December 31, 2017

A rich Digest to end 2017! There are several reviews on human gut microbiome and lots of papers on plant , root and soil microbiome. The airway microbiome is trending today and scientists are starting to examine rigorously the effect of herbal medicine on the gut microbiota. Happy Reading and Happy New Year!

General microbiology

Bacterial pathogens were detected from human exhaled breath using a novel protocol – Yunhao Zheng et al. – Journal of Aerosol Science

Bacteria Facilitate Enteric Virus Co-infection of Mammalian Cells and Promote Genetic Recombination – Andrea K. Erickson et al. – Cell Host & Microbe

Human airway microbiome

Review: Airway microbial metagenomics – Katarzyna Pienkowska et al. – Microbes and Infection

Respiratory syncytial virus and rhinovirus bronchiolitis are associated with distinct metabolic pathways – Christopher J Stewart et al. – Journal of Infectious Diseases

Tech Note: A breath of information: the volatilome – M. Mansurova et al. – Current Genetics

Short-term particulate matter exposure influences nasal microbiota in a population of healthy subjects – Jacopo Mariani et al. – Environmental Research

Exposure to traffic-related air pollution and the composition of the gut microbiota in overweight and obese adolescents – Tanya L. Alderete et al. – Environmental Research

Human gut microbiome

Gut microbiome contributes to impairment of immunity in pulmonary tuberculosis patients by alteration of butyrate and propionate producers – Abhijit Maji et al. – Environmental Microbiology

Review: Targeting the gut barrier for the treatment of alcoholic liver disease – Zhanxiang Zhou and Wei Zhong – Liver Research

Review: Microbial Regulation of Glucose Metabolism and Insulin Resistance – Crommen S and Simon MC – Genes

Review: Gut microbiota in the pathogenesis of inflammatory bowel disease – Nishida A et al. – Clinical Journal of Gastroenterology

Review: Human Intestinal Microbiota: Interaction Between Parasites and the Host Immune Response – Oswaldo Partida-Rodríguez et al. – Archives of Medical Research

Review: Gut dysbiosis and irritable bowel syndrome: the potential role of probiotics – Nicola Principi et al. – Journal of Infection

Review: Gut Microbiota in Obesity and Metabolic Abnormalities: A Matter of Composition or Functionality? – Sofia Moran-Ramo et al. – Archives of Medical Research

In vitro: An in vitro study to assess the impact of tetracycline on the human intestinal microbiome – Ji Young Jung et al. – Anaerobe

Human gut-microbiome-brain axis

Review: Targeting gut microbiome: A novel and potential therapy for autism – Yongshou Yang et al. – Life Sciences


Dark matter in host-microbiome metabolomics: Tackling the unknowns–A review – B.Y. Loulou Peisl et al. – Analytica Chimica Acta

Animal experiments

Mouse: Intestinal Ralstonia pickettii augments glucose intolerance in obesity – Shanthadevi D. Udayappan et al. – PLoS One

Pig: Structural Modulation of Gut Microbiota during Alleviation of Suckling Piglets Diarrhoea with Herbal Formula – Cui Liu et al. – Evidence-Based Complementary and Alternative Medicine

Rat: Effects of HLA-B27 on Gut Microbiota in Experimental Spondyloarthritis Implicate an Ecological Model of Dysbiosis – Gill T et al. – Arthritis and Rheumatology

Changes in mouse gut bacterial community in response to different types of drinking water – Marcela F. Dias et al. – Water Research

Mouse: Particle size determines the anti-inflammatory effect of wheat bran in a model of fructose over-consumption: Implication of the gut microbiota – Francesco Suriano & Audrey M. Neyrinck et al. – Journal of Functional Foods

Mouse: Mushroom polysaccharides from Ganoderma lucidum and Poria cocos reveal prebiotic functions – Imran Khan et al. – Journal of Functional Foods

Animal microbiome

Bacterial diversity of wild-caught Lutzomyia longipalpis (a vector of zoonotic visceral leishmaniasis in Brazil) under distinct physiological conditions by metagenomics analysis – Ana Clara Araújo Machado Pires et al. – Parasites & Vectors

