April 17, 2018

Today’s Digest is brief, but not without highlights. Brazilian and MIT scientists created artificial antimicrobial peptides using computer algorithms, ecologists model intransitive competition, and we urgently need to tackle flesh-eating bacteria. In addition, do check out several new issues’ table of contents now, if you have access.

General microbiology

** In silico optimization of a guava antimicrobial peptide enables combinatorial exploration for peptide design – William F. Porto et al. – Nature Communications

Press: Artificial antimicrobial peptides could help overcome drug-resistant bacteria – Anne Trafton – MIT News

Memories Are Made of This: Bacteria Remember Who Their Enemies Are with CRISPRs – Marcia Stone – BioScience

Human gut microbiome

Review: Drug‐induced enterocolitis: Prevention and management in primary care – Ignazio Grattagliano et al. – Journal of Digestive Diseases

Journal of Gastroenterology and Hepatology – Issue Information – TOC

Animal experiments

Gnotobiotic and Conventional Mouse Systems to Support Microbiota Based Studies – Richard Lavin et al. – Current Protocols in Immunology

Food Microbiology

Journal of Food Science – Issue Information – TOC

Plant, root and soil microbiome

Commentary: Taking the step: from Evo‐Devo to plant–microbe interaction evolution with the liverwort Marchantia – Mélanie Rich and Pierre‐Marc Delaux – New Phytologist

** Intransitive competition is common across five major taxonomic groups and is driven by productivity, competitive rank and functional traits – Santiago Soliveres et al. – Journal of Ecology

Preprint: Phylogenomics reveals dynamic evolution of fungal nitric oxide reductases and their relationship to secondary metabolism – Steven A Higgins et al. – bioRxiv

Phages and viruses

Preprint: Biology and taxonomy of crAss-like bacteriophages, the most abundant virus in the human gut – Emma Guerin et al. – bioRxiv

Preprint: Modelling phage-bacteria interactions driving predation and horizontal gene transfer – Jorge Moura de Sousa et al. – bioRxiv

Microbes in the news

Could Microbiota Predict Response to Anti-TNF Agents in Spondyloarthritis? – Kelly Davio – The Center for Biosimilars

You cannot escape poop bacteria – Sara Chodosh – Popular Science

Scientists Want to Replace Pesticides With Bacteria – Elizabeth G Dunn – Bloomberg Businessweek

Spikes of graphene can kill bacteria on implants – Science Daily

** Flesh-eating bacteria cases on the rise and we need an urgent response – Daniel O’Brien – The Conversation

Bacteria and feces found in fake cosmetics similar to popular makeup brands – Miriam Hernandez – ABC13

BESSY II sheds light on how the internal compass is constructed in magnetotactic bacteria – Science Daily

Connection Between Gut Bacteria And Autoimmunity Strengthens – Julianna LeMieux – American Council on Science and Health

In pictures: The bacteria living on your hands right now – Gaya Chandramohan – Channel NewsAsia


April 10, 2018

After a brief hiatus, your Digest is back! After screening several hundred papers, progress seems to concentrate on a selected fields, including human gut microbiome and plant/soil microbiome. The WHO advocates for a global atlas of zoonotic viruses, a PDF link to a book volume full of application of microbiome engineering in agriculture, environmental protection and industry, and 16s rDNA primers can cross-react with mitochondrial sequences in eukaryotic cells. Last but not least, what can we all do to help young scientists, including ourselves, cope with immense pressure and distress?

General microbiology

Role of Partially Saturated Canthaxanthin and Ergosterol in the Survival of Aspergillus carbonarius Mutant at Extreme Acidic Condition – A. Kumar et al. – Microbiology

Coupled iron-microbial catalysis for CO2 hydrogenation with multispecies microbial communities – Elise Blanchet et al. – Chemical Engineering Journal

An integrated membrane bioreactor system with iron-dosing and side-stream co-fermentation for enhanced nutrient removal and recovery: System performance and microbial community analysis – Ruo-hong Li et al. – Bioresource Technology

The Microbiome and Population Health: Considerations to Enhance Study Design and Data Analysis in Observational and Interventional Epidemiology – Ryan T Demmer – American Journal of Epidemiology

Robust, linear correlations between growth rates and β-lactam–mediated lysis rates – Anna J. Lee et al. – PNAS USA

Human oral microbiome

Apical periodontitis: preliminary assessment of microbiota by 16S rRNA high throughput amplicon target sequencing – Federico Mussano and Ilario Ferrocino et al. – BMC Oral Health

Human gut microbiome

A feasibility study: association between gut microbiota enterotype and antibody response to seasonal trivalent influenza vaccine in adults – Nick Shortt and Hazel Poyntz et al. – Clinical & Translational Immunology

Gut-dependent microbial translocation induces inflammation and cardiovascular events after ST-elevation myocardial infarction – Xin Zhou, Jing Li and Junli Guo et al. – Microbiome

Book chapter: Influence of the Gut Microbiome on Immune Development During Early Life – Shankar S. Iyer and Richard S. Blumberg – Physiology of the Gastrointestinal Tract (Sixth Edition)

Book chapter: Gut Barrier: Innate Immunity – Gerco den Hartog et al. – Physiology of the Gastrointestinal Tract (Sixth Edition)

Review: Molecular Pathophysiology of Epithelial Barrier Dysfunction in Inflammatory Bowel Diseases – Jessica Y. Lee et al. – Proteomes

