Category Archives: Events and jobs

November 18, 2017

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Featuring a bioinformatics paper from my former lab mate, as well as multiple, interesting pre-prints! See also a paper on rats in NYC and a study on peer review.

Events and jobs
Microbiology Technician I – Abbott – Plymouth, Minnesota, United States

Biology, Assistant Professor, Microbiology – College of Saint Benedict/Saint John’s University in Minnesota (3 year term, not tenure track)

PhD Studentship: Microbiome mediated resiliency of freshwater habitat – University of Birmingham

OMRF seeks participants as it launches new sarcoidosis clinic

General microbiome
Ecological Insights from the Evolutionary History of Microbial Innovations –
Mario E Muscarella – bioRxiv

Pregnancy and early life
Mode of delivery and child and adolescent psychological well-being: Evidence from Hong Kong’s “Children of 1997” birth cohort – Cherry Y. Leung – Scientific Reports

Multi-site human microbiome
Body size phenotypes comprehensively assess cardiometabolic risk and refine the association between obesity and gut microbiota – J de la Cuesta-Zuluaga – International Journal of Obesity

Human gut microbiome
Structural and functional differences in gut microbiome composition in patients undergoing haemodialysis or peritoneal dialysis – Vanessa Stadlbauer – Scientific Report

A role for bacterial urease in gut dysbiosis and Crohn’s disease – Josephine Ni – Science Translational Medicine

Animal experiments
Alteration of the intestinal microbiome characterizes preclinical inflammatory arthritis in mice and its modulation attenuates established arthritis – Rebecca Rogier – Scientific Reports

Dietary protein sources differentially affect microbiota, mTOR activity and transcription of mTOR signaling pathways in the small intestine – Soumya K. Kar – PLoS One

Blockade of CB1 cannabinoid receptor alters gut microbiota and attenuates inflammation and diet-induced obesity – Pegah Mehrpouya-Bahrami – Scientific Reports

Wild Microbiome Stems Tumorigenesis in Lab Mice – Cancer Discovery

Dietary chlorogenic acid regulates gut microbiota, serum-free amino acids and colonic serotonin levels in growing pigs – Yi Wu – International Journal of Food Sciences and Nutrition

Plant, root, and soil microbiomeSoil-mediated effects of global change on plant communities depend on plant growth form – Jes Hines – Ecosphere

Built environment
Spatial variation in the parasite communities and genomic structure of urban rats in New York City – L. P. Angley – Zoonoses and Public Health

Food microbiology
Digestion under saliva, simulated gastric and small intestinal conditions and fermentation in vitro of polysaccharides from the flowers of Camellia sinensis induced by human gut microbiota – Dan Chen – Food and Function

Review: Dietary and Endogenous Sphingolipid Metabolism in Chronic Inflammation – Gregory H. Norris – Nutrients

Review: Cardiovascular and Antiobesity Effects of Resveratrol Mediated through the Gut Microbiota – JK Bird – Advances in Nutrition

Review: Yogurt and Cardiometabolic Diseases: A Critical Review of Potential Mechanisms – MA Fernandez – Advances in Nutrition

Phages and viruses
Molecularly barcoded Zika virus libraries to probe in vivo evolutionary dynamics – Matthew T. Aliota – bioRxiv

Bioinformatics
A Bayesian method for detecting pairwise associations in compositional data – Emma Schwager – PLoS Computational Biology
Shout-out to my old lab mate, Emma!

MetQy: an R package to query metabolic functions of genes and genomes – Andrea Martinez-Vernon – bioRxiv

Genome announcements
Streptomyces tritici sp. nov., a novel actinomycete isolated from rhizosphere soil of wheat (Triticum aestivum L.) – Junwei Zhao – International Journal of Systematic and Evolutionary Biology

Rhodococcus psychrotolerans sp. nov., isolated from rhizosphere of Deschampsia antarctica – Leonardo Jose Silva – Antonie van Leeuwenhoek

Thalassotalea coralli sp. nov., isolated from the torch coral Euphyllia glabrescens – Der-Shyan Sheu – International Journal of Systematic and Evolutionary Biology

Microbes in the news
Lab-Grown Synthetic Nanobots May Officially End Antibiotic Resistance – Patrick Caughill – Futurism

Biolive yoghurt can help to lower blood pressure – Colin Fernandez – IOL

Dolphins: The final frontier for new types of bacteria? – Nicoletta Lanese – Scope

