity and microbiota in hydraulic fracturing flowback and produced water in the Denver–Julesburg Basin – Natalie M Hull – Science of The Total Environment

 

PLANT or SOIL MICROBIOME:

Preview – New Biological Insights Into How Deforestation in Amazonia Affects Soil Microbial Communities Using Metagenomics and Metagenome-Assembled Genomes – Marie E. Kroeger – Frontiers in Microbiology

Litter quality drives the differentiation of microbial communities in the litter horizon across an alpine treeline ecotone in the eastern Tibetan Plateau – Haifeng Zheng – Scientific Reports

Preview – Unravelling the composition of the root-associated bacterial microbiota of Phragmites australis and Typha latifolia – Laura Pietrangelo – Frontiers in Microbiology

 

BIOREMEDIATION:

Characterization and Dynamic Shift of Microbial Communities during Start-Up, Overloading and Steady-State in an Anaerobic Membrane Bioreactor – Nsanzumukiza Martin Vincent – Int. J. Environ. Res. Public Health

Review – Response of microbial communities to oil spill in the Gulf of Mexico: A review – Linda Adzigbli – Afr. J. Microbiol. Res

A two-staged system to generate electricity in microbial fuel cells using methane – Jaewook Myung – Chemical Engineering Journal

The influence of pressure on crude oil biodegradation in shallow and deep Gulf of Mexico sediments – Nguyen UT – PLoS One

Microbial Community Cohesion Mediates Community Turnover in Unperturbed Aquifers – Robert E. Danczak – mSystems

Energy efficiency: Importance of indigenous microorganisms contained in the municipal solid wastes – S.Zahedi – Waste management

Systematic characterization and proposed pathway of tetracycline degradation in solid waste treatment by Hermetia illucens with intestinal microbiota – Minmin Cai – Environmental Pollution

 

NUTRITION or DIET and TREATMENTS:

Functional Effects of the Buckwheat Iminosugar d-Fagomine on Rats with Diet-Induced Prediabetes – Ramos-Romero S – Mol Nutr Food Res

Long-Term Genistein Consumption Modifies Gut Microbiota, Improving Glucose Metabolism, Metabolic Endotoxaemia and Cognitive Function in Mice Fed a High-Fat Diet – López P – Mol Nutr Food Res

Brown rice-specific γ-oryzanol as a promising prophylactic avenue to protect against diabetes mellitus and obesity disease in humans – Masuzaki H – J Diabetes Investig

Intestinal Inflammation in Chilean Infants Fed With Bovine Formula vs. Breast Milk and Its Association With Their Gut Microbiota – Ossa JC – Front Cell Infect Microbiol.

Trigonelline inhibits intestinal microbial metabolism of choline and its associated cardiovascular risk – Anwar S – J Pharm Biomed Anal

Off-target effects of tribendimidine, tribendimidine plus ivermectin, tribendimidine plus oxantel-pamoate, and albendazole plus oxantel-pamoate on the human gut microbiota – Pierre H.H.Schneeberger – International Journal for Parasitology: Drugs and Drug Resistance

Isoquercetin and inulin synergistically modulate the gut microbiome to prevent development of the metabolic syndrome in mice fed a high fat diet – Si Tan – Scientific Reports

Glycation of fish protein impacts its fermentation metabolites and gut microbiota during in vitro human colonic fermentation – Yuhong Yang – Food Research International

Correlation between microbiota and flavours in fermentation of Chinese Sichuan Paocai – YangshengXiao – Food Research International

Review – Relationship between fatty acids intake and Clostridium coccoides in obese individuals with metabolic syndrome – Giovana Jamar – Food Research International

Review – Microbiota of milk powders and the heat resistance and spoilage potential of aerobic spore-forming bacteria – Faizan A.Sadiq – International Diary Journal

Review – The debate over neurotransmitter interaction in aspartame usage – Arbind Kumar Choudhary – Journal of Clinical Neuroscience

 

METHODS:

Reevaluating approaches to cystic fibrosis pulmonary exacerbations – Schechter MS – Pediatr Pulmonol

Review – Bioresponsive drug delivery systems in intestinal inflammation: State-of-the-art and future perspectives – Niranjan G.Kotla – Advance Drug Delivery Reviews