Impact of tart cherries polyphenols on the human gut microbiota and phenolic metabolites in vitro and in vivo – Alba C. Mayta-Apaza et al. – The Journal of Nutritional Biochemistry

Characterization of the duodenal bacterial microbiota in patients with pancreatic head cancer vs. healthy controls – Qi-Xiang Mei et al. – Pancreatology

Human multi-site microbiome

Microbiota potential for the treatment of sexual dysfunction – Hassan Tirandaz et al. – Medical Hypotheses

Animal experiments

Nile tilapia: Effects of Lactogen 13, a New Probiotic Preparation, on Gut Microbiota and Endocrine Signals Controlling Growth and Appetite of Oreochromis niloticus Juveniles – Gioacchini Giorgia et al. – Microbial Ecology

Effects of shenling baizhu powder herbal formula on intestinal microbiota in high-fat diet-induced NAFLD rats – Yupei Zhang et al. – Biomedicine & Pharmacotherapy

Gut Microbiota Promotes Tumor Growth in Mice by Modulating Immune Response – Vrishketan Sethi et al. – Gastroenterology

The effects of feeding monensin on rumen microbial communities and methanogenesis in bred heifers fed in a drylot – E.A. Melchior et al. – Livestock Science

Identification, characterization and selection of autochthonous lactic acid bacteria as probiotic for feedlot cattle – Natalia C. Maldonado et al. – Livestock Science

Glyphosate based- herbicide exposure affects gut microbiota, anxiety and depression-like behaviors in mice – Yassine Aitbali et al. – Neurotoxicology and Teratology

Animal microbiome

Characterization of the bacterial community in different parts of the gut of sea cucumber (Apostichopus Japonicus) and its variation during gut regeneration – Luo Wang et al. – Aquaculture Research

Review: The adherence and colonization of microorganisms in fish gastrointestinal tract – Xuemei Li et al. – Reviews in Aquaculture

Effect of Saccharomyces boulardii and Bacillus subtilis B10 on gut microbiota modulation in broiler – Chubin Qin and Li Gong et al. – Animal Nutrition

Metabolomics Study of Immune Responses of New Zealand Greenshell™ Mussels (Perna canaliculus) Infected with Pathogenic Vibrio sp. – Thao V. Nguyen et al. – Marine Biotechnology

Review: Use of antibiotics in broiler production: Global impacts and alternatives – Youcef Mehdi et al. – Animal Nutrition

Food Microbiome

PDF: High-Throughput rRNA Gene Sequencing Reveals High and Complex Bacterial Diversity Associated with Brazilian Coffee Bean Fermentation – Dão Pedro de Carvalho Neto et al. – Food Technology and Biotechnology

The impact of vegan production on the kimchi microbiome – Michelle Zabat et al. – Food Microbiology

Plant, root and soil microbiome

Soil abiotic variables are more important than Salicaceae phylogeny or habitat specialization in determining soil microbial community structure – Sonya Erlandson et al. – Molecular Ecology

RNA-based analyses reveal fungal communities structured by a senescence gradient in the moss Dicranum scoparium and the presence of putative multi-trophic fungi – Ko‐Hsuan Chen et al. – New Phytologist

Microbial diversity changes with rhizosphere and hydrocarbons in contrasting soils – Muhammad Atikul Islam Khan et al. – Ecotoxicology and Environmental Safety

Effects of redox potential on soil Cadmium solubility: Insight into microbial community – Delong Meng et al. – Journal of Environmental Sciences

Long-term phosphorus application to a maize monoculture influences the soil microbial community and its feedback effects on maize seedling biomass – Ming Lang et al. – Applied Soil Ecology

Book chapter: Differential Responses of Plants to Biotic Stress and the Role of Metabolites – Maham Saddique et al. – Plant Metabolites and Regulation Under Environmental Stress

Role of Phenolic Acids from the Rhizosphere Soils of Panax notoginseng as a Double-Edge Sword in the Occurrence of Root-Rot Disease – Ya-Meng Zhao et al. – Molecules

Forum: From Petri Dishes to Model Ecosystems – Oskar Siemianowski et al. – Trends in Plant Science

An Insight into Catechins Metabolic Pathways of Camellia sinensis Based on Genome and Transcriptome Analysis – Wenzhao Wang et al. – Journal of Agricultural and Food Chemistry

Seasonal characterization of sugarcane vinasse: Assessing environmental impacts from fertirrigation and the bioenergy recovery potential through biodigestion – Lucas Tadeu Fuess et al. – Science of The Total Environment

Soil microbial biomass: A key soil driver in management of ecosystem functioning – Jay Shankar Singh and Vijay Kumar Gupta – Science of The Total Environment

Phosphorus fertilising potential of fly ash and effects on soil microbiota and crop – Deborah Schönegger et al. – Resources, Conservation and Recycling

Response of the soil microbial community to different fertilizer inputs in a wheat-maize rotation on a calcareous soil – Shuikuan Bei et al. – Agriculture, Ecosystems & Environment

Water and extremophile microbiome

Bacterial Diversity and Functional Activity of Microbial Communities in Hot Springs of the Baikal Rift Zone – E. V. Lavrentyeva et al. – Microbiology

Microbial Community Composition and Rates of the Methane Cycle Microbial Processes in the Upper Sediments of the Yamal Sector of the Southwestern Kara Sea – A. S. Savvichev et al. – Microbiology

