May 14, 2017

A short digest this Sunday with most studies focusing on associations with microbiota and host health, plus a look at a novel sampling method for assessing human-pathogen interactions.


 General microbiome

Review: Using systems biology approaches to elucidate cause and effect in host-microbiome interactions – Elizabeth A. Witherden – Current Opinion in Systems Biology

Human gut microbiome

Dynamic gastrointestinal digestion of grape pomace extracts: bioaccessible phenolic metabolites and impact on human gut microbiota – Irene Gil-Sánchez – Journal of Food Composition and Analysis

Gut Microbiota in Parkinson Disease in a northern German cohort – Franziska Hopfner – Brain Research

Outlier based literature exploration for cross-domain linking of Alzheimer’s disease and gut microbiota – Donatella Gubiani – Expert Systems with Applications

Animal experiments

Review: This Gut Ain’t Big Enough for Both of Us. Or Is It? Helminth–Microbiota Interactions in Veterinary Species – Laura E. Peachey – Trends in Parasitology

Lactobacillus johnsonii CJLJ103 attenuates colitis and memory impairment in mice by inhibiting gut microbiota lipopolysaccharide production and NF-κB activation – Su-Min Lim – Journal of Functional Foods

Effects of potato dextrin on the composition and metabolism of the gut microbiota in rats fed standard and high-fat diets – Renata Barczynska – Journal of Functional Foods

Antibiotics-induced gut microbiota dysbiosis promotes tumor initiation via affecting APC-Th1 development in mice – Chengming Xu – Biochemical and Biophysical Research Communications

Plant, root, and soil microbiome

Effectiveness of a full-scale horizontal slow sand filter for controlling phytopathogens in recirculating hydroponics: From microbial isolation to full microbiome assessment – Francesc X. Prenafeta-Boldú – Science of The Total Environment

Functioning grouped soil microbial communities according to ecosystem type, based on comparison of fallows and meadows in the same region – Dominika Chmolowska – Science of The Total Environment

Effect of fumigation with chloropicrin on soil bacterial communities and genes encoding key enzymes involved in nitrogen cycling – Jun Li – Environmental Pollution


A novel sampling method for assessing human-pathogen interactions in the natural environment using boot socks and citizen scientists, with an application to the seasonality of Campylobacter – Natalia R Jones – Applied and Environmental Microbiology

Microbes in the news

The Coral Microbiome May Offer Protection in Warming Seas – Jeffrey Marlow – Discover

Grotty socks reveal surprising spread of gut-churning bacteria – Ben Guarino – Stuff

UK researchers develop low tech method for environmental sampling of campylobacter – ASM Press release

April 30, 2017

A review on how the human microbiome has changed from that of primates, plus articles on biofilm formation in soils, and the influence of microbiomes on bone and psychological health are just a few of the articles highlighted in todays Biks Picks!

Analysis of stability to cheaters in models of antibiotic degrading microbial communities – András Szilágyi – Journal of Theoretical Biology

Human vaginal microbiome

Vaginal ecosystem modeling of growth patterns of anaerobic bacteria in microaerophilic conditions – Audrie A. Medina-Colorado – Anaerobe

Human gut microbiome

Opinion: The shrinking human gut microbiome – Andrew H Moeller – Current Opinion in Microbiology

Review: Osteomicrobiology: The influence of gut microbiota on bone in health and disease – Rheinallt M. Jones – Bone

The Role of the Microbiome in Bipolar Disorder-A New Model – Robert Yolken – Biological Psychiatry

Gut Microbiome and Brain Functional Connectivity in Infants: A Preliminary Study Focusing on the Amygdala – Andrew Salzwedel – Biological Psychiatry

Gut Microbiota Distributions Predict Mood Disorder Symptoms and Mediate Dietary Interactions – Brittany Mason – Biological Psychiatry

Antimicrobial resistance in the Bacteroides fragilis group in faecal samples from patients receiving broad-spectrum antibiotics – Kia Cirkeline Møller Hansen – Anaerobe

Animal experiments

Impact of faecal microbiota transplantation on mouse digestive colonization with two extensively resistant bacteria – Rafael Mahieu – Journal of Infection

Changes of cecal microflora in chickens following Eimeria tenella challenge and regulating effect of coated sodium butyrate – Zuoyong Zhou – Experimental Parasitology

Plant, root, and soil microbiome

Preprint: Bacterial Biofilm Formation On Soil Fungi: A Widespread Ability Under Controls – Cora Miquel Guennoc – BioRxiv