Rapid analysis of photoautotroph microbial communities in soils by flow cytometric barcoding and fingerprinting – László Menyhárt – Applied Soil Ecology

Degradation studies of modified inulin as potential encapsulation material for colon targeting and release of mesalamine – MichaelWalz – Carbohydrate Polymers

Review – Advances in drug-induced cholestasis: Clinical perspectives, potential mechanisms and in vitro systems – M. LeonorFernández-Murga – Food and Chemical Toxicology

 

ANIMAL and BIRD MICROBIOME:

Characteristics of microbial communities and intestinal pathogenic bacteria for migrated Larus ridibundus in southwest China – Liao F – Microbiology Open

Gut microbiota correlates with fiber and apparent nutrients digestion in goose – Guojun Liu – Poultry Science

Feeding sows resistant starch during gestation and lactation impacts their faecal microbiota and milk composition but shows limited effects on their progeny – Julie Leblois – PLoS One

Analysis of temporal fecal microbiota dynamics in weaner pigs with and without exposure to enterotoxigenic Escherichia coli – J. Pollock – Journal of Animal Science

 

ANIMAL EXPERIMENTS:

Aryl hydrocarbon receptor/IL-22/Stat3 signaling pathway is involved in the modulation of intestinal mucosa antimicrobial molecules by commensal microbiota in mice – Wang J – Innate Immun.

Oral infection of mice with Fusobacterium nucleatum results in macrophage recruitment to the dental pulp and bone resorption – Larry Johnson – Biomedical Journal

Preview – Fecal Microbiota Transplantation is Associated with Reduced Morbidity and Mortality in Porcine Circovirus Associated Disease – Megan C. Niederwerder – Frontiers in Microbiology

Oral treatment with Lactobacillus rhamnosus 64 during the early postnatal period improves the health of adult rats with TNBS-induced colitis – Stanislava Stanojević – Journal of Functional Foods

Antibiotic-induced dysbiosis effects on the murine gastrointestinal tract and their systemic repercussions – Caio PupinRosa – Life Sciences

 

MICROBIOLOGY:

N-Acetyl-glucosamine influences the biofilm formation of Escherichia coli – Sicard JF – Gut Pathog

Benzoyl Peroxide Inhibits Quorum Sensing and Biofilm Formation by Gardnerella vaginalis 14018 – Ammar Algburi – Infectious Diseases in Obstetrics and Gynecology

 

PRE/PRO – BIOTICS:

Review : Benefaction of probiotics for human health: A review – George Kerry R – J Food Drug Anal

Review – Role of prebiotics in regulation of microbiota and prevention of obesity – Grethel T.Choque Delgado – Food Research International

Effects of the Administration of Probiotics on Fecal Microbiota Diversity and Composition in Healthy Individuals – Choong-Kyun Noh – J Neurogastroenterol Motil

 

METABOLOMICS:

Microbiome-related metabolite changes in gut tissue, cecum content and feces of rats treated with antibiotics – C.Behr – Toxicology and Applied Pharmacology

 

MULTI-OMICS PICKS:

Multiomics Modeling of the Immunome, Transcriptome, Microbiome, Proteome, and Metabolome Adaptations During Human Pregnancy – Mohammad Sajjad Ghaemi – Bioinformatics

July 6, 2018

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Today’s digest includes the spleen microbiome of wild mammals, the microbial phylogenetic diversity of natural clay, and the effects of non-nutritive sweeteners on the mouse gut microbiome. It also includes Nature’s picks for June’s best science images.

Pregnancy and early life

Maternal diet during pregnancy is related with the infant stool microbiome in a delivery mode-dependent manner – Sara N. Lundgren – Microbiome

Human skin microbiome

Skin commensal bacteria S. epidermidis promote survival of melanocytes bearing UVB‐induced DNA damage, while bacteria P. acnes inhibit survival of melanocytes by increasing apoptosis – Zhenping Wang – Photodermatology, Photoimmunology, and Photomedicine

Human gut microbiome

Review: Gut microbiota‐immune‐brain interactions in chemotherapy‐associated behavioral comorbidities – Kelley R. Jordan – Cancer