Nematode-associated microbial taxa do not correlate with host phylogeny, geographic region or feeding morphology in marine sediment habitats – Taruna Schuelke et al. – Molecular Ecology

Discriminating activated sludge flocs from biofilm microbial communities in a novel pilot-scale reciprocation MBR using high-throughput 16S rRNA gene sequencing – Ryan De Sotto et al. – Journal of Environmental Management

PDF: Divergent assemblage patterns of abundant and rare microbial sub-communities in response to inorganic carbon stresses in a simultaneous anammox and denitrification (SAD) system – Duntao Shu et al. – Bioresource Technology

Antibiotic resistance in wastewater treatment plants: Tackling the black box – Célia M. Manaia et al. – Environment International

Phages and viruses

** Building a global atlas of zoonotic viruses – Dennis Carroll et al. – Bulletin of WHO

Phages infecting Faecalibacterium prausnitzii belong to novel viral genera that help to decipher intestinal viromes – Jeffrey K. Cornuault et al. – Microbiome

Dual Insect specific virus infection limits Arbovirus replication in Aedes mosquito cells – Michaela J. Schultz et al. – Virology


** Taxon Disappearance from Microbiome Analysis Reinforces the Value of Mock Communities as a Standard in Every Sequencing Run – Yi-Chun Yeh et al. – mSystems

Hemolymph Microbiomes of Three Aquatic Invertebrates as Revealed by a New Cell Extraction Method – Xinxu Zhang et al. – Applied and Environmental Microbiology

Clinical impact of rapid bacterial identification by MALDI-TOF MS combined with the bêta-LACTA™ test on early antibiotic adaptation by an antimicrobial stewardship team in bloodstream infections – A. Mizrahi et al. – Infectious Diseases

Genetic engineering of bee gut microbiome bacteria with a toolkit for modular assembly of broad-host-range plasmids – Sean P. Leonard et al. – ACS Synthetic Biology

** Cross-Reactivity of Prokaryotic 16S rDNA-Specific Primers to Eukaryotic DNA: Mistaken Microbial Community Profiling in Environmental Samples – Shailendra Yadav et al. – Current Microbiology

Detection of Pathogenic Microorganisms by Microfluidics Based Analytical Methods – Dongxue Zhang et al. – Analytical Chemistry

** Book chapter PDF: Microbial, Plant, Environmental and Industrial Technologies – Debmalya Barh and Vasco Azevedo – Microbial Omics: Applications in Biotechnology

Metabolome- and genome-scale model analyses for engineering of Aureobasidium pullulans to enhance polymalic acid and malic acid production from sugarcane molasses – Jun Feng and Jing Yang et al. – Biotechnology for Biofuels

eDNA-based bioassessment of coastal sediments impacted by an oil spill – Yuwei Xie et al. – Environmental Pollution

Using natural biomass microorganisms for drinking water denitrification – Darleila Damasceno Costa et al. – Journal of Environmental Management


Cluster and Multiple Correspondence Analyses in Rheumatology: Paths to Uncovering Relationships in a Sea of Data – Lu Han et al. – Rheumatic Disease Clinics of North America

Microbes in the news

Faecal transplantation: do not try this at home – Talha Khan Burki – The Lancet Gastroenterology & Hepatology

Non-microbiology picks

** Editorial: Time to talk about why so many postgrads have poor mental health – Nature

Editorial: Using Preprints for Journal Clubs – Arturo Casadevall and Neil Gow – mBio


March 20, 2018

Still short and sweet. Highlights include combining bacterial and archaeal membranes, a reference catalog for the rumen microbiome and your gut microbiome keeping you awake at night, but really?


Research Associate, Microbiology – Kintai Therapeutics – Cambridge, MA

Partners with relevant publications are needed – Faculty of Agriculture, Ain Shams University – Egypt

Biomedical Scientist or Trainee Biomedical Scientist (Microbiology) – York Teaching Hospital, UK

General microbiology

Identification of Biofilm Inhibitors by Screening Combinatorial Libraries of Metal Oxide Thin Films – Michal M. Dykas et al. – Applied Materials and Interfaces

** Converting Escherichia coli into an archaebacterium with a hybrid heterochiral membrane – Antonella Caforio et al. – PNAS, USA

Press: Scientists engineer new life form with mixed Bacteria and Archaea membrane – Tibi Puiu – ZME Science

Preprint: Antibiotic-induced cell chaining triggers pneumococcal competence by reshaping quorum sensing to autocrine signaling – Arnau Domenech et al. – bioRxiv

Animal microbiome

** Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection – Rekha Seshadri et al. – Nature Biotechnology

Press: A reference catalog for the rumen microbiome – Joint Genome Institute, DOE

Water and extremophile microbiome

Preprint: Growth arrest in the active rare biosphere – Bela Hausmann et al. – bioRxiv

Phages and viruses

Preprint: Avian keratin disorder of Alaska black-capped chickadees is associated with Poecivirus infection – Maxine Zylberberg et al. -bioRxiv


Essay: Which experimental systems should we use for human microbiome science? – Angela E. Douglas – PLoS Biology

Preprint: Efficient genome editing of Magnetospirillum magneticum AMB-1 by CRISPR-Cas9 system for analyzing magnetotactic behavior – Haitao Chen et al. – bioRxiv

Microbes in the news

Could the Microbiome Treat Side Effects of Stem Cell Transplants? – Alexander Burik – Labiotech

