September 12, 2017

Today’s post is short and sweet. A European Food Safety Authority panel releases a report on deoxynivalenol (DON), a review on the effects of obesity on depression, and fish oil might be good for your gut microbiota.

General microbiology

Viable But Non-Culturable Cells Are Persister Cells – Jun-Seob Kim et al. – bioRxiv

Regulated release of cryptococcal polysaccharide drives virulence and suppresses immune cell infiltration into the central nervous system – Steven T. Denham et al. – bioRxiv

*Scientific Opinion: Risks to human and animal health related to the presence of deoxynivalenol and its acetylated and modified forms in food and feed – EFSA Panel on Contaminants in the Food Chain et al. – EFSA Journal

Strategies for editing virulent staphylococcal phages using CRISPR-Cas10 – S.M. Nayeemul Bari et al. – ACS Synthetic Biology

Compensatory evolution facilitates the acquisition of multiple plasmids in bacteria – Alfonso Santos-Lopez et al. – bioRxiv

Human gut microbiome

The Role of Gut Microbiome in the Pathogenesis of Prostate Cancer: a Prospective, Pilot Study – Golombos DM et al. – Urology

Review: Pathogenesis of Helicobacter pylori infection – Vania Camilo et al. – Helicobacter

Helicobacter Special Issue: XXXth International Workshop on Helicobacter & Microbiota in Inflammation & Cancer

*Biological and clinical implications of herbal medicine and natural products for the treatment of inflammatory bowel disease – Bao-Jian Guo et al. – Annals of The New York Academy of Sciences

Plant non-starch polysaccharides that inhibit key enzymes linked to type 2 diabetes mellitus – Dan Liu et al. – Annals of The New York Academy of Sciences

Mini-Review: Role of microbiota in the pathogenesis of functional disorders of the lower GI tract: Work in progress – Jonna Jalanka and Robin Spiller – Neurogastroenterology and Motility

*Omega-3 fatty acids correlate with gut microbiome diversity and production of N-carbamylglutamate in middle aged and elderly women – Cristina Menni et al. – Scientific Reports

Press: Omega 3 helps the gut stay healthy, study finds – Medical Xpress

Human gut-microbiome-brain axis

*Review: Effects of obesity on depression: a role for inflammation and the gut microbiota – Schachter J et al. – Brain, Behavior, and Immunity

Preimmunization with a heat-killed preparation of Mycobacterium vaccae enhances fear extinction in the fear-potentiated startle paradigm – Fox JH et al. – Brain, Behavior, and Immunity

Animal experiments

Rapamycin treatment attenuates age-associated periodontitis in mice – An JY et al. – Geroscience

Animal microbiome

Disparity in the nasopharyngeal microbiota between healthy cattle on feed, at entry processing and with respiratory disease – Zeineldin M et al. – Veterinary Microbiology

Increased microbiome diversity at the time of infection is associated with improved growth rates of pigs after co-infection with porcine reproductive and respiratory syndrome virus (PRRSV) and porcine circovirus type 2 (PCV2) – Ober RA et al. – Veterinary Microbiology

Plant, root and soil microbiome

Seasonal and inter-annual variability in litter decomposition and nitrogen availability in a mid-Appalachian watershed – Jeff W. Atkins et al. – Ecosphere

Probiotics, Prebiotics and Synbiotics

Probiotic Supplementation in Chronic Kidney Disease: A Double-blind, Randomized, Placebo-controlled Trial – Borges NA et al. – Journal of Renal Nutrition

Apple pectin-derived oligosaccharides produce carbon dioxide radical anion in Fenton reaction and prevent growth of Escherichia coli and Staphylococcus aureus – Martinov J et al. – Food research international

Microbes in the news

Researchers found omega 3 helps the gut stay healthy – Pharmabiz

Microbes on the market

Tata and OptiBiotix seal deal for India prebiotic expansion – Gary Scattergood+ – Food Navigator Asia

Startups focus on the microbiome – Olivia Tucker – Version Weekly



September 1, 2017

A rich Digest to start your September. A special issue of Immunological Reviews on the host-microbiome interaction, water can be dangerous – both in Texas and your washing machines, and how about some music inspired by the microbiome?