10 Things You Should Never Say to Someone With a Chronic Illness—Seriously – Karen Duffy – Health

Bacterium in a beetle makes it a leaf-eater – Science Daily
Paper: Drastic Genome Reduction in an Herbivore’s Pectinolytic Symbiont – Hassan Salem – Cell

How the Immune System Identifies Invading Bacteria – HHMI
Paper: The structural basis of flagellin detection by NAIP5: A strategy to limit pathogen immune evasion – Jeannette L. Tenthorey – Science

Dog owners have lower mortality, study finds – Katie Silver – BBC
No actual mention of microbiome in paper, which is: Dog ownership and the risk of cardiovascular disease and death – a nationwide cohort study – Mwenya Mubanga – Scientific Report

Microbes on the market
Evelo taps Mayo Clinic expertise for therapeutic bacteria programs – Phil Taylor – FierceBiotech

Human Microbiome Market Global Therapeutics, Drugs Review To 2025 – MedGadget

Researchers receive $500,000 grant to study the “microbiome of death” – Matt Wood – ScienceLife

Science, publishing, and career
Reviewer bias in single- versus double-blind peer review – Andrew Tomkins – PNAS

November 17, 2017

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Jobs and events

Lab Assistant – Microbiology, Dublin Ohio

General microbiome

Evolution of the hygiene hypothesis into biota alteration theory: what are the paradigms and where are the clinical applications? – Chantal Villeneuve, Microbes and Infection

Human gut microbiome

Identifying predictive features of Clostridium difficile infection recurrence before, during, and after primary antibiotic treatment – Sepideh Pakpour, Microbiome

Gastric microbiome of Indian patients with Helicobacter pylori infection, and their interaction networks – Anubhav Das, Scientific Reports

Discovery of an expansive bacteriophage family that includes the most abundant viruses from the human gut – Natalya Yutin, Nature Microbiology

Fecal Transplantation for Treatment of Clostridium Difficile Infection in Elderly and Debilitated Patients – Tali Friedman-Korn, Digestive Diseases and Sciences

Myocardial infarction and gut microbiota: an incidental connection – Sepideh ZununiVahed, Pharmacological Research

Anxiety, Depression, and the Microbiome: A Role for Gut Peptides – Gilliard Lach, Neurotherapeutics

The nursing home elder microbiome stability and associations with age, frailty, nutrition and physical location – John P. Haran, Journal of Medical Microbiology

Human nearly-sterile sites

Risk of Subsequent Sepsis within 90 Days of a Previous Hospital Stay by Type of Antibiotic Exposure – James Baggs, Clinical Infectious Diseases

Human vaginal microbiome

Microbial Diversity of Genital Ulcers of HSV-2 Seropositive Women – Supriya D. Mehta, Scientific Reports

Animal experiments

The green tea modulates large intestinal microbiome and exo/endogenous metabolome altered through chronic UVB-exposure – Eun Sung Jung, PLOS ONE

Acute Administration of the Nonpathogenic, Saprophytic Bacterium, Mycobacterium vaccae, Induces Activation of Serotonergic Neurons in the Dorsal Raphe Nucleus and Antidepressant-Like Behavior in Association with Mild Hypothermia – Philip H. Siebler, Cellular and Molecular Neurobiology

Maternal High Fat Diet and its Consequence on the Gut Microbiome: A Rat Model – Phyllis E. Mann, Gut Microbes

Environmental Burkholderia cenocepacia Strain Enhances Fitness by Serial Passages during Long-Term Chronic Airways Infection in Mice – Alessandra Bragonzi, International Journal of Molecular Sciences

Enteric Delivery of Regenerating Family Member 3 alpha Alters the Intestinal Microbiota and Controls Inflammation in Mice With Colitis – Marion Darnaud, Gastroenterology

Animal microbiome

Novel viruses in salivary glands of mosquitoes from sylvatic Cerrado, Midwestern Brazil – Andressa Zelenski de Lara Pinto, PLOS ONE

New evidence showing that the destruction of gut bacteria by antibiotic treatment could increase the honey bee’s vulnerability to Nosema infection – Jiang Hong Li, PLOS ONE

Relative importance of honeydew and resin for the microbial activity in wood ant nest and forest floor substrate – a laboratory study – Veronika Jílková, Soil Biology and Biochemistry