Rapid Starch Increases, Decreases in Horse Diets Upset Gut Microbiome – Kristen M. Janicki – the Horse

** Could it be your gut keeping you awake at night? – Kate Leaver – the Guardian

Molecular cuisine for gut bacteria – ScienceDaily

Bacteria churn out a million potential protein drugs – KATRINA KRÄMER – ChemistryWorld

Bacteria that can kill wild sheep and goats has never turned up in Alaska — until now – Zaz Hollander – Anchorage Daily News

News Bites: New molecule able to kill drug-resistant bacteria, FDA approves at-home breast cancer risk test – Chu Meiyi – MIMS Today

Non-antibiotic drugs promote antibiotic resistance – The Economist

Microbes on the market

Microbiome Therapeutics Market Overview with Qualitative analysis, Competitive landscape & Forecast 2023 – Healthcare Journal

March 14, 2018

Today’s Digest adds to the growing literature of microbiome research. Highlights include the synergistic relationship between fungi and an invasive plant, enteral nutrition may help maintain the gastrointestinal function of critically ill patients, and the NCI calls for advancing epidemiologic research on the human microbiome.


Student Trainee Microbiology Student Trainee Usda Pathways Internship Program Job in SAINT LOUIS, MO – Opening from 3/12-3/16, 2018

General microbiology

Antibiotic-induced population fluctuations and stochastic clearance of bacteria – Jessica Coates et al. – eLife

Press: Biophysicists discover how small populations of bacteria survive treatment – Science Daily

Preprint: Division of labor during biofilm matrix production – Anna Dragos et al. – bioRxiv

Isolation and characterization of two novel groups of kanamycin-resistance ColE1-like plasmids in Salmonella enterica serotypes from food animals – Chin-Yi Chen et al. – PLoS One

Human nasal microbiome

Genomic differences between nasal Staphylococcus aureus from hog slaughterhouse workers and their communities – Yaqi You et al. – PLoS One

Human oral microbiome

In vitro: pH changes of mixed biofilms of Streptococcus mutans and Candida albicans after exposure to sucrose solutions in vitro – Thamires Priscila Cavazana et al. – Archives of Oral Biology

Human lung microbiome

Fluctuations in airway bacterial communities associated with clinical states and disease stages in cystic fibrosis – Lisa A. Carmody et al. – PLoS One

Human gut microbiome

** Review: Effects of enteral nutrition on gastrointestinal function in patients who are critically ill – Michael Schörghuber and Sonja Fruhwald – The Lancet Gastroenterology & Hepatology

An overview on the interplay between nutraceuticals and gut microbiota – Adrian Catinean et al. – PeerJ

Animal experiments

Aronia berry (Aronia mitschurinii ‘Viking’) inhibits colitis in mice and inhibits T cell tumour necrosis factor-α secretion – Derek A. Martin et al. – Journal of Functional Foods

Mouse: Diet, Genetics, and the Gut Microbiome Drive Dynamic Changes in Plasma Metabolites – Shiho Fujisaka et al. – Cell Reports

Animal microbiome

Pathology and bacteria related to digital dermatitis in dairy cattle in all year round grazing system in Brazil – Tiago F. Moreira et al. – PLoS One

Food microbiology

The potential use of leaf extracts of two Newtonia (Fabaceae) species to treat diarrhoea – K.E. Motlhatlego et al. – South African Journal of Botany

Editorial: The interactions between food components and human nutrition – Charles Brennan – International Journal of Food Science & Technology

Plant, root and soil microbiome

** The unspecificity of the relationships between the invasive Pennisetum setaceum and mycorrhizal fungi may provide advantages during its establishment at semiarid Mediterranean sites – G. Rodríguez-Caballero et al. – Science of the Total Environment

Review: Environmental and public health related risk of veterinary zinc in pig production – Using Denmark as an example – John Jensen et al. – Environment International

Hydrophobins contribute to root colonization and stress responses in the rhizosphere-competent insect pathogenic fungus Beauveria bassiana – Soumya Moonjely et al. – Microbiology

Perspective: Tracing the role of human civilization in the globalization of plant pathogens – Alberto Santini et al. – ISME

Water and extremophile microbiome

Review: Surface water flooding, groundwater contamination, and enteric disease in developed countries: A scoping review of connections and consequences – L. Andrade et al. – Environmental Pollution

Domestic wastewater treatment and power generation in continuous flow air-cathode stacked microbial fuel cell: Effect of series and parallel configuration – Edson Baltazar Estrada-Arriaga et al. – Journal of Environmental Management

Effect of particle size and heterogeneity on sediment biofilm metabolism and nutrient uptake scaled using two approaches – Samuel P. Parker et al. – Ecosphere

Phages and viruses

Differential impact of lytic viruses on prokaryotic morphopopulations in a tropical estuarine system (Cochin estuary, India) – Vijayan Jasna et al. – PLoS One


A Bayesian Semiparametric Regression Model for Joint Analysis of Microbiome Data – Juhee Lee and Marilou Sison-Mangus – Frontiers in Microbiology

A systems pharmacology model for inflammatory bowel disease – Violeta Balbas-Martinez et al. – PLoS One

Microbes in the news

** Of Microbes and Men: Advancing Epidemiologic Research on the Human Microbiome – Victoria Fisher – National Cancer Institute

Opinion: Inflammatory bowel disease: complexity and variability need integration – Claudio Fiocchi – Frontiers in Medicine