Microbiology jobs in Kansas – New Scientist Jobs

Post Doctoral Researcher – The Ohio State University

Laboratory Assistant III – Microbiology – Contingent – Allegiance Health – Jackson, MI

Microbiology Lab Technician (Up to $2500, Global MNC, No experience required)

General microbiology

Towards a universal molecular microbiological test – Richard J. N. Allcock et al. – Journal of Clinical Microbiology

Human microbiome inspired antibiotics with improved β-lactam synergy against MDR Staphylococcus aureus -Chu J et al. – ACS Infectious Diseases

Pregnancy and early life

Feasibility of Metatranscriptome Analysis from Infant Gut Microbiota: Adaptation to Solid Foods Results in Increased Activity of Firmicutes at Six Months – Floor Hugenholtz et al. – International Journal of Microbiology

Human skin microbiome

Application of sebomics for the analysis of residual skin surface components to detect potential biomarkers of type-1 diabetes mellitus – Satyajit S. Shetage et al. – Scientific Reports

Human near-sterile sites

Bone Remodeling and the Microbiome – Pacifici R – Cold Spring Harbor Perspectives in Medicine

Human lung microbiome

Comparing microbiota profiles in induced and spontaneous sputum samples in COPD patients – Solveig Tangedal et al. – Respiratory Research

Human gut microbiome

Analysis of endoscopic brush samples identified mucosa-associated dysbiosis in inflammatory bowel disease – Kyohei Nishino et al. – Journal of Gastroenterology

*Review: Host-microbiota interactions and adaptive immunity – Kathy D. McCoy et al. – Immunological Reviews (Special Issue: Microbiome-Immune System Interplay)

Animal experiments

Mouse: Commensal bacteria make GPCR ligands that mimic human signalling molecules – Louis J. Cohen et al. – Nature

Review: Exposure of livestock to GM feeds: Detectability and measurement – Anna Nadal et al. – Food and Chemical Toxicology

Comparison of the Luminal and Mucosa-Associated Microbiota in the Colon of Pigs with and without Swine Dysentery -Eric R. Burrough et al. – Frontiers in Veterinary Science

Moderate Exercise Has Limited but Distinguishable Effects on the Mouse Microbiome – Emily V. Lamoureux et al. – mSystems

Animal microbiome

Metagenomic analysis reveals a green sulfur bacterium as a potential coral symbiont – Lin Cai et al. – Scientific Reports

Genomic diversification of giant enteric symbionts reflects host dietary lifestyles – David Kamanda Ngugi et al. – PNAS

Culture Media and Individual Hosts Affect the Recovery of Culturable Bacterial Diversity from Amphibian Skin – Daniel Medina et al. – Frontiers in Microbiology

Impact of egg disinfection of hatching eggs on the eggshell microbiome and bacterial load – R. Olsen et al. – Poultry Science

Plant, root and soil microbiome

Antioxidant and Antibacterial Activity of Organic Extracts of Roots of Glycyrrhiza Glabra Linn – Zafar Iqbal et al. – American Journal of Applied and Industrial Chemistry

Effect of red clover on the microbial transformation of phenanthrene and octadecane in the soil – A. V. Nazarov et al. – Eurasian Soil Science

Biogeography of plant-associated fungal symbionts in mountain ecosystems: A meta-analysis – Stephanie N. Kivlin et al. – Diversity and Distribution

Water and extremophile microbiome

Biodiversity analysis of the unique geothermal microbial ecosystem of the Blue Lagoon (Iceland) using next-generation sequencing (NGS) – Katarzyna A. Palinska et al. – Hydrobiologia

Impacts of tropospheric ozone exposure on peatland microbial consumers – Richard J. Payne et al. – Soil Biology and Biochemistry

Progress and perspectives in aquatic microbial ecology: highlights of the SAME 14, Uppsala, Sweden, 2015 – Eva S. Lindström & Paul A. del Giorgio – Aquatic Microbial Ecology