Drosophila Perpetuates Nutritional Mutualism by Promoting the Fitness of Its Intestinal Symbiont Lactobacillus plantarum – Gilles Storelli et al. – Cell Metabolism

Analysis of the influence of living environment and age on vaginal fungal microbiome in giant pandas (Ailuropoda melanoleuca) by high throughput sequencing – Danyu Chen et al. – Microbial Pathogenesis

Plant, root and soil microbiome

Phosphate levels influence the utilisation of rice rhizodeposition carbon and the phosphate-solubilising microbial community in a paddy soil – Xi-En Long et al. – Soil Biology and Biochemistry

Plant community and soil conditions individually affect soil microbial community assembly in experimental mesocosms – Aspen T. Reese et al. – Ecology and Evolution

Responses of bulk and rhizosphere soil microbial communities to thermoclimatic changes in a Mediterranean ecosystem – Javier Pascual et al. – Soil Biology and Biochemistry

Remediation of arsenic in mung bean (Vigna radiata) with growth enhancement by unique arsenic-resistant bacterium Acinetobacter lwoffii – Joyati Das and Priyabrata Sarkar – Science of the Total Environment

* Opinion: Why we need a National Living Soil Repository – Daniel K. Manter et al. – PNAS

Long-term effects of nitrogen fertilization on aggregation and localization of carbon, nitrogen and microbial activities in soil – Yidong Wang et al. – Science of the Total Environment

Vineyard microbiome variations during different fertilisation practices revealed by 16s rRNA gene sequencing – Loredana Canfora et al. – Applied Soil Ecology

* Co-occurrence patterns of soybean rhizosphere microbiome at a continental scale – Baogang Zhang et al. – Soil Biology and Biochemistry

Review: Symbiotic nitrogen fixation by rhizobia — the roots of a success story – Catherine Masson-Boivin and Joel L Sachs – Current Opinion in Plant Biology

Water and extremophile microbiome

PDF: From extreme environments to human pathogens: an evolutionary journey – Donato Giovannelli and Costantino Vetriani – Biochemical Society

Comparison of Iris pseudacorus wetland systems with unplanted systems on pollutant removal and microbial community under nanosilver exposure – Juan Huang et al. – Science of the Total Environment

Impacts of design configuration and plants on the functionality of the microbial community of mesocosm-scale constructed wetlands treating ibuprofen – Liang Zhang et al. – Water Research

Microbial community evolution in partial nitritation/anammox process: From sidestream to mainstream – Yandong Yang et al. – Bioresource Technology

Spatiotemporal changes in bacterial community and microbial activity in a full-scale drinking water treatment plant – Luanfeng Hou et al. – Science of the Total Environment

Built environment microbiome

Microbiological air contamination in university premises and the evaluation of drug resistance of staphylococci occurring in the form of a bioaerosol – Katarzyna Wolny-Koładka et al. – Indoor and Built Environment

Phages and viruses

Virome analysis of lily plants reveals a new potyvirus – Yongqiang Li et al. – Archives of Virology

Comparative Analysis of 37 Acinetobacter Bacteriophages – Dann Turner et al. – Viruses

Antiviral systems in vector mosquitoes – Tong Liu et al. – Developmental & Comparative Immunology

Microbes in the news

Launceston associate professors studying gut microbiome in elderly Tasmanians – Carly Dolan – Examiner

Biofilm made of mulberry silk to destroy dengue virus – TNN – Times of India

Rhode Island Health Department finds E. coli bacteria, issues boil water notice – PATRICIA RESENDE & TONY GUGLIOTT – NBC 10

Op-Ed: Survival tips in the age of drug-resistant bacteria – Kevin Kavanagh – Lexington Herald Leader

One Big Family: This Beautiful Interactive Diagram Shows How Every Organism Is Related – Fiona McMillan – Forbes

Researchers propose different approach to beat antibiotic-resistant superbugs – News Medical



December 29, 2017

It’s a bit quiet towards the end of the year, but not without highlights. Could we fight antibiotic resistance by targeting mild infections using alternative drugs? Do we want to correct our own genes using CRISPR and what’s the future for penicillin?