Involvement of T helper 17 cells in inflammatory arthritis depends on the host intestinal microbiota – Heather Evans‐Marin – Arthritis and Rheumatology

Analysis of the Gut Microbiome of Rural and Urban Healthy Indians Living in Sea Level and High Altitude Areas – Bhabatosh Das – Scientific Reports

Animal experiments

Non-nutritive sweeteners possess a bacteriostatic effect and alter gut microbiota in mice – Qiao-Ping Wang – PLoS One

Effects of naturally-produced lovastatin on feed digestibility, rumen fermentation, microbiota and methane emissions in goats over a 12-week treatment period – Su Chui Len Candyrine – PLoS One

Perinatal short-chain fructooligosaccharides program intestinal microbiota and improve enteroinsular axis function and inflammatory status in high-fat diet-fed adult pigs – Cindy Le Bourgot – FASEB

Bifidobacterium bifidum TMC3115 Can Characteristically Influence Glucose and Lipid Profile and Intestinal Microbiota in the Middle-Aged and Elderly – Ke Wang – Probiotics and Antimicrobial Proteins

Isoquercetin and inulin synergistically modulate the gut microbiome to prevent development of the metabolic syndrome in mice fed a high fat diet – Si Tan – Scientific Reports

Animal microbiome

The spleen microbiota of small wild mammals reveals distinct patterns with tick-borne bacteria – Yan Ge – PLoS Neglected Tropical Diseases

Drosophila melanogaster establishes a species-specific mutualistic interaction with stable gut-colonizing bacteria – Inês S. Pais – PLoS Biology

Plant, root, and soil microbiome

Phylogenetic diversity and metabolic potential of microbiome of natural healing clay from Chamliyal (J&K) – Sakshi Sharma – Archives of Microbiology

Bioinformatics

Taxonomic and Functional Compositions Impacted by the Quality of Metatranscriptomic Assemblies – Maggie C. Y. Lau – Frontiers in Microbiology

Techniques

Development of outbred CD1 mouse colonies with distinct standardized gut microbiota profiles for use in complex microbiota targeted studies – Marcia L. Hart – Scientific Reports

Non-microbiology picks

Astronauts, atmospheres and axolotls — June’s best science images – Nature

July 02, 2018

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Good morning! Today’s Microbiome Digest will cover the general microbiome, HIV infection and multi-site bacterial microbiota, crucial role of lung microbiome in asthma, gut microbiome in type 1 diabetes, Link between diet and metabolic syndrome, Wild and Captive Baboon Gut Microbiota and Their Antibiotic Resistomes, HmmUFOtu: a tool for taxonomic assignment and OTU picking and a news on plastic eating bacteria …

Events and jobs

Post-Doctoral Research Position, Oregon State University, with Dr. Stephen Giovannoni

Postdoctoral Researcher Position Characterizing Microbial Candidate Phlya at Stanford University

General microbiome

Issue: The microbiome: more than a gut reaction – John R. Wingard – Blood

Evaluation at scale of microbiome-derived metabolites as biomarker of flavan-3-ol intake in epidemiological studies – Javier I. Ottaviani – Scientific Reports

All disease begins in the gut: Influence of gastrointestinal disorders and surgery on oral drug performance – Grace B. Hatton – International Journal of Pharmaceutics

Designing microbial consortia with defined social interactions – Wentao Kong – Nature Chemical Biology

Multi-site human microbiome

HPV infection and bacterial microbiota in the placenta, uterine cervix and oral mucosa – Heidi Tuominen – Scientific Reports

Human respiratory microbiome

State of the Art: Does lung microbiome play a causal or casual role in asthma? – Maria Di Cicco – Pediatric Pulmonology

Human vaginal microbiome

Increased richness and diversity of the vaginal microbiota and spontaneous preterm birth – Aline C. Freitas – Microbiome

Human gut microbiome

Review: Gut microbiome in type 1 diabetes: A comprehensive review – Zheng P – Diabetes Metab Res Rev

Review: Altered Gut Microbiota: A Link Between Diet and the Metabolic Syndrome – Velasquez Manuel T – Metabolic Syndrome and Related Disorders

Chapter: Microbiota, Obesity and NAFLD – Louis H. S. Lau – Obesity, Fatty Liver and Liver Cancer