*Prevalence of β-lactamase genes in domestic washing machines and dishwashers and the impact of laundering processes on antibiotic resistant bacteria – Laura Rehberg et al. – Journal of Applied Microbiology

Built environment microbiome

A high-flow-rate impinger for the study of concentration, viability, metabolic activity, and ice nucleation activity of airborne bacteria – Tina Šantl-Temkiv et al. – Environmental Science & Technology

Phages and viruses

Structure, proteome and genome of Sinorhizobium meliloti phage ΦM5: A virus with LUZ24-like morphology and a highly mosaic genome – Matthew C. Johnson et al. – Journal of Structural Biology

Microbes in the news

Welcome Mat: Franklin art fair returns on Labor Day – Maureen Feighan – The Detroit News

Methane emissions tackled with gas-guzzling bacteria – Monash University – Science Daily

Altered Gut Bacteria Could Indicate Parkinson’s – Sylvia Booth Hubbard – News Max

*Health officials are warning Texans to stay out of Harvey floodwaters for a disturbing reason – Erin Brodwin – Business Insider

*Study shows nurses’ scrubs become contaminated with bacteria in hospitals – Medical Express

Cheaters take advantage – Irene Vacca – Nature Reviews Microbiology

Bacteria – Dot Wordsworth – The Spectator

New Oral Microbiome Study Could Provide Better Estimate of Time since Death – University of Tennessee

*Scientists Made Music From the Human Microbiome, and It’s Seriously Cool – Gears of Biz

How A Mother’s Letter Inspired A Scientist To Revolutionize Consumer Microbiome Testing – Afif Ghannoum – Forbes

Non-microbiology pick

Advocating for Diversity and Inclusion in Faculty Hiring – Darryl Yong and Sumun Pendakur – Notices of the AMS

August 27, 2017

Quite a few reviews and news pieces to supplement your Sunday. Separation of mom and infant shortly after birth may run afoul of our evolutionary history, the gut-microbiome-brain axis is hot today, and can we use bacteria to generate electricity for us?

General microbiology

Review: Plant Hormones: Key Players in Gut Microbiota and Human Diseases? – Emilie Chanclud and Benoît Lacombe – Trends in Plant Science

Review: Microbe-mitochondrion crosstalk and health: An emerging paradigm – Prashant Bajpai et al. – Mitochondrion

Food microbiology

Diversity of bacterial communities in French chicken cuts stored under modified atmosphere packaging – Amélie Rouger et al. – Food Microbiology

Pregnancy and early life

*Review: Mother-newborn separation at birth in hospitals: A possible risk for neurodevelopmental disorders? – Noémi Császár-Nagy and István Bókkon – Neuroscience & Biobehavioral Reviews

Cancer and microbiome

Review: Probiotic species in the modulation of the anticancer immune response – Luciana Marinelli and Gian Carlo Tenore – Seminars in Cancer Biology

Human gut microbiome

Special Issue on Crohn’s Disease – Gastroenterology Clinics of North America

Review: Insights into defective serological memory after acute lymphoblastic leukaemia treatment: The role of the plasma cell survival niche, memory B-cells and gut microbiota in vaccine responses – Shanie Saghafian-Hedengren et al. – Blood Reviews

Review: Circadian Clocks and Metabolism: Implications for Microbiome and Aging – Georgios K. Paschos and Garret A. FitzGerald – Trends in Genetics

Human gut-microbiome-brain axis

*Microbial regulation of microRNA expression in the amygdala and prefrontal cortex – Alan E. Hoban et al. – Microbiome

Press: Feeling anxious? Your gut bacteria might be to blame – Honor Whiteman – Medical News Today

Review: The microbiota–gut–brain axis in obesity – Cristina Torres-Fuentes and Harriët Schellekens et al. – The Lancet Gastroenterology & Hepatology

Commentary: The Microbiome as a Key Regulator of Brain, Behaviour and Immunity: Commentary on the 2017 Named Series – Michael T. Bailey and John F. Cryan – Brain, Behavior, and Immunity

Animal experiments

Probiotics Modulete Gut Microbiota and Improve Insulin Sensitivity in DIO Mice: Probiotics Modulete Microbiota and Insulin Action – Renata A. Bagarolli et al. – The Journal of Nutritional Biochemistry