Associate Professor – Microbiology – Dental College -chennai

General microbiology

Efficient Hydrogen-Dependent Carbon Dioxide Reduction by Escherichia coli – Magali Roger et al. – Current Biology

Press: Bacteria under pressure run reaction in reverse to sequester carbon – John Timmer – Ars Technica

The Role of Type VI Secretion System Effectors in Target Cell Lysis and Subsequent Horizontal Gene Transfer – Peter David Ringel et al. – Cell Reports

Press: Predatory Bacteria Acquire Drug Resistance Directly from Rivals – Genetic Engineering & Biotechnology News

* Alternative therapeutics for self-limiting infections—An indirect approach to the antibiotic resistance challenge – Kristofer Wollein Waldetoft and Sam P. Brown – PLoS Biology

Author interview: Alternatives to Antibiotics: Why managing mild maladies matters – Beth Baker – PLoS Research News

Animal experiments

Under control: how a dietary additive can restore the gut microbiome and proteomic profile, and improve disease resilience in a marine teleostean fish fed vegetable diets – María Carla Piazzon et al. – Microbiome

Animal microbiome

Mosquito vector-associated microbiota: Metabarcoding bacteria and eukaryotic symbionts across habitat types in Thailand endemic for dengue and other arthropod-borne diseases – Panpim Thongsripong et al. – Ecology and Evolution

Plant, root and soil microbiome

Rhizosphere-associated Alcaligenes and Bacillus strains that induce resistance against blast and sheath blight diseases, enhance plant growth and improve mineral content in rice – Kaleem U. Kakar et al. – Journal of Applied Microbiology

Microbes in the news

A week of holiday junk food could derail your gut microbiome—but there’s hope – Claire Maldarelli – Popular Science

Microbiota and Cancer – Andrea S. Blevins Prime – Cancer Therapy Advisor

Maternal Antibiotic Exposure Affects Infant Fecal Microbiota Following Vaginal Delivery – Jessica Martin – Infectious Disease Advisor

Microbe expert claims we should wash them ‘AT LEAST’ once a week at a high temperature to avoid dust mites and bacteria – Unity Blott – Daily Mail

* CORRECTING THE GENES – Santanu Chakraborty – Bangalore Mirror

Govt study finds faecal bacteria in 97 percent ‘filtered’ water jars in Dhaka – Bdnews24

* 200 million lives saved – but prognosis for penicillin is not healthy – Harry Ridgewell and Angela Long (collaborator) – Wiki Tribune

Microbes on the market

Report on sale: Human Microbiome Therapeutics Market is expected to Witness a CAGR of 14.19 % Till 2022 including Key Players: Rebiotix, Seres Therapeutics – Craig Francis – Social Articles Tracking & PR

Report on sale: Microbiome Drugs Market by Production, Capacity Utilization Rate, Ex-Factory Price, Revenue, Cost, Gross and Gross Margin Analysis – Amit Pawar – Social Articles Tracking & PR


November 14, 2017

Today seems unusually quiet. But, a few highlights still stand out. Scientists discover a new mechanism of antibiotic resistance. The HHS in the US released a progress report on fighting against antibiotic resistance. Finally, please enjoy the stunning beauty of microbes under the microscope.


Grants Alert – Federal Grants & Contracts


Technologist (Microbiology) – Tampa Florida

General microbiology

New issue of Global Change Biology Bioenergy

* The multiple antibiotic resistance operon of enteric bacteria controls DNA repair and outer membrane integrity – Prateek Sharma et al. – Nature Communications

Press: New mechanisms discovered that bacteria use to protect themselves from antibiotics –

* National Action Plan Drives Progress in Fight Against Antibiotic-Resistant Bacteria – Christopher M. Jones – HHS

Na+-induced structural transition of MotPS for stator assembly of the Bacillus flagellar motor – Naoya Terahara et al. – Science Advances

Press: How bacteria get their groove: Mechanism behind flagellar motility – Osaka University – Science Daily

Phages and viruses

Phage Genome Annotation Using the RAST Pipeline – Katelyn McNair et al. – Bacteriophages