Chapter: The Influence of Gut Microbial Metabolism on the Development and Progression of Non-alcoholic Fatty Liver Disease – Wei Jia – Obesity, Fatty Liver and Liver Cancer

Method: Assessing the Mouse Intestinal Microbiota in Settings of Type-2 Immune Responses – Mei San Tang – Type 2 Immunity

Ancient Thali Diet: Gut Microbiota, Immunity, and Health – Kaitlyn Shondelmyer – Yale Journal of Biology & Medicine

Altered gut microbiome composition in children with refractory epilepsy after ketogenic diet – Yunjian Zhang – Epilepsy Research

The Stringent Response Determines the Ability of a Commensal Bacterium to Survive Starvation and to Persist in the Gut – Whitman B. Schofield – Cell Host & Microbe

Review: Update on the Gastrointestinal Microbiome in Systemic Sclerosis – Chiara Bellocchi – Current Rheumatology Reports

Review: The Gut Microbiome Alterations and Inflammation-Driven Pathogenesis of Alzheimer’s Disease—a Critical Review – Marta Sochocka – Molecular Neurobiology

The controversial role of Enterococcus faecalis in colorectal cancer – Carolina Vieira de Almeida – Therapeutic Advances in Gastroenterology

Animal experiments

Pea-protein alginate encapsulation adversely effects development of clinical signs of Citrobacter rodentium-induced colitis in mice treated with probiotics – Natallia Varankovich – Canadian Journal of Microbiology

Maternal Soluble Fiber Diet during Pregnancy Changes the Intestinal Microbiota, Improves Growth Performance, and Reduces Intestinal Permeability in Piglets – Chuanshang Cheng – Applied and Environmental Microbiology

Overlapping community composition of gut and fecal microbiomes in lab-reared and field-collected German cockroaches – Madhavi L. Kakumanu – Applied and Environmental Microbiology

TRIF deficiency protects non-obese diabetic mice from type 1 diabetes by modulating the gut microbiota and dendritic cells – Elke Gülden – Journal of Autoimmunity

Mucosal homeostasis is altered in the ileum of gnotobiotic mice – Chasen J. Greig – Journal of Surgical Research

Animal microbiome

Factors influencing bacterial microbiome composition in a wild non-human primate community in Taï National Park, Côte d’Ivoire – Jan F. Gogarten – The ISME Journal

Characterization of Wild and Captive Baboon Gut Microbiota and Their Antibiotic Resistomes – Pablo Tsukayama – mSystems

Genetic variability and ontogeny predict microbiome structure in a disease-challenged montane amphibian – Sarah M. Griffiths – The ISME Journal

Plant, root, and soil microbiome

Review: Multifaceted Impacts of Bacteriophages in the Plant Microbiome – Britt Koskella – Annual Review of Phytopathology

‘Concord’ grapevine nutritional status and chlorosis rank associated with fungal and bacterial root zone microbiomes – R.W.Lewis – Plant Physiology and Biochemistry

Draft Genome Sequences of Two Novel Cellulolytic Streptomyces Strains Isolated from South African Rhizosphere Soil – Mobolaji F. Adegboye – Genome Announcements

Differences in microbial key players in anaerobic degradation between biogas and sewage treatment plants – Christian Buettner – International Biodeterioration & Biodegradation

Water and extremophile microbiome

The impact of the Deepwater Horizon blowout on historic shipwreck-associated sediment microbiomes in the northern Gulf of Mexico – Leila J. Hamdan – Scientific Reports

Stoichio-Metagenomics of ocean waters: a molecular evolution approach to trace the dynamics of nitrogen conservation in natural communities – Hannes Dittberner – Frontiers in Microbiology

 Probiotics / prebiotics

Review: Impact of Prebiotics on Poultry Production and Food Safety – Steven C. Ricke – Yale Journal of Biology & Medicine

Isolation and Partial Characterization of Lactic Acid Bacteria from the Gut Microbiota of Marine Fishes for Potential Application as Probiotics in Aquaculture – Sergio Alonso – Probiotics and Antimicrobial Proteins