*Mice: Metabolic, Epigenetic, and Transgenerational Effects of Gut Bacterial Choline Consumption – Kymberleigh A. Romano et al. – Cell Host & Microbe

*Mice: An Oxidative Central Metabolism Enables Salmonella to Utilize Microbiota-Derived Succinate – Luisella Spiga and Maria G. Winter et al. – Cell Host & Microbe

Piglets: Gut antimicrobial effects and nutritional value of black soldier fly (Hermetia illucens L.) prepupae for weaned piglets – Thomas Spranghers et al. – Animal Feed Science and Technology

Plant, root and soil microbiome

Preprint: Plant genes influence microbial hubs that shape beneficial leaf communities – Benjamin Brachi et al. – bioRxiv

Tree roots select specific bacterial communities in the subsurface critical zone – O. Nicolitch et al. – Soil Biology and Biochemistry

Water and extremophile microbiome

Product quality and microbial dynamics during vermicomposting and maturation of compost from pig manure – Iria Villar et al. – Waste Management

Phages and viruses

Immobilization of bacteriophage in wound-dressing nanostructure – Frederico Nogueira et al. – Nanomedicine: Nanotechnology, Biology and Medicine

Microbes in the news

Hunter-gatherer gut microbes change with seasons, researchers say – Andrew Joseph – STAT

Top stories: Life-saving mini-organs, seasonal gut bacteria, and the world’s smallest antennas – Giorgia Guglielmi – Science

Does gut bacteria cause autism? Pathogens in the stomach alter the brain’s development and may increase the risk of condition – Alexandra Thompson – Daily Mail

President Trump’s proposed budget would kill Florida’s beach bacteria testing program – Amy Bennett Williams – News-Press

*Could Cyborg Bacteria Help Us Turn Sunlight into Fuel? – Steve Williams – Care2

Researchers suggest microbiological version of “Anna Karenina principle” – Xinhua Net

Trillions of Bacteria in Your Body are Alien to Science, Study Finds – WSP

Could you go a month without bathing? – Yvonne van Dongen – Stuff

Without fecal transplant, life can be a pain in the butt – Travis Paterson – Victoria News

August 14, 2017

A burst of articles for your Monday digest. Quite a few highlights emerge from this Digest. There can be racial disparity in gastrointestinal cancer risk. The stress we experience now might influence our children’s aging in the future. And you might want to think twice about choosing between 16S and metagenomic sequencing, depending on the type of samples you have.


Research Technician – Molecular Biology and Microbiology Department – Tufts University

General microbiology

*Letter: Pilot study to determine whether microbial contamination levels in hospital washrooms are associated with hand-drying method – M.H. Wilcox et al. – Journal of Hospital Infection

History matters: heterotrophic microbial community structure and function adapt to multiple stressors – Alexander Feckler et al. – Global Change Biology

Pregnancy and early life

Impact of intrapartum antimicrobial prophylaxis upon the intestinal microbiota and the prevalence of antibiotic resistance genes in vaginally delivered full-term neonates – Alicja Nogacka et al. – Microbiome

Pregnancy-induced changes in metabolome and proteome in ovine uterine flushings – Jared J. Romero – Biology of Reproduction

Evolution of newborns urinary metabolomic profiles according to age and growth – Aurélien Scalabre et al. – Journal of Proteome Research

Human oral microbiome

Effect of fermented milk containing Lactobacillus rhamnosus SD11 on oral microbiota of healthy volunteers: A randomized clinical trial – P. Rungsri et al. – Journal of Dairy Science

Human lung microbiome

Microbiome in lung explants of idiopathic pulmonary fibrosis: a case-control study in patients with end-stage fibrosis – Kitsios GD – Thorax

Human gut microbiome

**Racial Disparity in Gastrointestinal Cancer Risk – Hassan Ashktorab et al. – Gastroenterology

Master Thesis: A study of the effects of diet on human gut microbial community structure and mercury metabolism – Ria Saha – University of Ottawa

*Investigation into the stability and culturability of Chinese enterotypes – Yeshi Yin
et al. – Scientific Reports