Microbes in the news

* Seeing the Beautiful Intelligence of Microbes – John Rennie & Lucy Reading-Ikkanda – Quanta Magazine

FDA Acts to Advance Potential Inhaled Treatment of Resistant Bacteria Tied to Lung Infections – Janet Stewart – Cystic Fibrosis News Today

Strong Evidence Emerging That Gut Microbiome Is a Key Variable in Immunotherapy Efficacy – Theodore Bosworth – Medscape

How the Gut Microbiome Affects Outcomes in HIV – Jeannette Y. Wick – Special Pharmacy Times

Microbes on the market

With a grain of salt: Would you put bacteria on your face? This brand thinks you should – Victoria Hall – Telegraph


November 7, 2017

Here’s your daily Digest. Highlights include an attempt to establish the causal link between gut microbiota and colorectal cancer in mice, an electric bandage to fight biofilm and antimicrobial resistance, and a group B Streptococcus vaccine that could save tens of thousands of babies per year.

General microbiology

Oral epithelial cells orchestrate innate type 17 responses to Candida albicans through the virulence factor candidalysin – Akash H. Verma et al. – Science Immunology

Methicillin Resistant Staphylococcus aureus Sequence Type (ST) 5 Isolates from Health Care and Agricultural Sources Adhere Equivalently to Human Keratinocytes – Samantha J. Hau et al. – Applied and Environmental Microbiology

Human gut microbiome

Human microbiome signatures of differential colorectal cancer drug metabolism – Leah Guthrie et al. – npj Biofilms and Microbiomes

Whole grain-rich diet reduces body weight and systemic low-grade inflammation without inducing major changes of the gut microbiome: a randomised cross-over trial – Henrik Munch Roager et al. – Gut

Multi-site human microbiome

Review: Human microbiome, infections, and rheumatic disease – Ana Clara Camine et al. – Clinical Rheumatology

Review: The Microbiome and Bone and Joint Disease – Christopher J. Hernandez – Current Rheumatology Reports

Animal experiments

Gavage of fecal samples from patients with colorectal cancer promotes intestinal carcinogenesis in germ-free and conventional mice – Sunny H. Wong and Liuyang Zhao – Gastroenterology

Animal microbiome

An integrative study on biologically recovered polyhydroxyalkanoates (PHAs) and simultaneous assessment of gut microbiome in yellow mealworm – Su Yean Ong et al. – Journal of Biotechnology

Plant, root and soil microbiome

Shifts in microbial communities in soil, rhizosphere and roots of two major crop systems under elevated CO2 and O3 – Peng Wang et al. – Scientific Reports

Year-round shotgun metagenomes reveal stable microbial communities in agricultural soils and novel ammonia oxidizers responding to fertilization – Luis H. Orellana et al. – Applied and Environmental Microbiology

Water and extremophile microbiome

High altitude, hyper-arid soils of the Central-Andes harbor mega-diverse communities of actinobacteria – Alan T. Bull et al. – Extremophiles

Sediment nitrogen cycling rates and microbial abundance along a submerged vegetation gradient in a eutrophic lake – Lu Yao et al. – Science of The Total Environment


Electric Field Based Dressing Disrupts Mixed-Species Bacterial Biofilm Infection and Restores Functional Wound Healing – Barki, Kasturi Ganesh et al. – Annals of Surgery

Press: Study shows electric bandages can fight biofilm infection, antimicrobial resistance – MedicalXpress


Preprint: A novel multi SNP based method for the identification of subspecies and associated lineages and sub-lineages of the Mycobacterium tuberculosis complex by whole genome sequencing – Samuel I. W. Lipworth et al. – bioRxiv

Microbes in the news

Your Eyes Have Their Own Microbiome. Here’s What You Need To Do To Take Care Of It – Sam Berne – MBG Health

Does a Healthy Gut Equal a Long, Healthy Life? – Jim Pietrangelo – Healthline

Unlocking the Secrets of the Microbiome – Jane E. Brody – New York Times

Specific gut bacteria can help or hinder cancer treatments – Rich Haridy – New Atlas

Proprietary Prebiotic Fiber Tested in National Institutes of Health Pilot Study with End-Stage Renal Disease Patients – Kimberly J. Decker – Nutritional Outlook