Stress: How social conflict alters gut bacteria – Maria Cohut – Medical News Today

High-Fiber Generates Gut Bacteria Good for Type 2 Diabetes – Becky McCall – Medscape

New pathway may lead to improved probiotic products – Tim Lundeen – Feedstuffs

Probiotic potential: Specific gut microbes could cut severity of parasitic infections in developing countries – Nathan Gray – NUTRAingredients

Wandering Gut Bacteria Could Be Behind Conditions Like Lupus – Abby Norman – Futurism

Model Can Predict Which Bacteria will Engraft after FMT – Rachel Lutz – MD Magazine

Can Coral Microbes Protect Reefs From Climate Change? – Amelia Urry – NewsDeeply

Study: Several important vaginal metabolites elevated in smokers – Bob Kronemyer – Modern Medicine

Doctors collect viruses from pond and employ them to combat a man’s antibiotic resistance infection in man’s heart – Mark Kaufman – Mashable

Making good bacteria more resilient – Gali Weinreb – Globes

Study links decline of ‘good’ bacteria in infants to higher long-term increases in pH of poo – Tim Cutcliffe – NUTRAingredients

Microbes on the market

German biotech company wants to turn old PCs into gold – Jeremy Gray – Handelsblatt Global – European Business & Finance News


February 16, 2018

Happy Lunar New Year of the Dog!

Today’s Digest contains many news pieces, and also features a major paper on strain tracking post fecal microbiota transplantation, a review on antibacterial proteins shaping the intestinal microbiota, and a call for action to build communities for bioinformatics programming.


Postdoctoral Scholars of Microbiology, School of Life Sciences – University of Nevada Las Vegas

General microbiology

Book chapter: Agro-industrial Lignocellulosic Waste: An Alternative to Unravel the Future Bioenergy – Nidhi V. Maheshwari – Biofuels: Greenhouse Gas Mitigation and Global Warming

Review: Evolutionary Mechanisms Shaping the Maintenance of Antibiotic Resistance – Paulo Durão et al. – Trends in Microbiology

A single amino acid change in the response regulator PhoP acquired during Yersinia pestis evolution affects PhoP target gene transcription and polymyxin B susceptibility – Fukuto HS et al. – Journal of Bacteriology

Validated measurements of microbial loads on environmental surfaces in intensive care units before and after disinfecting cleaning – H. Frickmann et al. – Journal of Applied Microbiology

Human gut microbiome

Review: Proceedings of the 2017 ASPEN Research Workshop—Gastric Bypass: Role of the Gut – Ajay Kumar Jain et al. – Journal of Parenteral & Enteral Nutrition

A Phase 1 Study in Healthy Subjects to Assess the Safety, Tolerability, Pharmacokinetics, and Pharmacodynamics of Multiple Oral Doses of DS-2969b, a Novel GyrB Inhibitor – Vandell AG et al. – Antimicrobial Agents and Chemotherapy

* Antibacterial Weapons: Targeted Destruction in the Microbiota – Benoit Chassaing and Eric Cascales – Trends in Microbiology

Perspective: How to train your microbiome to eat broccoli – Sam H. Au – Science Translational Medicine

* Strain Tracking Reveals the Determinants of Bacterial Engraftment in the Human Gut Following Fecal Microbiota Transplantation – Christopher S. Smillie – Cell Host & Microbe

Press: Model of fecal transplantation predicts which bacteria will flourish – Medical Xpress

Preprint: Spatial variation of the native colon microbiota in healthy adults – Kaitlin J Flynn et al. – bioRxiv

Preprint: The intestinal microbiota predisposes to traveller’s diarrhoea and to the carriage of multidrug-resistant Enterobacteriaceae after travelling to tropical regions – Stefano Leo et al. – bioRxiv

Animal experiments

Extracellular cholesterol oxidase production by Streptomyces aegyptia, in vitro anticancer activities against rhabdomyosarcoma, breast cancer cell-lines and in vivo apoptosis – Noura El-Ahmady El-Naggar et al. – Scientific Reports

Molecular analyses of two bacterial sampling methods in ligature-induced periodontitis in rats – Carla Raquel Fontana et al. – Clinical and Experimental Dental Research

Animal microbiome

Preprint: Drosophila melanogaster establishes a species-specific mutualistic interaction with stable gut-colonizing bacteria – Ines Silva Pais et al. – bioRxiv

Plant, root and soil microbiome

Removal of metals and their pools in plant in response to plant diversity in microcosms of floating constructed wetlands – Wenjuan Han et al. – Ecological Engineering

The Sesamum indicum rhizosphere associated bacterium: A source of Antifungal compound – Renu Chaudhary et al. – Current Topics in Medicinal Chemistry

Intensifying rotations increases soil carbon, fungi, and aggregation in semi-arid agroecosystems – Steven T. Rosenzweig et al. – Agriculture, Ecosystems & Environment

Impact of oxytetracycline and bacterial bioaugmentation on the efficiency and microbial community structure of a pesticide-degrading biomixture – Víctor Castro-Gutiérrez et al. – Environmental Science and Pollution Research

Indigenous endophytic seed bacteria promote seedling development and defend against fungal disease in browntop millet (Urochloa ramosa L.) – S.K. Verma and J.F. White – Journal of Applied Microbiology

Water and extremophile microbiome

Halophilic starch degrading bacteria isolated from Sambhar Lake, India, as potential anode catalyst in Microbial fuel cell: A promising process for saline water treatment – Ankisha Vijay et al. – Bioresource Technology