Bangladesh Environmental Enteric Dysfunction (BEED) study: protocol for a community-based intervention study to validate non-invasive biomarkers of environmental enteric dysfunction – Mahfuz M – BMJ Open


“Omics” in Human Colostrum and Mature Milk: Looking to Old Data with New Eyes – Flaminia Bardanzellu et al. – Nutrients

Animal experiments

Stability and efficacy of frozen and lyophilized fecal microbiota transplant (FMT) product in a mouse model of Clostridium difficile infection (CDI) – Zhi-Dong Jiang et al. – Anaerobe

Rat: The activity of Hou-Po-Da-Huang-Tang is improved through intestinal bacterial metabolism and Hou-Po-Da-Huang-Tang selectively stimulate the growth of intestinal bacteria associated with health – Xing-Yan Liu et al. – Biomedicine & Pharmacotherapy

Mouse: Navy and black bean supplementation primes the colonic mucosal microenvironment to improve gut health – Jennifer M. Monk et al. – The Journal of Nutritional Biochemistry

Mouse: Human Gut-Derived Commensal Bacteria Suppress CNS Inflammatory and Demyelinating Disease – Ashutosh Mangalam et al. – Cell Reports

Mouse: Nlrp6- and ASC-Dependent Inflammasomes Do Not Shape the Commensal Gut Microbiota Composition – Michail Mamantopoulos et al. – Immunity

Fluoride Depletes Acidogenic Taxa in Oral but Not Gut Microbial Communities in Mice – Koji Yasuda et al. – mSystems

The In-Feed Antibiotic Carbadox Induces Phage Gene Transcription in the Swine Gut Microbiome – Timothy A. Johnson et al. – mBio

Animal microbiome

*The Effects of Captivity on the Mammalian Gut Microbiome – Valerie J. McKenzie et al. – Integrative and Comparative Biology

Gene and transcript abundances of bacterial type III secretion systems from the rumen microbiome are correlated with methane yield in sheep – Janine Kamke et al. – BMC Research Notes

High diversity and unique composition of gut microbiomes in pygmy (Kogia breviceps) and dwarf (K. sima) sperm whales – Patrick M. Erwin et al. – Scientific Reports

Virome comparisons in wild-diseased and healthy captive giant pandas – Wen Zhang and Shixing Yang et al. – Microbiome

Gut microbiomes of free-ranging and captive Namibian cheetahs: diversity, putative functions, and occurrence of potential pathogens – Wasim uddin et al. – Molecular Ecology

Plant, root and soil microbiome

Ecological and functional effects of fungal endophytes on wood decomposition – Lauren C. Cline et al. – Functional Ecology

Spatial Distribution Patterns of Root-Associated Bacterial Communities Mediated by Root Exudates in Different Aged Ratooning Tea Monoculture Systems – Yasir Arafat et al. – International Journal of Molecular Sciences

Book chapter: The Rhizosphere and Plant Nutrition Under Climate Change – Tarek Alshaal et al. – Essential Plant Nutrients

Fungal Diversity in Tomato Rhizosphere Soil under Conventional and Desert Farming Systems – Elham A. Kazerooni et al. – Frontiers in Microbiology

Banana Fusarium Wilt Disease Incidence Is Influenced by Shifts of Soil Microbial Communities Under Different Monoculture Spans – Zongzhuan Shen et al. – Microbial Ecology

*Characterisation and risk assessment of polycyclic aromatic hydrocarbons (PAHs) in soils and plants around e-waste dismantling sites in southern China – Yujie Wang et al. – Environmental Science and Pollution Research

Water and extremophile microbiome

**Large-scale differences in microbial biodiversity discovery between 16S amplicon and shotgun sequencing – Michael Tessler et al. – Scientific Reports

Interplay of hydrology, community ecology and pollutant attenuation in the hyporheic zone – Ignacio Peralta-Maraver et al. – Science of The Total Environment

Responses of coral-associated bacterial communities to local and global stressors – Jamie McDevitt-Irwin et al. – Frontiers in Marine Science