Common Cutaneous Bacteria Isolated from Snakes Inhibit Growth of Ophidiomyces ophiodiicola – Aubree J. Hill, EcoHealth

Plant, root, and soil microbiome

Fungal community reveals less dispersal limitation and potentially more connected network than that of bacteria in bamboo forest soils – Xian Xiao, Molecular Ecology

Influence of compost and biochar on microbial communities and the sorption/degradation of PAHs and NSO-substituted PAHs in contaminated soils – Gabriel Sigmund, Journal of Hazardous Materials

Epiphytic Bacteria Alter Floral Scent Emissions – Carola Helletsgruber, Journal of Chemical Ecology

In vitro bacterization of banana (Musa spp.) with native endophytic and rhizospheric bacterial isolates: Novel ways to combat Fusarium wilt – M. Kavino, European Journal of Plant Pathology

Foliar microbiome transplants confer disease resistance in a critically-endangered plant – Geoffrey Zahn, PeerJ

The response of soil microbial communities to variation in annual precipitation depends on soil nutritional status in an oligotrophic desert – Cristina Montiel-González, PeerJ

Entomopathogenic Fungi as Dual Control Agents against Both the Pest Myzus persicae and Phytopathogen Botrytis cinerea – Hwi-Geon Yun, Mycobiology

Glycomyces rhizosphaerae sp. nov., isolated from the root and rhizosphere soil of wheat (Triticum aestivum L.) – Wenchao Li, International Journal of Systematic and Evolutionary Microbiology

Water and extremophile microbiome

A comparison between biostimulation and bioaugmentation in a solid treatment of anaerobic sludge: Drug content and microbial evaluation – G. Llorens-Blanch, Waste Management

Iron Chloride Flocculation of Bacteriophages from Seawater – Bonnie T. Poulos, Bacteriophages

Multi-Level Contact Oxidation Process Performance When Treating Automobile Painting Wastewater: Pollutant Removal Efficiency and Microbial Community Structures – Yufang Zhu, Water

Insights from the Genomes of Microbes Thriving in Uranium-Enriched Sediments – Brodie Sutcliffe, Microbial Ecology

Biogeography at the limits of life: Do extremophilic microbial communities show biogeographical regionalization? – Dave R. Clark, Global Ecology and Biogeography

Diversity of microbiota found in coffee processing wastewater treatment plant – Josiane Ferreira Pires, World Journal of Microbiology and Biotechnology

Food microbiology

Epiphytic fungal community in Vitis vinifera of the Portuguese wine regions – M. Oliveira, Letters in Applied Microbiology

Bioinformatics

HgtSIM: a simulator for horizontal gene transfer (HGT) in microbial communities – Weizhi Song, PeerJ

Techniques

Significance estimation for large scale metabolomics annotations by spectral matching – Kerstin Scheubert, Nature

Single primer isothermal amplification (SPIA) combined with next generation sequencing provides complete bovine coronavirus genome coverage and higher sequence depth compared to sequence-independent single primer amplification (SISPA) – Mette Myrmel, PLOS ONE

Developing selective media for quantification of multispecies biofilms following antibiotic treatment – Eva Vandeplassche, PLOS ONE

Microbes in the news

Microbiology: Bacteria disarm host-defence proteins – John D. MacMicking, Nature News and Views

Probiotics: Health boost or waste of cash? – Anne Allred, 5-ON-YOUR-SIDE

Cygnus Open for Business; Crew Unloading New Bacteria, Plant and Tech Studies – Mark Garcia, NASA blog

Bacteria Hysteria

Your supermarket is filled with germs — here are 7 facts that will make you dread grocery shopping –  Joanna Fantozzi, Insider

November 14, 2017

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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.

Jobs

Grants Alert – Federal Grants & Contracts

QA LAB SENSORY & MICROBIOLOGY TECHNICIAN LEAD – MEMPHIS PRODUCTION CENTER AT COCA-COLA CONSOLIDATED – Jobs.net

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 – Phys.org

* 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 4, 2017

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Events and jobs

Microbiology Lab Technician – Manpower – Evansville

Research Associate in Plant and Arthropod Microbiome – Indiana University

 

General microbiome

Review: New Insights into Graft-Versus-Host Disease and Graft Rejection – E Perkey – Annual Review of Pathology

Microbial network of the carbonate precipitation process induced by microbial consortia and the potential application to crack healing in concrete. – J Zhang – Scientific Reports