Laboratory persistence in soil of thiacloprid, pendimethalin and fenarimol incubated with treated wastewater and dissolved organic matter solutions. Contribution of soil biota – José Antonio Rodríguez-Liébana – Chemosphere

Food microbiology

Effect of different marinating conditions on the evolution of spoilage microbiota and metabolomic profile of chicken breast fillets – Anastasia E. Lytou – Food Microbiology

Probiotics / prebiotics

A combination of the probiotic and prebiotic product can prevent the germination of Clostridium difficile spores and infection – M. Rätsep – Anaerobe

Gut microbiota-mediated pharmacokinetics of ginseng saponins – Dong-Hyun Kim – Journal of Ginseng Research

Microbes in the news

Rumblings of Parkinson’s: Gut Microbiome Shifts in Early Stage of Disease – ALZFORUM

Yersinia pestis, the plague bacteria, can survive inside Acanthamoeba for protection -OutBreakNewsToday

March 19, 2017

A nice collection of articles this Sunday. We look at the potential benefits of Fecal Microbiota Transplantation,  a number of probiotic articles, and microbiota manipulations in animals. 


Events and jobs

Pharmaceutical Microbiology Laboratory Manager – Derbyshire / Edinburgh

General microbiome

Role of the small intestine, colon and microbiota in determining the metabolic fate of polyphenols – Gary Williamson – Biochemical Pharmacology

Fecal microbiota transplantation (FMT) could reverse the severity of experimental necrotizing enterocolitis (NEC) via oxidative stress modulation – Xiaomei Li –

Free Radical Biology and Medicine

PREPRINT: Bacterial physiological adaptations to contrasting edaphic conditions identified using landscape scale metagenomics – Ashish A Malik – BioRxiv

Human respiratory microbiome

Review: Normal Oral Flora and the Oral Ecosystem – Lakshman Samaranayake – Dental Clinics of North America

Oral Bacterial Infections : Diagnosis and Management – Glendee Reynolds-Campbell – Dental Clinics of North America

Human gut microbiome 

The gut microbiota metabolism of pomegranate or walnut ellagitannins yields two urolithin-metabotypes that correlate with cardiometabolic risk biomarkers: comparison between normoweight, overweight-obesity and metabolic syndrome – María V. Selma – Clinical Nutrition

Animal experiments

Effects of dietary inclusion of the yeasts Saccharomyces cerevisiae and Wickerhamomyces anomalus on gut microbiota of rainbow trout – David Huyben –


Host Intestinal Epithelium Derived Mirnas Shape The Microbiota And Its Implication In Cardiovascular Diseases – Lianbi Zhao – Journal of the American College of Cardiology

The effect of penicillin administration in early life on murine gut microbiota and blood lymphocyte subsets – Jaroslaw Daniluk – Anaerobe

Effect of bioaugmentation by cellulolytic bacteria enriched from sheep rumen on methane production from wheat straw – E. Gozde Ozbayram – Anaerobe

Animal microbiomes

Hunting for healthy microbiomes: determining the core microbiomes of Ceratina, Megalopta, and Apis bees and how they associate with microbes in bee collected pollen – Peter Graystock – Conservation Genetics

Water and extremophile microbiome  

Bacterial Microbiota Associated with the Glacier Ice Worm Is Dominated by Both Worm-Specific and Glacier-Derived Facultative Lineages – Takumi Murakami – Microbes and Environments

Food microbiology

Biopreservation potential of lactic acid bacteria from Andean fermented food of vegetal origin – Alba Yépez – Food Control

Metaproteomic analysis of microbiota in the fermented fish, Siniperca chuatsi – Chaofan Ji – LWT – Food Science and Technology

Probiotics / prebiotics 

The use of potential probiotic Lactobacillus plantarum DW12 for producing a novel functional beverage from mature coconut water – Duangporn Kantachote – Journal of Functional Foods

Autochthonous lactic acid bacteria with probiotic aptitudes as starter cultures for fish-based products – Barbara Speranza – Food Microbiology

Functional probiotic products based on fermented buckwheat with Lactobacillus rhamnosus – Zuzana Matejčeková – LWT – Food Science and Technology


Organism and Microbiome Analysis: Techniques and Implications for Chronic Rhinosinusitis – Ashleigh A. Halderman – Otolaryngologic Clinics of North America

Microbes in the news

Vitamin May be Key to Killing Cancer-Causing Bacteria Carole Ellis ContagionLive

Changes in gut microbiota after unhealthy diet may protect from metabolic disease – Medical Press

Porridge really is that good for you – The Independent

Antibiotics and the honeybee microbiome – Kerry Evans – Labroots

January 31, 2017

Todays picks include nice reviews on microbiome engineering, and one on skin microbiomes in humans and animals. Biodegredation of mononitrophenol isomers by a tailor-made microbial consortium.  Quite a lot of microbiome news – from autism to inflammatory bowel disease.