Sequestration and utilization of carbon dioxide by chemical and biological methods for biofuels and biomaterials by chemoautotrophs: Opportunities and challenges – Indu Shekhar Thakur et al. – Bioresource Technology

Small eukaryotic phytoplankton communities in tropical waters off Brazil are dominated by symbioses between Haptophyta and nitrogen-fixing cyanobacteria – Catherine Gérikas Ribeiro et al. – ISME

Neobodonids are dominant kinetoplastids in the global ocean – Olga Flegontova et al. – Environmental Microbiology

Food microbiology

Review: Whole genome sequencing as a typing tool for foodborne pathogens like Listeria monocytogenes – The way towards global harmonisation and data exchange – StefanieLüth et al. – Trends in Food Science & Technology

Phages and viruses

Book chapter: Tick-Borne Viruses and Host Skin Interface – Mária Kazimírová et al. – Skin and Arthropod Vectors

Preprint: The virome of Drosophila suzukii, an invasive pest of soft fruit – Nathan C Medd et al. – bioRxiv


Microfluidics-based liquid chromatography/mass spectrometry multiple reaction monitoring approach for the relative quantification of Burkholderia cenocepacia secreted virulence factors – Sofie Depluverez et al. – Rapid Communications in Mass Spectrometry

Microbes in the news

Surgeon sets new frontiers in battle against bacteria! – WBWire

The effect of antibacterials on the skin – Zoe Diana Draelo – Dermatology Times

Donor, Recipient Strain Analyses Offer Fecal Transplant Engraftment Clues – Genome Web

Australian Scientist Gets $1 Million to See if Probiotics Can Help Children with CF – Carolina Henriques – Cystic Fibrosis News Today

Do probiotics work? Answers to this and other gut-wrenching questions – Joanna Clay – USC News

Monitoring bacteria on whale skin – EurekAlert

Bacteria Hidden Under Our Feet May Be a New Weapon Against Superbugs – Kristin Houser – Futurism

Which probiotic is right for you? These are the exact bacteria strains to look for – Emily Laurence – Well and Good

How can we harness the power of bacteria-killing viruses? – Claire O’Connell – Sillcon Republic

Manipulating gut bacteria may cut obesity, diabetes risk – The Peninsula

Microbes on the market

Carbiotix launches world’s lowest cost microbiome test – Nathan Gray – Nutra Ingredients

Scientific Communication and Education

* Preprint: Building a local community of practice in scientific programming for Life Scientists – Sarah L.R. Stevens et al. – bioRxiv


February 12, 2018

A rich Digest to start your work week. Highlights include a review in Lancet cautionary about precision nutrition, an NIH metagenome FTP site, and a sampling of songbirds that reveals high prevalence of antibiotic resistant bacteria.


Intellectual Property x The Microbiome – SF Bay Area Microbiome Meetup

General microbiology

Expanding our Understanding of the Role of the Microbiome in Health and Disease – Rob Knight – Archives of Medical Research

* NIH Metagnome FTP site

* The Ecosystem Services of Animal Microbiomes – E.A. McKenney et al. – Molecular Ecology

Preprint: Experimental Evolution of Cell Shape in Bacteria – Paul Richard Yulo et al. – bioRxiv

Human skin microbiome

In vitro: Yeasts from skin colonization are able to cross the acellular dermal matrix – Isabele Carrilho Jarros et al. – Microbial Pathogenesis

Human vaginal microbiome

Review: Immunology of the Uterine and Vaginal Mucosae – Jordan Z. Zhou et al. – Trends in Immunology

Human gut microbiome

The Role of Diet in the Treatment of Irritable Bowel Syndrome : A Systematic Review – Rajdeep Singh et al. – Gastroenterology Clinics of North America

Review: Metabolic Surgery : Weight Loss, Diabetes, and Beyond – Manan Pareek et al. – Journal of the American College of Cardiology

Review: Environmental Noise and the Cardiovascular System – Thomas Münzel et al. – Journal of the American College of Cardiology

The effects of synbiotic supplementation on insulin resistance/sensitivity, lipid profile and total antioxidant capacity in women with gestational diabetes mellitus: a randomized double blind placebo controlled clinical trial – Zohoor Nabhani et al. – Diabetes Research and Clinical Practice

* Precision nutrition for prevention and management of type 2 diabetes – Dong D Wang and Frank B Hu – The Lancet Diabetes & Endocrinology

The Small Intestine Converts Dietary Fructose into Glucose and Organic Acids – Cholsoon Jang et al. – Cell Metabolism

Review: Therapeutic implications of the gastrointestinal microbiome – Purna C Kayshap and Eamonn MM Quigley – Current Opinion in Pharmacology

Risk factors for Clostridium difficile infection in intestinal transplant recipients during the first year post transplant – Luis Guzman et al. – Transplant Infectious Disease


Review: Advances in computational metabolomics and databases deepen the understanding of metabolisms – Hiroshi Tsugawa – Current Opinion in Biotechnology

Animal experiments

Rat: Onion quercetin monoglycosides alter microbial activity and increase antioxidant capacity – Katarzyna Grzelak-Błaszczyk et al. – The Journal of Nutritional Biochemistry

Preview: Cultivating a Relationship with Gut Bacteria – Catherine E. Schretter and Sarkis K. Mazmanian – Cell Metabolism