Effects of Prebiotics vs a Diet Low in Fodmaps in Patients with Functional Gut Disorder – Jose-Walter Huaman – Gastroenterology

Bioinformatics

HmmUFOtu: An HMM and phylogenetic placement based ultra-fast taxonomic assignment and OTU picking tool for microbiome amplicon sequencing studies – Qi Zheng – Genome Biology

Techniques

Review: Culturing the human microbiota and culturomics – Jean-Christophe Lagier – Nature Reviews Microbiology

Microbes in the news

Plastic-eating bacteria discovered by student could help solve global pollution crisis

Sewage microbes make a fuel booster

Our intestinal microbiome influences metabolism — through the immune system

 

Ashok’s non-microbiology picks

Efficacy and Safety of Dupilumab in Glucocorticoid-Dependent Severe Asthma – Klaus F. Rabe – The NEW ENGLAND JOURNAL of Medicine

June 29, 2018

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A variety of reviews on the human skin and gut microbiota, effects of probiotics on depressive behaviors, microbiota changes in deer populations in China.

Human skin microbiome

Review: Microbiome in the Gut-Skin Axis in Atopic Dermatitis – So-Yeon Lee – Allergy and Asthma Immunology Research

Human gut microbiome

Pre-print: The Genetic Basis for the Cooperative Bioactivation of Plant Lignans by a Human Gut Bacterial Consortium – Elizabeth N Bess – bioRxiv

Review: Mechanistic Insights in the Success of Fecal Microbiota Transplants for the Treatment of Clostridium difficile Infections – Amoe Baktash – Frontiers in Microbiology

Review: Reciprocal Interactions Between Gut Microbiota and Host Social Behavior – Emmanuelle Münger – Frontiers in Integrative Neuroscience

Review: Gut microbiota bile acid metabolism controls cancer immunosurveillance – Anna Dart – Nature Reviews Microbiology

Animal experiments

Pulmonary Arterial Hypertension Affects the Rat Gut Microbiome – María Callejo – Scientific Reports

Animal microbiome

Comparative Analysis of Gut Microbiota Changes in Père David’s Deer Populations in Beijing Milu Park and Shishou, Hubei Province in China – Meishan Zhang – Frontiers in Microbiology

Ixodes scapularis does not harbor a stable midgut microbiome – Benjamin D Ross – The ISME Journal

Plant, root, and soil microbiome

Different Height Forms of Spartina alterniflora Might Select Their Own Rhizospheric Bacterial Communities in Southern Coast of China – Li’an Lin – Microbial Ecology

Survey of sediment oxygenation in rhizospheres of the saltmarsh grass – Spartina anglica – Ketil Koop-Jakobsen – Science of the Total Environment

Probiotics/prebiotics

Probiotics decrease depressive behaviors induced by constipation via activating the AKT signaling pathway – Nana Xu – Metabolic Brain Disease

Phages and viruses

Pre-print: Seroprevalence of fourteen human polyomaviruses determined in blood donors – Sergio S Kamminga – bioRxiv

Bioinformatics

A distinct abundant group of microbial rhodopsins discovered using functional metagenomics – Alina Pushkarev – Nature

Techniques

Selection of validated hypervariable regions is crucial in 16S-based microbiota studies of the female genital tract – Simon Graspeuntner – Scientific Reports

More microbes

Cryo-EM structure of an essential Plasmodium vivax invasion complex – Jakub Gruszczyk – Nature

Microbes in the news

Genetically modified bacteria enlisted in fight against disease – Sara Reardon – Nature

A short course of laxatives has long-lasting effects on microbiome – Nature

June 27, 2018

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In today’s Microbiome Digest you can read about: cyanobacterial blooms by J. Huisman, designer microbial consortia by W. Kong,  the significance of the intestinal microbiome for vaccinology by Vanessa C. Harris, indigenous microbes residing in oil sands by Xiaoxuan Yu, effects of sliver nanoparticles on soil microbiome by J.Y. Xu,  WHAM!: a web-based visualization tool for metagenomics by J.C. Devlin. Yet another interesting read you can find in Science & Publishing  –> “Death of scientific journals after 350 years” by S. Silver. Enjoy!