Review: A Call to Arms: Quest for a Cryptococcal Vaccine – MC Caballero Van Dyke – Cell

 

 

Human respiratory microbiome

Impact of the Respiratory Microbiome on Host Responses to Respiratory Viral Infection. – M Pichon – Vaccines

 

 

Human gut microbiome

Review: Atherosclerosis: Association between the gut microbiome and atherosclerosis – WT Barrington – Nature Reviews

Improvement in cardiometabolic risk markers following a multifunctional diet is associated with gut microbial taxa in healthy overweight and obese subjects. – N Marungruang – European Journal of Nutrition

Opinion: NOD2 and bacterial recognition as therapeutic targets for Crohn’s disease. – M de Bruyn – Expert Opinion on Therapeutic Targets.

 

Animal experiments 

Microbial diversity and composition in different gut locations of hyperlipidemic mice receiving krill oil. – C Lu – Applied Microbiology and Biotechnology

Evaluating the contribution of gut microbiome to the variance of porcine serum glucose and lipid concentration. – X Huang – Scientific Reports

Gut microbiome influences efficacy of PD-1-based immunotherapy against epithelial tumors. – B Routy – Science

 

Animal microbiome 

The bacterium Wolbachia exploits host innate immunity to establish a symbiotic relationship with the dengue vector mosquito Aedes aegypti. – X Pan – The ISME Journal

Enzymatic dynamics into the Eisenia fetida (Savigny, 1826) gut during vermicomposting of coffee husk and market waste in a tropical environment. – B Ordoñez-Arévalo – Environmental Science and Pollution Research International

Microbial community and ovine host response varies with early and late stages of Haemonchus contortus infection. – S El-Ashram – Veterinary Research Communications

 

Plant, root and soil microbiome

The spent culture supernatant of Pseudomonas syringae contains azelaic acid – SG Javvadi – bioRxiv

Stratified Bacterial and Archaeal Community in Mangrove and Intertidal Wetland Mudflats Revealed by High Throughput 16S rRNA Gene Sequencing – Z Zhou – Frontiers in Microbiology

Genome Sequencing of Microbacterium sp. Yaish 1, a Bacterial Strain Isolated from the Rhizosphere of Date Palm Trees Affected by Salinity – GA Jana – Genome Announcements

A New Proposal for the Pathogenic Mechanism of Non-Coeliac/Non-Allergic Gluten/Wheat Sensitivity: Piecing Together the Puzzle of Recent Scientific Evidence. – V Leccioli – Nutrients

Identification of novel small RNAs in Burkholderia cenocepacia KC-01 expressed under iron limitation and oxidative stress conditions. – S Ghosh – Microbiology

Conductive particles enable syntrophic acetate oxidation between Geobacter and Methanosarcina from coastal sediments – AE Rotaru – bioRxiv

 

Water and extremophile microbiome

A dynamic microbial community with high functional redundancy inhabits the cold, oxic subseafloor aquifer. – BJ Tully – The ISME Journal

 

 

Phages and viruses

Co-existence of freshwater and marine T4-like myoviruses in a typical subtropical estuary. – L Liu – FEMS Microbiology Ecology

 

Techniques

Optimisation of 16S rRNA gut microbiota profiling of extremely low birth weight infants. – C Alcon-Giner – BMC Genomics

Metagenomic analysis reveals potential interactions in an artificial coculture. – M Ren – AMB Express

Review: Phage Hunters: computational strategies for finding phages in large-scale ‘omics datasets – BL Hurwitz – Virus Research

Defining the Transcriptional Landscape during Cytomegalovirus Latency with Single-Cell RNA Sequencing – M Shnayder – bioRxiv

 

Microbes in the news

Can microbiology tell us exactly what killed the Aztecs? – OUP Blog

Tuning the Microbiome Improves Melanoma Immunotherapy Response – GEN

November 3, 2017

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Events and jobs

Assistant Professor in Food Microbiology/Safety – The University of Texas Rio Grande Valley – Close Date: 12/3/2017

Assistant Professor Microbiology – University of New Haven, Connecticut

Microbiology Technician On-Call – Battle Creek, MI – Michigan

 

General microbiome

Closely related methicillin-resistant Staphylococcus aureus isolates from retail meat, cows with mastitis, and humans in Japan – T Sato – PLoS One