Events and jobs

Microbiome Scientist Job – Merck – Cambridge, MA


General microbiome

Review: Microbiome engineering: Current applications and its future – Jee Loon Foo – Biotechnology Journal

Simultaneous biodegradation of three mononitrophenol isomers by a tailor-made microbial consortium immobilized in sequential batch reactors – H. Fu – Letters in Applied Microbiology

Human skin microbiome

Review: The cutaneous ecosystem: the roles of the skin microbiome in health and its association with inflammatory skin conditions in humans and animals – Aline Rodrigues Hoffmann – Veterinary Dermatology


Animal experiments

A metagenomic study of the preventive effect of Lactobacillus rhamnosus GG on intestinal polyp formation in ApcMin/+ mice – Y. Ni – Journal of Applied Microbiology

Water and extremophile microbiome

Biofilms for Monitoring Presence of Microsporidia in Environmental Water – Joseph A. Moss – Journal of Eukaryotic Microbiology

Haptophyte Diversity and Vertical Distribution Explored by 18S and 28S Ribosomal RNA Gene Metabarcoding and Scanning Electron Microscopy – Sandra Gran-Stadniczeñko – Journal of Eukaryotic Microbiology


Preprint: In-Depth Resistome Analysis by Targeted Metagenomics – Val F Lanza – bioRxiv

Microbes in the news

Could Fecal Microbiota Transplant Benefit Autistic Children? – MPR

Premature birth risk linked to bacteria in vagina and cervix – Catharine Paddock – MNT

New evidence of how gut microbes affect Inflammatory Bowel Disease – Kate Sweeney – BuisnessWeekly

Boost your immunity with foods that are alive – Rachel Yan – 9News

Rebalancing gut microbiome lengthens survival in mouse model of ALS – ScienceDaily

Carbohydrate That Promotes Biofilm May Be Key to Treating Pseudomonas Infections – Magdalena Kegel – CysticFibrosisNewsToday



January 28, 2017

Among todays picks; Microbiota Transfer Therapy improves gastrointestinal and autism symptoms. Primate microbiota is linked to degree of host sociality. Identifying microbial community changes in space and time opens a door to predicting ecosystem level functioning. Native soil microbes help native plants compete with exotics. Metal toxicity and stress response adaptations represent an important selective force for influencing diversity within marine Synechococcus populations.

Events and jobs

Postdoctoral fellowships in microbiome/neuroscience – Northwestern University

Medical Lab Technician in Microbiology – Medical University of South Carolina

Microbiology Technologist – CK Group, Surrey

General microbiome

Predicting the structure and function of coalesced microbial communities –Pawel Sierocinski – bioRxiv

Multi-site human microbiome

Frozen: Thawing and Its Effect on the Postmortem Microbiome in Two Pediatric Cases – Jennifer L. Pechal – Journal of Forensic Sciences

Human vaginal microbiome

Appreciable uncertainty regarding benefits and risks in the treatment of bacterial vaginosis to prevent preterm birth – Thor Haahr -Acta Obstetricia et Gynecologica Scandinavica

Human gut microbiome

Microbiota Transfer Therapy alters gut ecosystem and improves gastrointestinal and autism symptoms: an open-label study – Dae-Wook Kang – Microbiome

Dysregulation of Systemic and Mucosal Humoral Responses to Microbial and Food Antigens as a Factor Contributing to Microbial Translocation and Chronic Inflammation in HIV-1 Infection. – Zdenek Hel – PLOS PATHOGENS

Impact of the Microbiota and Gastric Disease Development by Helicobacter pylori. – Teresa Alarcón –  Current Topics in Microbiology and Immunology

Helicobacter pylori-Induced Changes in Gastric Acid Secretion and Upper Gastrointestinal Disease. – Adam J. Smolka –  Current Topics in Microbiology and Immunology