Briny pool bacteria can clean up and power up – King Abdullah University of Science & Technology – EurekAlert

2 million Chinese mothers carry strep bacteria that can be fatal to newborns, study finds – Laurie Chen – South China Morning Post

* Vaccine for bacteria carried by 20% of pregnant women ‘could prevent 100,000 baby deaths’ – Sarah Boseley – The Irish Times

Research finds link between gut fungi, bacteria and obesity – Camille Bienvenu –

Microbes on the market

Microbiome Therapeutics prepares to launch ‘microbiome modulator’ – Stephen Daniells – NutraIngredients


October 31, 2017

Today’s Digest is short, but not without highlights. The highlights all go to antibiotics. Ed Yong wrote about the history of methicillin resistance, colistin resistance was found to be increasing in Chinese hospitals, and fox poop could save us from vegetable and fruit waste.

General microbiology

A CRISPR–Cas9-based gene drive platform for genetic interaction analysis in Candida albicans – Rebecca S. Shapiro et al. – Nature Microbiology

Reduction of bacterial burden by copper alloys on high-touch athletic center surfaces – Zina Ibrahim et al. – American Journal of Infection Control

Press: New Study Shows Copper Surfaces on Athletic Equipment Reduce Bacteria by 94 Percent – Business Wire

Plant, root and soil microbiome

Assessing and characterising the repertoire of constitutive promoter elements in soil metagenomic libraries in Escherichia coli – Caua Antunes Westmann et al. – bioRxiv


Reproducibility and repeatability of six high-throughput 16S rDNA sequencing protocols for microbiota profiling – Sajan Raju et al. – bioRxiv

Microbes in the news

Flesh-eating bacteria kills man helping repair Harvey-damaged homes – Claire Z. Cardona – Dallas News

Gut bacteria found to have a role in both PTSD and Alzheimer’s disease – Rich Haridy – New Atlas

* Bacteria Can Evolve Resistance to Drugs Before Those Drugs Are Used – Ed Yong – The Atlantic

* New Study Detects Increase in MCR-1 Positive Multidrug-Resistant Bacteria in Humans – Samar Mahmoud – Contagion Live

Vaginal Microbiota Profile Predictive of Chlamydia Susceptibility – Jessica Martin – Infectious Disease Advisor

* War on waste: Antimicrobial borne by feral foxes slows decay saving food and money – Jennifer Nichols – ABC News

Microbes on the market

Video: Bioengineers recreated spider silk by fermenting E. Coli bacteria – Mashable

Kane Biotech Inc. Provides Overview of Biofilm Industry, Clinical Development and Growth Drivers in New SNNLive Video Interview with – Global Newswire

Evivo™ Gains Health Canada Approval, Providing First International Expansion Opportunity – Global Newswire


October 27, 2017

A dynamic Digest today. A variety of articles in human and other microbiome research. The ongoing discussion on reproducible research and P value. For us junior scientists, what are our career prospects?

General microbiology

Review: Development and regulation of single- and multi-species Candida albicans biofilms – Matthew B. Lohse et al. – Nature Reviews Microbiology

Preprint: Metabolic Interactions Between Dynamic Bacterial Subpopulations – Adam Z Rosenthal et al. – bioRxiv

Human skin microbiome

Review: Staphylococcal Biofilms in Atopic Dermatitis – Tammy Gonzalez et al. – Current Allergy and Asthma Reports

Human oral microbiome

Sociodemographic variation in the oral microbiome – Audrey Renson et al. – bioRxiv

Human lung microbiome

Review: New opportunities for managing acute and chronic lung infections – William O. C. M. Cookson et al. – Nature Reviews Microbiology

Human gut microbiome

Gut microbiota and host metabolism: what relationship? – Mithieux G – Neuroendocrinology

Review: Pharmabiotics as an Emerging Medication for Metabolic Syndrome and Its Related Diseases – Thi Thanh Binh Nguyen and Yan Yan Jin et al. – Molecules

Review: The Gastrointestinal Tract as an Integrator of Mechanical and Hormonal Response to Nutrient Ingestion – Adrian Vella and Michael Camilleri – Diabetes