Effect of two seaweed polysaccharides on intestinal microbiota in mice evaluated by illumina PE250 sequencing – Zhongshan Zhang et al. – International Journal of Biological Macromolecules

Green Tea Polyphenols Modulate Colonic Microbiota Diversity and Lipid Metabolism in High-Fat Diet Treated HFA Mice – Li Wang et al. – Journal of Food Science

Animal microbiome

* Antibiotic resistant bacteria are widespread in songbirds across rural and urban environments – Diana L. Carter et al. – Science of The Total Environment

Effects of chlorogenic acids-enriched extract from Eucommia ulmoides leaves on growth performance, stress response, antioxidant status and meat quality of lambs subjected or not to transport stress – H.W. Liu et al. – Animal Feed Science and Technology

Characterisation of Bergeyella spp. isolated from the nasal cavities of piglets – M. Lorenzo de Arriba et al. – The Veterinary Journal

Horse: The relationships between faecal egg counts and gut microbial composition in UK Thoroughbreds infected by cyathostomins – L.E. Peachey et al. – International Journal for Parasitology

The effects singular or combined administration of fermentable fiber and probiotic on mucosal immune parameters, digestive enzyme activity, gut microbiota and growth performance of Caspian white fish (Rutilus frisii kutum) fingerlings – Ali Taheri Mirghaed et al. – Fish & Shellfish Immunology

Diagnostics and Treatments in Chronic Diarrhea and Weight Loss in Horses – Olimpo Oliver-Espinosa – Veterinary Clinics: Equine Practice

Plant, root and soil microbiome

Diversifying crop rotation increased metabolic soil diversity and activity of the microbial community – Luciana D’Acunto et al. – Agriculture, Ecosystems & Environment

The impact of reconstructed soils following oil sands exploitation on aspen and its associated belowground microbiome – Franck Stefani et al. – Scientific Reports

Water and extremophile microbiome

Antibiotic resistome in landfill leachate from different cities of China deciphered by metagenomic analysis – Renxin Zhao et al. – Water Research

Microbiomes in extremely acidic environments: functionalities and interactions that allow survival and growth of prokaryotes at low pH – Raquel Quatrini and D Barrie Johnson – Current Opinion in Microbiology

Effect of heat shock on hot water plumbing microbiota and Legionella pneumophila control – Pan Ji et al. – Microbiome

Food microbiology

Variability within the dominant microbiota of sliced cooked poultry products at expiration date in the Belgian retail – Wim Geeraerts et al. – Food Microbiology

Modelling the growth of Listeria monocytogenes in Mediterranean fish species from aquaculture production – Araceli Bolívar et al. – International Journal of Food Microbiology

Prebiotic in fruit juice: processing challenges, advances, and perspectives – Thatyane Vidal Fonteles and Sueli Rodrigues – Current Opinion in Food Science


Multi-omics approach to elucidate the gut microbiota activity. Metaproteomics and metagenomics connection – Maria Guirro et al. – Electrophoresis

Microbes in the news

Can Your Gut Protect You Against Cancer? – Michelle Schoffro Cook – Care2

Millions of Mosquitoes to Be Released in Florida for Good Cause – Inside Edition

Using Special UV Light in Public Spaces Could Kill Flu Viruses, Bacteria – Jakob Nielson – Apex Tribune


January 26, 2018

Here’s your daily Digest after a burst of articles. High-intensity swimming can impact immunity and microbial diversity in mice. Intestinal microbiota can alter host epigenetic in mice. A sad story of an eight year old boy killed by flesh eating bacteria…

Jobs and events

The Human Microbiome – Heidelberg, Germany


General microbiology

Peptidoglycan compositional analysis of Enterococcus faecalis biofilm by stable isotope labeling by amino acids in bacterial culture – James D. Chang et al. – Biochemistry

Pregnancy and early life

Vaginal dysbiosis increases risk of preterm fetal membrane rupture, neonatal sepsis and is exacerbated by erythromycin – Richard G. Brown et al. – BMC Medicine

Human skin microbiome

* Review: Skin microbiota–host interactions – Y. Erin Chen et al. – Nature

Human vaginal microbiome

Probiotics in the Prevention and Treatment of Postmenopausal Vaginal Infections: Review Article – Jun-Mo Kim and Yoo Jin Park – Journal of Menopausal Medicine

Human oral microbiome

Silver Fluoride as a Treatment for Dental Caries – J.A. Horst – Advances in Dental Research

Therapeutic Strategies Targeting Cariogenic Biofilm Microenvironment – Y. Liu & Z. Ren et al. – Advances in Dental Research

Video protocol: Oral Biofilm Sampling for Microbiome Analysis in Healthy Children – Elisabeth Santigli et al. – JoVE

Human gut microbiome

Review: Clostridium difficile control measures: current and future methods for prevention – Erik R. Dubberke & Carlos Mejia-Chew – Expert Review of Anti-infective Therapy

Review: Colorectal Cancers: An Update on Their Molecular Pathology – Kentaro Inamura – Cancers

Review: Role of microbiota-derived lipopolysaccharide in adipose tissue inflammation, adipocyte size and pyroptosis during obesity – Lars-Georg Hersoug et al. – Nutrition Research Reviews

* Review: Role of priority effects in the early-life assembly of the gut microbiota – Daniel Sprockett et al. – Nature Reviews Gastroenterology & Hepatology

Review: Upper Respiratory Symptoms, Gut Health and Mucosal Immunity in Athletes – Candice Colbey et al. – Sports Medicine