Built environment microbiome

Variability of indoor fungal microbiome of green and non-green low-income homes in Cincinnati, Ohio – Kanistha Coombs et al. – Science of The Total Environment

Food microbiome

Bacterial diversity of the Colombian fermented milk “Suero Costeño” assessed by culturing and high-throughput sequencing and DGGE analysis of 16S rRNA gene amplicons – Karina Edith Motato – Food Microbiology


*Metagenomic assembly through the lens of validation: recent advances in assessing and improving the quality of genomes assembled from metagenomes – Nathan D. Olson et al. – Briefings in Bioinformatics

Big data management challenges in health research—a literature review – Xiaoming Wang et al. – Briefings in Bioinformatics

Microbes in the news

*FDA: Don’t use these liquid drug or dietary supplement products for infants – Sara Nealeigh – Bradenton Herald

Core bacteria in the gut of horses showed some stability over time in study – HorseTalk

Are Doctors Wrong About Finishing Your Antibiotics? – Paul A. Offit – Daily Beast

*Bacteria at the beach: High levels found at nearly a dozen locations in past two weeks – Sarah Reese – NWI Times

Microbes on the market

OptiBiotix Health PLC (OPTI) Rating Reiterated by FinnCap – Anthony Sawyer – Week Herald

Non-microbiology picks

**Review: Transgenerational Effects of Early Environmental Insults on Aging and Disease Incidence – Mirela Ambeskovic et al. – Neuroscience & Biobehavioral Reviews

Air-quality implications of widespread adoption of cool roofs on ozone and particulate matter in southern California – Scott A. Epstein et al. – PNAS

August 8, 2017

Our daily digest for you, with highlights on gut microbiota signatures in Japanese infants with food allergy, salt mash communities affected by the Deepwater Horizon oil spill and a proposed stricter P value for claiming a ‘significant’ result.


Microbiology Laboratory Technicians – Australian Clinical Labs

General microbiology

Light controlled 3D micromotors powered by bacteria – Gaszton Vizsnyiczai et al. – Nature Communications

Press: Herding Bacteria Brings Power to 3D-Printed Micromotors – Michael Molitch-Hou –

Review: Zika Virus Protease: An Antiviral Drug Target – Congbao Kang et al. – Trends in Microbiology

Call for papers: Advances in Understanding and Controlling Bacteria-Material Interactions, with a Focus on how Bacteria Sense a Surface – Frontiers

Preprint: Saccharomyces cerevisiae strain YH166: a novel wild yeast for the production of tropical fruit sensory attributes in fermented beverages – Kara Osburn – bioRxiv

Pregnancy and early life

Review: Early-life adversity, epigenetics, and visceral hypersensitivity – S. Liu et al. – Neurogastroenterology & Motility

*Signatures in the gut microbiota of Japanese infants who developed food allergies in early childhood – Masaru Tanaka et al. – FEMS Microbiology Ecology

Animal experiments

Mouse: Dietary perturbations alter the ecological significance of ingested Lactobacillus plantarum in the digestive tract – Xiaochen Yin et al. – Scientific Reports

Abstract: A commensal Bifidobacterium longum strain improves gluten-related immunopathology in mice through expression of a serine protease inhibitor – McCarville JL et al. – Applied Environmental Microbiology

Carrageenan-induced colitis is associated with decreased population of anti-inflammatory bacterium, Akkermansia muciniphila, in the gut microbiota of C57BL/6J mice – Qingsen Shang et al. – Toxicology Letters

Mouse: Estrogen protection against EAE modulates the microbiota and mucosal-associated regulatory cells – Gil Benedek et al. – Journal of Neuroimmunology

Feed-additive probiotics accelerate yet antibiotics delay intestinal microbiota maturation in broiler chicken – Pengfei Gao, Chen Ma and Zheng Sun et al. – Microbiome

Stable engraftment of human microbiota into mice with a single oral gavage following antibiotic conditioning – Christopher Staley et al. – Microbiome

Animal microbiome

Supplemental thymol and carvacrol increases ileum Lactobacillus population and reduces effect of necrotic enteritis caused by Clostridium perfringes in chickens – Dafei Yin et al. – Scientific Reports