Molecular, microbiological and clinical characterization of Clostridium difficile isolates from tertiary care hospitals in Colombia – Clara Lina Salazar et al. – PLoS One

Animal experiments

Polyphenol- and caffeine-rich post-fermented Pu-er tea improves diet-induced metabolic syndrome by remodeling intestinal homeostasis in mice – Xiaoyu Gao et al. – Infection and Immunity

Animal microbiome

Exogenous dietary lysozyme improves the growth performance and gut microbiota in broiler chickens targeting the antioxidant and non-specific immunity mRNA expression – Mervat A. Abdel-Latif et al. – PLoS One

Prohibition of antibiotic growth promoters has affected the genomic profiles of Lactobacillus salivarius inhabiting the swine intestine – Jun-Yeong Lee et al. – PLoS One

Plant, root and soil microbiome

Effects of stand age and soil properties on soil bacterial and fungal community composition in Chinese pine plantations on the Loess Plateau – Peng Dang et al. – PLoS One

Tide as Steering Factor in Structuring Archaeal and Bacterial Ammonia-Oxidizing Communities in Mangrove Forest Soils Dominated by Avicennia germinans and Rhizophora mangle – Magalí S. Marcos et al. – Microbial Ecology

Phages and viruses

Preprint: Diagnostic Potential & the Interactive Dynamics of the Colorectal Cancer Virome – Geoffrey D. Hannigan et al. – bioRxiv

Microbes in the news

Does Chinese Urbanization Change the Microbiome? – Usha B. Nair – Medical News Bulletin

*Healthy ageing? Microbiome study shows same patterns irrespective of age – Nathan Gray – Nutra

Modified bacteria convert petroleum directly into building blocks for plastics – Wageningen University

Releasing the Antibiotics That Lie Dormant in Bacteria – Micronow

Bacteria have a sense of touch – EurekAlert

How Dog and Cat ‘Kisses’ Can Turn Deadly – Erika Engelhaupt – National Geographic

Xin’s non-microbiology picks

*Many junior scientists need to take a hard look at their job prospects – Nature Editorial

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


October 25, 2017

A short Digest for today. The evolution of E. coli in the lab for over 60,000 generations, the necessity of including a mock community for every sequencing run, and plenty of news pieces.

Events and jobs

Free Webinar: Not Just for Neurons – Electrical Signaling in Bacterial Biofilm Communities – Select Science

Laboratory Assistant-Microbiology – Raritan New Jersey

General microbiology

*The dynamics of molecular evolution over 60,000 generations – Benjamin H. Good et al. – Nature

Press: The evolution experiment that has been watching bacteria mutate for 30 years – Rich Haridy – New Atlas

Bacterial pathogenesis: Activating Helicobacter effector delivery – Irene Vacca – Nature Reviews Microbiology

Human gut microbiome

Discovery of α-L-arabinopyranosidases from human gut microbiome expands the diversity within glycoside hydrolase family 42 – Alexander Holm Viborg et al. – Journal of Biological Chemistry

Letter: Low eukaryotic viral richness is associated with faecal microbiota transplantation success in patients with UC – Nádia Conceição-Neto et al. – Gut


*Preprint: Taxon disappearance from microbiome analysis indicates need for mock communities as a standard in every sequencing run – Yi-Chun Yeh et al. – bioRxiv

Microbes in the news

Strength in numbers: How biofilms outfox antibiotics – Yella Hewings-Martin – Medical News Today

Lung microbiome plays major role in asthma severity and response to treatment – News Medical

New way to prevent unfavorable intestinal microbiota – Hokkaido University – EurekAlert

VIDEO: Gut microbiome research sped by technology, informatics, but diet a major confounder – Eamonn M.M. Quigley – Healio

New Study Shows Link Between Gut Bacteria And Breast Cancer – CBS New York

Harvey-linked flesh-eating bacteria claims Galveston man – Todd Ackerman – Chron

Major changes in balance of gut bacteria occur soon after serious injury/trauma – Medical Xpress

‘Achilles heel’ found in antibiotic-resistant bacteria – John von Radowitz – Irish Independent