Letter:A global resource allocation strategy governs growth transition kinetics of Escherichia coli – DW Erickson – Nature

Inter-species population dynamics enhance microbial horizontal gene transfer and spread of antibiotic resistance – RM Cooper – eLife

 

Pregnancy and early life

Gut microbiome of mothers delivering prematurely shows reduced diversity and lower relative abundance of Bifidobacterium and Streptococcus – C Dahl – PLoS One

 

 

Human vaginal microbiome

Association of high-risk sexual behaviour with diversity of the vaginal microbiota and abundance of Lactobacillus. – JM Wessels – PLoS One

Associations between sexual habits, menstrual hygiene practices, demographics and the vaginal microbiome as revealed by Bayesian network analysis – N Noyes – bioRxiv

Opinion: Committee Opinion No. 725: Vaginal Seeding – KR Wharton – Obstetrics and Gynecology

 

Human gut microbiome

“Omic” investigations of protozoa and worms for a deeper understanding of the human gut “parasitome”. – V Marzano – PLoS Neglected Tropical Diseases

Comparison of the human gastric microbiota in hypochlorhydric states arising as a result of Helicobacter pylori-induced atrophic gastritis, autoimmune atrophic gastritis and proton pump inhibitor use – BN Parsons – PLoS Pathogens

Modeling the temporal dynamics of the gut microbial community in adults and infants – L Shenhav – bioRxiv

The ethnic distribution of sessile serrated polyps in the United States is inversely associated with Helicobacter pylori prevalence – A Sonnenberg – Colorectal Disease

Gut microbiome in gestational diabetes: A Cross-sectional study of mothers and offspring 5 years post-partum. – S Hasan – Acta obstetricia et gynecologica Scandinavica

Protective Roles of Intestinal Microbiota derived Short Chain Fatty Acids in Alzheimer’s Disease-type Beta-Amyloid Neuropathological Mechanisms. – L Ho – Expert Review of Neurotherapeutics

 

Animal experiments 

Microbiota control immune regulation in humanized mice – E Gülden – Journal of Clinical Investigation Insight

Effects of essential oils from Liquidambar orientalis Mill. leaves on growth performance, carcass and some organ traits, some blood metabolites and intestinal microbiota in broilers. –  A Altop – British Poultry Science

PD-1 deficiency protects experimental colitis via alteration of gut microbiota. – SJ Park – Journal of biochemistry and molecular biology.

The Mouse Model of Infection with Citrobacter rodentium – N Bouladoux – Current Protocols in Immunology

Glyphosate has limited short-term effects on commensal bacterial community composition in the gut environment due to sufficient aromatic amino acid levels. – LN Nielsen – Environmental Pollution

 

Animal microbiome 

Strong responses of Drosophila melanogaster microbiota to developmental temperature – NN Moghadam – Fly (Austin)

Amphibian skin defences show variation in ability to inhibit growth of Batrachochytrium dendrobatidis isolates from the Global Panzootic Lineage. – RE Antwis – Microbiology (Reading, England)

Midgut Bacterial Diversity of Wild Populations of Phlebotomus (P.) papatasi, the Vector of Zoonotic Cutaneous Leishmaniasis (ZCL) in Turkey. – M Karakuş – Scientific Reports

Rapid regrowth and detection of microbial contaminants in equine fecal microbiome samples – KF Beckers – PLoS One

 

Plant, root and soil microbiome

Deinococcus hibisci sp. nov., isolated from rhizosphere of Hibiscus syriacus L. (mugunghwa flower). – G Moya – International Journal of Systematic and Evolutionary Microbiology

Priority effects can persist across floral generations in nectar microbial meta-communities – T Hirokazu – Oikos

Endosphere microbiome comparison between symptomatic and asymptomatic roots of Brassica napus infected with Plasmodiophora brassicae – Y Zhao – PLoS One

Microbial community-level regulation explains soil carbon responses to long-term litter manipulations – K Georgiou – Nature Communications

 

Water microbiome and extremophiles

Cultivation and genomics of the first freshwater SAR11 (LD12) isolate – MW Hinson – bioRxiv

Lessons from simple marine models on the bacterial regulation of eukaryotic development – A Woznica – bioRxiv

Chapter: Sponge Disease and Climate Change – HM Luter – Climate Change, Ocean Acidification and Sponges

 