General microbiome

Designing microbial consortia with defined social interactions –  Wentao Kong – Nature Chemical Biology

Pregnancy and early life

Antibiotics in early life: dysbiosis and the damage done – Hadar Neuman – FEMS Microbiology Reviews

Human ear microbiota

The unsolved problem of otitis media in indigenous populations: A systematic review of upper respiratory and middle ear microbiota in indigenous children – Andrea Coleman – bioRxiv

Human respiratory microbiome

Does lung microbiome play a causal or casual role in asthma? – Maria Di Cicco – Pediatric Pulmonology

Human gut microbiome

Alterations in the gut bacterial microbiome in fungal Keratitis patients – Sama Kalyana Chakravarthy – PLOS One

Altered intestinal microbiota composition, antibiotic therapy and intestinal inflammation in children and adolescents with cystic fibrosis – Maiara Brusco de Freitas – PLOS One

Nonaplex PCR using Cliffhanger primers to identify diarrhoeagenic Escherichia coli from crude lysates of human faecal samples – Uffe Vest Schneider – PLOS One

Review: The Significance of the Intestinal Microbiome for Vaccinology: From Correlations to Therapeutic Applications – Vanessa C. Harris – Drugs

Review: Update on the Gastrointestinal Microbiome in Systemic Sclerosis – Chiara Bellocchi – Current Rheumatology Reports

Gut microbiota components are associated with fixed airway obstruction in asthmatic patients living in the tropics – Emiro Buendía – Scientific Reports

Role of Microbiota and Tryptophan Metabolites in the Remote Effect of Intestinal Inflammation on Brain and Depression – Barbora Waclawiková – Pharmaceuticals

The study of bacteria in biopsies from Slovak colorectal adenoma and carcinoma patients – L. Wachsmannova-  Neoplasma

Amplification of Antimicrobial Resistance in Gut Flora of Patients Treated with Ceftriaxone – J. Meletiadis – Antimicrobial Agents and Chemotherapy

Animal experiments 

Metabolome disruption of pregnant rats and their offspring resulting from repeated exposure to a pesticide mixture representative of environmental contamination in Brittany – Nathalie Bonvallot – PLOS One

Dietary supplementation with raspberry extracts modifies the fecal microbiotain obese diabetic db/db mice –    Jose F. Garcia-Mazcorro – Journal of Microbiology and Biotechnology

Effects of dietary yeast nucleotides supplementation on intestinal barrier function, intestinal microbiota, and humoral immunity in specific pathogen-free chickens – Che Wu – Poultry Science

Magnesium lithospermate B improves the gut microbiome and bile acid metabolic profiles in a mouse model of diabetic nephropathy – Jing Zhao – Acta Pharmacologica Sinica

Animal microbiome

Evaluation of the impact of dental prophylaxis on the oral microbiota of dogs – Rebecca Flancman – PLOS One

Improving the standards for gut microbiome analysis of fecal samples: insights from the field biology of Japanese macaques on Yakushima Island – Takashi Hayakawa – Primates

Plant, root, and soil microbiome

Indigenous microorganisms residing in oil sands tailings biodegrade residual bitumen – Xiaoxuan Yu – Chemosphere

Interactive effects of Magnaporthe inoculation and nitrogen doses on the plant enzyme machinery and phyllosphere microbiome of resistant and susceptible rice cultivars – Shobit Thapa – Archives of Microbiology

Large-scale replicated field study of maize rhizosphere identifies heritable microbes – William A. Walters – PNAS

Long-term effects of sliver nanoparticles on the abundance and activity of soil microbiome – Jing Yang Xu – Journal of Environmental Sciences

Long-term effects of environmentally relevant concentrations of silver nanoparticles on microbial biomass, enzyme activity, and functional genes involved in the nitrogen cycle of loamy soil – Anna-Lena Grün – Journal of Environmental Sciences

Sphingomonas tabacisoli sp. nov., a member of the genus Sphingomonas, isolated from rhizosphere soil of Nicotiana tabacum L. – Xing-Kui Zhou – International Journal of Systematic and Evolutionary Microbiology

Effects of Bacillus subtilis and nanohydroxyapatite on the metal accumulation and microbial diversity of rapeseed (Brassica campestris L.) for the remediation of cadmium-contaminated soil – Wei Liu – Environmental Science and Pollution Research