Review: Microbiota in obesity: interactions with enteroendocrine, immune and central nervous systems – R. J. Mulders et al. – Obesity Reviews

Factors Associated with the Use of Fecal Microbiota Transplant in Patients with Recurrent Clostridium difficile Infections – Sehrish Jamot et al. – Infection Control & Hospital Epidemiology

Animal experiments

Zebrafish: Dysregulation of Intestinal Health by Environmental Pollutants: Involvement of the Estrogen Receptor and Aryl Hydrocarbon Receptor – Lianguo Chen et al. – Environmental Science & Technology

Probiotic/prebiotic correction for adverse effects of iron fortification on intestinal resistance to Salmonella infection in weaning mice – Feifei Lin et al. – Food & Function

Beneficial effects of consumption of acerola, cashew or guava processing by-products on intestinal health and lipid metabolism in dyslipidaemic female Wistar rats – Kamila Sabino Batista et al. – British Journal of Nutrition

Rat: Berberine Modulates Gut Microbiota and Reduces Insulin Resistance via the TLR4 Signaling Pathway – Dan Liu & Yiyi Zhang et al. – Experimental and Clinical Endocrinology & Diabetes

Early microbial colonization affects DNA methylation of genes related to intestinal immunity and metabolism in preterm pigs – Xiaoyu Pan et al. – DNA Research

Mouse: Innate and adaptive lymphocytes sequentially shape the gut microbiota and lipid metabolism – Kairui Mao et al. – Nature

* Influence of excessive exercise on immunity, metabolism and gut microbial diversity in an overtraining mice model – Xin Yuan et al. – Scandinavian Journal of Medicine & Science in Sports

* Mouse: An obesity-associated gut microbiome reprograms the intestinal epigenome and leads to altered colonic gene expression – Yufeng Qin et al. – Genome Biology

* Gut Microbiota-Derived Short Chain Fatty Acids Induce Circadian Clock Entrainment in Mouse Peripheral Tissue – Yu Tahara et al. – Scientific Reports

Time-course responses of ileal and fecal microbiota and metabolite profiles to antibiotics in cannulated pigs – Kan Gao et al. – Applied Microbiology and Biotechnology

Preprint: Toxoplasma gondii infection triggers chronic cachexia and sustained commensal dysbiosis in mice – Jessica A Hatter et al. – bioRxiv

Animal microbiome

Rapid and Specific Methods to Differentiate Foodborne Pathogens, Campylobacter jejuni, Campylobacter coli, and the New Species Causing Spotty Liver Disease in Chickens, Campylobacter hepaticus – Thi Thu Hao Van et al. – Foodborne Pathogens and Disease

Microbial community and short-chain fatty acid profile in gastrointestinal tract of goose – H Yang et al. – Poultry Science

Exploration of the faecal microbiota and biomarker discovery in equine grass sickness – Joy Leng et al. – Journal of Proteome Research

Plant, root and soil microbiome

Amendment of Agricultural Soil with Metal Nanoparticles: Effects on Soil Enzyme Activity and Microbial Community Composition – Bahareh Asadishad et al. – Environmental Science & Technology

Induction of abiotic stress tolerance in plants by endophytic microbes – Rusi Lata et al. – Letters in Applied Microbiology

Opinion piece: Plant pathogen effector proteins as manipulators of host microbiomes? – Nick C. Snelders et al. – Molecular Plant Pathology

Water and extremophile microbiome

Metabarcoding analysis on European coastal samples reveals new molecular metazoan diversity – David Lopez-Escardo et al. – bioRxiv

Food microbiome

Fungal networks shape dynamics of bacterial dispersal and community assembly in cheese rind microbiomes – Yuanchen Zhang et al. – Nature Communications

Phages and viruses

Distinct Effects of Type I and III Interferons on Enteric Viruses – Harshad Ingle et al. – Viruses


GC-MS Analysis of Short-Chain Fatty Acids in Feces, Cecum Content, and Blood Samples – Lisa R. Hoving et al. – Clinical Metabolomics

NMR Analysis of Fecal Samples – Hye Kyong Kim et al. – Clinical Metabolomics


Spherical: an iterative workflow for assembling metagenomic datasets – Thomas C. A. Hitch and Christopher J. Creevey – BMC Bioinformatics

Microbes in the news

Middle Eastern diet increases gut microbiota diversity, shows benefit in cirrhosis – Healio

Bacterial DNA sequencing could help design ‘friendlier’ nanoparticles – Belle Dumé – Nanotechweb

Consumption of Dietary Fiber May Prevent Metabolic Syndrome – Anamika P – TGHN

Researchers Discover 10 New Immune Systems in Bacteria – Jim Daley – The Scientist

New Ocean-Dwelling, Bacteria-Killing Tailless Virus Hid in Plain Sight – Mindy Weisberger – Live Science

New method developed to detect bacteria in food and water – Ananya Mandal – News Medical

eNose Successfully Recognizes Bacteria in Common Soft Tissue Infections – Michaela Fleming – Contagion Live

Are There Zombie Viruses In The Thawing Permafrost? – Michaeleen Doucleff – NPR

* ‘He was so strong’: Boy, 8, dies from flesh-eating bacteria – by Associated Press – New York Post

Publishing and education

Preprint: Harmonizing semantic annotations for computational models in biology – Maxwell L Neal et al. – bioRxiv