Sleepy, circadian disrupted and sick: Could intestinal microbiota play an important role in shift worker health? – Amy C. Reynolds – Molecular Metabolism

Oxidation During Digestion of Meat: Interactions with the Diet and Helicobacter pylori Gastritis, and Implications on Human Health – Thomas Van Hecke – Comprehensive Reviews in Food Science and Food Safety

Glucosinolate and Desulfo-glucosinolate Metabolism by a Selection of Human Gut Bacteria. – Vijitra Luang-In – Current Microbiology

Animal experiments

Species-specific immunity to Helicobacter suis – Iris Bosschem – Helicobacter

Animal microbiome 

The Association of Specific Constituents of the Fecal Microbiota with Immune-Mediated Brain Disease in Dogs. – Nick D. Jeffery – PLOS ONE

Patterns in Gut Microbiota Similarity Associated with Degree of Sociality among Sex Classes of a Neotropical Primate. – Katherine R. Amato – Microbial Ecology

Plant, root, and soil microbiome

Antimicrobial Activities of Some Actinomycetes Isolated from Different Rhizospheric Soils in Tunisia. – Ines Trabelsi – Current Microbiology

Native plants fare better against an introduced competitor with native microbes and lower nitrogen availability. – W. Gaya Shivega – AoB PLANTS

Identity of biocrust species and microbial communities drive the response of soil multifunctionality to simulated global change – Yu-Rong Liu – Soil Biology and Biochemistry

Distinct roles for soil fungal and bacterial communities associated with the suppression of vanilla Fusarium wilt disease – Wu Xiong – Soil Biology and Biochemistry

Prolonged exposure does not increase soil microbial community response to warming along geothermal gradients – Dajana Radujkovic – bioRxiv

Water and extremophile microbiome

Coupling Spatiotemporal Community Assembly Processes to Changes in Microbial Metabolism – Emily B. Graham – Frontiers in Microbiology 

Copper toxicity response influences mesotrophic Synechococcus community structure – Rhona K. Stuart – Environmental Microbiology

Identification and bioactive potential of marine microorganisms from selected Florida coastal areas – Anna Christensen – MicrobiologyOpen

Diversity and mineral substrate preference in endolithic microbial communities from marine intertidal outcrops (Isla de Mona, Puerto Rico) – Estelle Couradeau –


Review: Mining for CRISPR–Cas – Ashley York – Nature Reviews Microbiology

Data Mining Techniques Applied to Hydrogen Lactose Breath Test – Cristina Rubio-Escudero – PLOS ONE

Profiling Living Bacteria Informs Preparation of Fecal Microbiota Transplantations – Nathaniel D. Chu – PLOS ONE

Statistical test for tolerability of effects of an antifungal biocontrol strain on fungal communities in three arable soils – Kai Antweiler – Microbial Biotechnology

Molecular beacons to identify gifted microbes for genome mining – Richard H Baltz – The Journal of Antibiotics

Phages and viruses

Fecal virome of healthy chickens reveals a large diversity of the eukaryote viral community, including novel circular single-stranded DNA viruses –  Diane Lima – Journal of General Virology

Studies on the Virome of the Entomopathogenic Fungus Beauveria bassiana Reveal Novel dsRNA Elements and Mild Hypervirulence – Ioly Kotta-Loizou – PLOS PATHOGENS

Microbes in the news 

Microbiome Science Could Bring a Revolution in Medical Care –  Lois Parshley – NBC NEWS

Is showering everyday bad for you? New research says yes  – Sarah Young – The INDEPENDENT

Rapidly identifying life-threatening bacteria in hospitals –

Bacteria May Be Altering Your Brain To Suppress Your Appetite When You’re Sick – Josh Davis – IFL Science

Stanford Medicine and uBiome Investigate Relationship Between Gut Bacteria and Diabetes – Julie Taylor – Prweb

Microbes in the news

*Pathogen-Mediated Inhibition of Anorexia Promotes Host Survival and Transmission – Sheila Rao – Cell

Microbes on the market 

Global Human Microbiome Market Is Expected to Witness a Steady Growth By 2020 – MedGadget

Daily Dog Diet Significantly Influences Canine Gut Microbiome, Report Says – Kalyan Kumar – Tech Times

Pete’s non-microbiology picks

Terrestrial discharges mediate trophic shifts and enhance methylmercury accumulation in estuarine biota – Sofi Jonsson – Science Advances