Interactive effects of Magnaporthe inoculation and nitrogen doses on the plant enzyme machinery and phyllosphere microbiome of resistant and susceptible rice cultivars – Shobit Thapa – Archives of Microbiology

Water and extremophile microbiome

Heliorhodopsins are absent in diderm (Gram-negative) bacteria: Some thoughts and possible implications for activity – Jose Flores-Uribe – bioRxiv

Comparative genomics analyses indicate differential methylated amine utilisation trait within the member of the genus Gemmobacter – Eileen Kröber – bioRxiv

Functional annotation of hypothetical proteins from the Exiguobacterium antarcticum strain B7 reveals proteins involved in adaptation to extreme environments, including high arsenic resistance – Wana Lailan Oliveira da Costa – PLOS One

Factors affecting infection of corals and larval oysters by Vibrio coralliilyticus – Blake Ushijima – PLOS One

“Twisted Tales: Insights into Genome Diversity of Ciliates Using Single-Cell ‘omics” –  Xyrus X Maurer-Alcalá – Genome Biology and Evolution

Integrated methodological approach reveals microbial diversity and functions in aerobic groundwater microcosms adapted to vinyl chloride – Xikun Liu – FEMS Microbiology Ecology

Specialized proteomic responses and an ancient photoprotection mechanism sustain marine green algal growth during phosphate limitation – Jian Guo –  Nature Microbiology

Warming and oligotrophication cause shifts in freshwater phytoplankton communities – Laura Verbeek – Global Change Biology

Review: Cyanobacterial blooms – Jef Huisman – Nature Reviews Microbiology

Research letter: Airborne Microbes Contribute to N2 Fixation in Surface Water of the Northern Red Sea – Eyal Rahav – Geophysical Research Letters

Bloom of a denitrifying methanotroph, “Candidatus Methylomirabilis limnetica”, in a deep stratified lake – Jon S. Graf – Environmental Microbiology

Extensive nitrification and active ammonia oxidizers in two contrasting coastal systems of the Baltic Sea – Elisabeth Happel – Environmental Microbiology

Microbial life under ice: Metagenome diversity and in situ activity of Verrucomicrobia in seasonally ice‐covered lakes – Patricia Tran – Environmental Microbiology

Rapid thermal adaptation in a marine diatom reveals constraints and tradeoffs – Daniel R. O’Donnell – Global Change Biology

A Virus Infecting Marine Photoheterotrophic Alphaproteobacteria (Citromicrobium spp.) Defines a New Lineage of ssDNA Viruses – Qiang Zheng – Frontiers in Microbiology / Virology

Built environment 

Coupled laboratory and field investigations resolve microbial interactions that underpin persistence in hydraulically fractured shales – Mikayla A. Borton – PNAS

Phages and viruses

Two point mutations in the Hantaan virus glycoproteins afford the generation of a highly infectious recombinant vesicular stomatitis virus vector – Megan M Slough – bioRxiv

ΦCrAss001, a member of the most abundant bacteriophage family in the human gut, infects Bacteroides – Andrey Shkoporov – bioRxiv

In silico characterisation of the two-component system regulators of Streptococcus pyogenes – Sean J. Buckley- PLOS One

Host-microbiome interactions

Opinion: Classic Models for New Perspectives: Delving into Helminth–Microbiota–Immune System Interactions – Alba Cortés – Trends in Parasitology

Review: Helminth–Bacterial Interactions: Cause and Consequence – Alexis Rapin – Trends in Immunology

Bioinformatics

WHAM!: a web-based visualization suite for user-defined analysis of metagenomic shotgun sequencing data – Joseph C. Devlin – BMC Genomics

MicroPheno: predicting environments and host phenotypes from 16S rRNA gene sequencing using a k-mer based representation of shallow sub-samples – Ehsaneddin Asgari – Bioinformatics

Science, publishing, and career 

The Impact of Grant Funding on the Publication Activity of Awarded Applicants: A Systematic Review of Comparative Studies and Meta-analytical Estimates – Ruslan Saygitov – bioRxiv

Death of scientific journals after 350 years – Simon Silver – FEMS Microbiology Letters