Probiotics / prebiotics

Lactobacillus plantarum HNU082-derived improvements in the intestinal microbiome prevent the development of hyperlipidaemia – Y Shao – Food & Function

Can Probiotic Supplements Improve Outcomes in Rheumatoid Arthritis? – A Schorpion – Current Rheumatology Reports

 

 

Techniques

A novel baiting microcosm approach used to identify the bacterial community associated with Penicillium bilaii hyphae in soil – B Ghodsalavi – PLoS One

Bacterium-triggered remodeling of chromatin identifies BasR, a novel regulator of fungal natural product biosynthesis – J Fischer – bioRxiv

Transcriptome analysis of sheep oral mucosa response to Orf virus infection – H Jia – PLoS One

A mechanism for prime-realignment during influenza A virus replication – J Oymans – bioRxiv

 

Microbes in the news

How caries-causing bacteria can survive in dental plaque – EurekAlert

Nicotine’s hold: What the gut and gender have to do with it – Phys.org

‘Big Chicken’ Connects Poultry Farming To Antibiotic-Resistant Bacteria – npr

Microbiology: Crowdsourcing Earth’s microbes – Nature

Fresh off the petri dish: Spend your Thursdays creating art with bacteria – FSU Torch

 

Non-microbiology picks

Nigritoxin is a bacterial toxin for crustaceans and insects – Y Labreuche – Nature Communications

The Polycomb group protein CBX6 is an essential regulator of embryonic stem cell identity – A Santanach – Nature Communications

 

November 2, 2017

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Second day of November we have quite a few job offers, nice set of microbiome news, two reviews in “gut microbiome” sector. Two (personal) highlights today would be the Thomas J. Browning’s  paper about phytoplankon nutrient co-limitation and Luke R. Thompson’s paper about The Earth Microbiome Project. Enjoy…

Events and jobs

Research Technician, University of York, UK

Postdoctoral Researcher – Molecular Microbiologist, University of Oxford, Oxford, UK

Bioinformatics Postdoc, Max Planck Institute for Infection Biology, Berlin, Germany

Microbiology Postdoctoral Scholar,  The University of California, Berkeley, California, US

Bioinformatics Analyst, Ares Genetics GmbH, Vienna, Austria

Assistant Professor of Microbiology, The University of Alabama in Huntsville, Huntsville, Alabama, US

Tenure-track Assistant Professor of Microbiology, Miami University, Miami, Ohio, US

Tenure Track Assistant Professor in Microbiology, The University of British Columbia, Vancouver,  Canada

General microbiome

Impaired competence in flagellar mutants of Bacillus subtilis is connected to the regulatory network governed by DegU – Theresa Hoelscher – bioRxiv

Gene network analysis identifies a central post-transcriptional regulator of cellular stress survival – Matthew Z. Tien – bioRxiv

Detection of cytosolic Shigella flexneri via a C-terminal triple-arginine motif of GBP1 inhibits actin-based motility – Anthony Piro – bioRxiv

Inter-species population dynamics enhance microbial horizontal gene transfer and spread of antibiotic resistance – Robert M Cooper – eLIFE

A communal catalogue reveals Earth’s multiscale microbial diversity – Luke R. Thompson – Nature

Human gut microbiome

Rapid Assessment of Microbiota Changes in Individuals with Autism Spectrum Disorder Using Bacteria-derived Membrane Vesicles in Urine – Yunjin Lee – Experimental Neurobiology

Review: Dietary and microbial metabolites in the regulation of host immunity – Jun Kunisawa – frontiers in Microbiology

Review: Gut microbiota as a potential target of metabolic syndrome: the role of probiotics and prebiotics – Mingqian He – Cell & Bioscience

Progression of Parkinson’s disease is associated with gut dysbiosis: Two-year follow-up study – Tomomi Minato – PLOS One

Animal experiments

Rapid regrowth and detection of microbial contaminants in equine fecal microbiome samples – Kalie F. Beckers – PLOS One

Cecal Microbiota in Broilers Fed with Prebiotics – Dany Mesa – Frontiers in Genetics

Commensal Lactobacillus Controls Immune Tolerance during Acute Liver Injury in Mice – Nobuhiro Nakamoto – Cell Reports

Food restriction followed by refeeding with a casein- or whey-based diet differentially affects the gut microbiota of pre-pubertal male rats – Majdi Masarwi – The Journal of Nutritional Biochemistry