Plant, root and soil microbiome

Impact of Land-use Change on Vertical Soil Bacterial Communities in Sabah – Hoe Seng Tin et al. – Microbial Ecology

Water and extremophile microbiome

Pilot-scale investigation of sludge reduction in aerobic digestion system with endospore-forming bacteria – Kyu Won Seo et al. – Chemosphere

*Abstract: Salt marsh bacterial communities before and after the Deepwater Horizon oil spill – Engel AS et al. – Salt marsh bacterial communities before and after the Deepwater Horizon oil spill

Phages and viruses

A virulence-associated filamentous bacteriophage of Neisseria meningitidis increases host-cell colonisation – Emmanuelle Bille & Julie Meyer et al. – PLoS Pathogens

Microbes in the news

Cleaning a Dirty Sponge Only Helps Its Worst Bacteria, Study Says – Joanna Klein – NYT

McDonald’s, KFC, Burger King drinks test positive for fecal bacteria – WHDH

Congrats, happy couples: You really do share everything, even skin bacteria – Ellen Scott – Metro

Seasonal bacteria causes odd taste in Sacramento water – KCRA Staff – KCRA3

IIT Delhi team develops a new antibacterial drug-delivery system – R. Prasad – The Hindu

Antibiotics use by India’s poultry farms endangering human lives, says expert – Charu Bahri – Hindustan Times

Can We Encode Medical Records Into Our DNA? – Cathy Cassata – Healthline

Papaya Outbreak Grows to 109 Infected People. But How Does Salmonella Get Inside Produce? – Heather Williams – UnsafeFoods

Microbes on the market

PhoneSoap uses a UV sanitizing system to keep your phone bacteria-free – Ricci Rox – NoteBookCheck

Non-microbiology pick

*The Reproducibility Of Research And The Misinterpretation Of P Values – David Colquhoun – bioRxiv

July 24, 2017

Here’s our Digest to start your Monday. The importance of managing the antibiotic resistance in perinatal and neonatal care, review on the plant-microbiota holobiont and poo bacteria found in three big fast food chains.


Microbiology Lab Technician – Johnson County Community College – Overland Park, KS

Research Fellow – Microbiome Program Job – Mayo Clinic, Rochester MN

Pregnancy and infant microbiome

Book Chapter: Bacterial Infections in the Neonate – Morven S. Edwards & Carol J. Baker – Principles and Practice of Pediatric Infectious Diseases (Fifth Edition)

**Review: Antibiotic stewardship in perinatal and neonatal care Jayashree Ramasethu & Tetsuya Kawakita – Seminars in Fetal and Neonatal Medicine

Human liver microbiome

Sequencing the gut metagenome as a non-invasive diagnosis for advanced nonalcoholic steatohepatitis – Lixin Zhu et al. – Hepatology

Human gut microbiome

Comparative phenotypic analysis of “Clostridium neonatale” and Clostridium butyricum isolates from neonates – S. Schönherr-Helleca and G. Klein et al. – Anaerobe

The association of type II diabetes with gut microbiota composition – Fatemeh Navab-Moghadama et al. – Microbial Pathogenesis

The role of intestinal bacteria in the development and progression of gastrointestinal tract neoplasms – Kosuke Mima & Shuji Ogino et al. – Surgical Oncology

Review: The Microbiome in Crohn’s Disease : Role in Pathogenesis and Role of Microbiome Replacement Therapies – Sahil Khanna & Laura E. Raffals – Gastroenterology Clinics of North America

Review: The Gastric and Intestinal Microbiome: Role of Proton Pump Inhibitors – Artem Minalyan – Current Gastroenterology Reports

Animal experiments

The aerial parts of Salvia miltiorrhiza Bge. strengthen intestinal barrier and modulate gut microbiota imbalance in streptozocin-induced diabetic mice – Jun-Fei Gu et al. – Journal of Functional Foods

Intervention of probiotic L. reuteri fermented milk as an adjuvant to combat protein energy malnourishment induced gut disturbances in albino mice – S. Garg et al. – Journal of Functional Foods