Animal microbiome 
Evidence for a conserved microbiota across the different developmental stages of Plodia interpunctella – Valeria Mereghetti -Insect Science

Plant, root, and soil microbiome

Stable isotope informed genome-resolved metagenomics reveals that Saccharibacteria utilize microbially processed plant derived carbon – Evan P. Starr – bioRxiv

Water and extremophile microbiome 

Analysis of bacterial communities and characterization of antimicrobial strains from cave microbiota – Muhammad Yasir – Brazilian Journal of Microbiology

Highly divergent 16S rRNA sequences in ribosomal operons of Scytonema hyalinum (Cyanobacteria) – Jeffrey R. Johansen – PLOS One

Study of Microbial diversity in Ganga river water sample by the use of Metagenomics technique – Jamilah Ali Ahmed Zaed – Journal of Pharmacognosy and Phytochemistry

Niche specialization of bacteria in permanently ice-covered lakes of the McMurdo Dry Valleys, Antarctica – Miye Kwon – Environmental Microbiology

Influence of bicarbonate on the abundance of microbial communities capable of reducing U(VI) in groundwater – Dianxin Li – RSC Advances

Monitoring microbial responses to ocean deoxygenation in a model oxygen minimum zone – Steven J. Hallam – Scientific Data

Synechococcus plasticity under environmental changes – Cristiana Callieri – FEMS Microbiology Letters

Nutrient co-limitation at the boundary of an oceanic gyre – Thomas J. Browning -Nature

Evaluation of different 16S rRNA gene V regions for exploring bacterial diversity in a eutrophic freshwater lake – Junyi Zhang – Science of The Total Environment

Microbial community structures and functions of wastewater treatment systems in plateau and cold regions – Dexin Fang – Bioresource Technology

Adaptability as the key to success for the ubiquitous marine nitrite oxidizer Nitrococcus — Jessika Füssel – Science Advances

Food microbiology

Characterization of Enterococcal Community Isolated from an Artisan Istrian Raw Milk Cheese: Biotechnological and Safety Aspects – Mirna Mrkonjic Fuka – Food Technology and Biotechnology

Probiotics / prebiotics
Lactobacillus reuteri suppresses E. coli O157:H7 in bovine ruminal fluid: Toward a pre-slaughter strategy to improve food safety? – Yolande Bertin – PLOS One

Bioinformatics

MetaCherchant: analyzing genomic context of antibiotic resistance genes in gut microbiota – Evgenii I Olekhnovich – Bioinformatics

Techniques

Quantification of diverse virus populations in the environment using the polony method – Nava Baran – Nature Microbiology

Microbes in the news 

Microbiome Link with Colorectal Cancer Drug Toxicity Points to Predictive Tests and Prevention – Genetic Engineering and Biotechnology News

Gut bacteria composition could predict toxicity of chemotherapy drugs in cancer patients – News Medical

Versatile marine bacteria could be an influence on global warming, scientists discover – Science Daily

By 2100, climate change could alter key microbial interactions in the ocean  – Phys Org

Microbes on the market 

Symbiotix Biotherapies Receives $5 Million in Institutional Financing to Advance its Development of Molecular Therapeutics that Modulate Regulatory T Cell Activity

Tina’s (non)microbiology picks 

Concept Inventory Development Reveals Common Student Misconceptions about Microbiology – Amy G. Briggs – Journal of Microbiology & Biology Education

Announcing the winner of this year’s ‘Dance Your Ph.D.’ contest – John Bohannon – Science

 

November 1, 2017

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Happy November everybody! We have an interesting collection of articles today. Co-cultivation of plant beneficial fungi as an effective strategy to modulate the production of bioactive metabolites and a review on the benefits of berries and their phytochemicals on the digestive and immune systems. Enjoy!