Western Diet–Induced Dysbiosis in Farnesoid X Receptor Knockout Mice Causes Persistent Hepatic Inflammation after Antibiotic Treatment – Prasant K. Jena et al. – The American Journal of Pathology

The title seems an overstatement: Microbial regulation of hippocampal miRNA expression: Implications for transcription of kynurenine pathway enzymes – Gerard M. Moloney et al. – Behavioural Brain Research

Helicobacter species are potent drivers of colonic T cell responses in homeostasis and inflammation – Jiani N. Chai et al. – Science Immunology

Press: How ‘Bad’ Gut Bacteria Can Change Their Evil Ways – Christopher Wanjek – LiveScience

Animal microbiome

Exploring a possible link between the intestinal microbiota and feed efficiency in pigs – Ursula M. McCormack et al. – Applied and Environmental Microbiology


Plant, root and soil microbiome

Review: Insights into plant phosphate sensing and signaling – Byung-Kook Ham et al. – Current Opinion in Biotechnology

Responses of rice paddy micro-food webs to elevated CO2 are modulated by nitrogen fertilization and crop cultivars – Zhengkun Hu et al. – Soil Biology and Biochemistry

**Review: Understanding the holobiont: the interdependence of plants and their microbiome – Carmen Sánchez-Cañizares et al. – Current Opinion in Microbiology

Water and extremophile microbiome

Operation-driven heterogeneity and overlooked feed-associated populations in global anaerobic digester microbiome – Ran Mei et al. – Water Research

Preprint: Cytosine methylation within marine sediment microbial communities: potential epigenetic adaptation to the environment – Ian M. Rambo – bioRxiv

Phages and viruses

Bacteriophages in the human gut: our fellow travelers throughout life and potential biomarkers of heath or disease – Babak Bakhshinejad & Saeedeh Ghiasvand – Virus Research

Microbes in the news

Florida man contracts flesh-eating bacteria through blisters from hiking
Cherise Leclerc – WMUR9

Florida Seawater Bacteria Case Count Rises – Sherri Lonon – Patch

Shock as lab tests find of poo bacteria in products at McDonald’s, KFC and Burger King – Zara Whelan – Daily Post

Vaginal Probiotics Could Slow Zika & Other STD Infections – Sheryl Wood – Invisiverse

NASA Identifies What Kind of Fungi Could Grow in a Mars Habitat – Cynthia Wallentine – Invisiverse

July 18, 2017

A short Digest today, but with very interesting papers. Strain diversity implicated in atopic dermatitis, infant gut microbiome associated with cognitive development? And the sourdough microbiome.

General microbiology

Use of oxygen isotopes to differentiate between nitrous oxide produced by fungi or bacteria during denitrification – Lena Rohe et al. – Rapid Communications in Mass Spectrometry

Human skin microbiome

Staphylococcus aureus and Staphylococcus epidermidis strain diversity underlying pediatric atopic dermatitis – Allyson Byrd et al. – Science Translational Medicine

Human gut-microbiome-brain axis

Infant Gut Microbiome Associated with Cognitive Development – Alexander L. Carlson et al. – Biological Psychiatry

Press: In baby’s dirty diapers, the clues to baby’s brain development – UNC Health Care – EurekaAlert

Animal experiments

Peripartum Antibiotics Promote Gut Dysbiosis, Loss of Immune Tolerance, and Inflammatory Bowel Disease in Genetically Prone Offspring – Jun Miyoshi et al. – Cell Reports

Press: Higher IBD Risk in Offspring Associated With Antibiotic Use in Pregnancy – IDSE News Staff – IDSE

Microbes in the news

More Than Bread: Sourdough As a Window Into The Microbiome – Marcus Woo – NPR

Promising but take caution: Probiotics and Weight Loss – Philip J. Gregory – Medscape

Review article discusses potential role, benefits of non-rhizobia bacteria in root nodules of legume –

Microbes on the market

Enterome, Nestlé Health Science Launch Microbiome Diagnostics Partners to Develop New IBD Treatments – Carolina Henriques – IBD News Today

Essential Science: Big investments for human microbiome research – Tim Sandle – Digital Journal