Events and jobs

Microbiology Lab Assistant – Seattle, Washington – Labcorp

General microbiome

The Microbiome in Posttraumatic Stress Disorder and Trauma-Exposed Controls: An Exploratory Study – Hemmings, Sian M.J – Pyschosomatic Medicine

Human respiratory microbiome

Review : CF Airway Microbiome: Overturning the Old, Opening the Way for the New – George A. O’Toole – Journal of Bacteriology

Human oral microbiome

Effect of maltitol-containing chewing gum use on the composition of dental plaque microbiota in subjects with active dental caries – Erica M. Prosdocimi – Journal of Oral Microbiology

Human gut microbiome

The circulating microbiome signature and inferred functional metagenomics in alcoholic hepatitis – Puneet Puri – Hepatology

Diet, Environments, and Gut Microbiota. A Preliminary Investigation in Children Living in Rural and Urban Burkina Faso and Italy – Carlotta De Filippo – Frontiers in Microbiology

Gut microbiome of mothers delivering prematurely shows reduced diversity and lower relative abundance of Bifidobacterium and Streptococcus – Cecilie Dahl – Plos One

Review : Systematic review of the effects of the intestinal microbiota on selected nutrients and non-nutrient – Colette Shortt – European Journal of Nutrition

Cereal products derived from wheat, sorghum, rice and oats alter the infant gut microbiota in vitro – Hasinika K. A. H. Gamage – Scientific Reports

Animal experiments

Antibiotic treatment disrupts bacterial communities in the colon and rectum of SIV-infected macaques – Alexander S. Zevin – FEMS Microbiology Letters

Ophiopogonin D alleviates high-fat diet–induced metabolic syndrome and changes the structure of gut microbiota in mice – Siyu Chen – The FASEB Journal

Animal microbiome

Bacterial Species Identified on the Skin of Bottlenose Dolphins Off Southern California via Next Generation Sequencing Techniques – Corey D. Russo – Microbial Ecology

Skin and fur bacterial diversity and community structure on American southwestern bats: effects of habitat, geography and bat traits – Ara S. Winter – PeerJ

Analysis of the Microbial Diversity in the Fecal Material of Giraffes – Jessica M. Schmidt – Current Microbiology

Morphological and genetic factors shape the microbiome of a seabird species (Oceanodroma leucorhoa) more than environmental and social factors – Douglas S. Pearce – Microbiome

Metabolomics

Plasma Metabolites From Choline Pathway and Risk of Cardiovascular Disease in the PREDIMED (Prevention With Mediterranean Diet) Study – Marta Guasch-Ferré – Journal of the American Heart Association

Plant, root, and soil microbiome

Strong Regionality and Dominance of Anaerobic Bacterial Taxa Characterize Diazotrophic Bacterial Communities of the Arcto-Alpine Plant Species Oxyria digyna and Saxifraga oppositifolia – Manoj Kumar – Frontiers in Microbiology

An endophytic Bacillus strain promotes growth of oil palm seedling by fine root biofilm formation – MdHoirul Azri – Rhizosphere

Effect of auxin producing and phosphate solubilizing bacteria on mobility of soil phosphorus, growth rate, and P acquisition by wheat plants – Guzel R. Kudoyarova – Acta Physiologiae Plantarum

Contrasting effects of ammonium and nitrate additions on the biomass of soil microbial communities and enzyme activities in subtropical China – Chuang Zhang – Biogeosciences

Impact of land use change and soil organic carbon quality on microbial diversity in soils across Europe – Márton Szoboszlay – FEMS Microbiology Ecology

Microbial Diversity and Community Structure of Sulfate-Reducing and Sulfur-Oxidizing Bacteria in Sediment Cores from the East China Sea – Yu Zhang – Frontiers in Microbiology

Rhizosphere-associated Pseudomonas induce systemic resistance to herbivores at the cost of susceptibility to bacterial pathogens – Cara H. Haney – Molecular Ecology

*Co-Culture of Plant Beneficial Microbes as Source of Bioactive Metabolites – F. Vinale – Scientific Reports

Introducing BASE: the Biomes of Australian Soil Environments soil microbial diversity database – Andrew Bissett – Gigascience

Water and extremophile microbiome

Anaerobic digestion of spent mushroom substrate under thermophilic conditions: performance and microbial community analysis – Zheng Xiao – Applied Microbiology and Biotechnology

Metagenomic characterization of biofilter microbial communities in a full-scale drinking water treatment plant – Seungdae Oh – Water Research

Distinct microbial communities in the active and permafrost layers on the Tibetan Plateau – Yong-Liang Chen – Molecular Ecology

Community composition and assembly processes of the free-living and particle-attached bacteria in Taihu Lake – Dayong Zhao – FEMS Microbiology Ecology

Food Microbiology

Anti-obesity Effect of Exopolysaccharides Isolated from Kefir Grains – Juha Lim – J. Agric. Food Chem

Modulating Effects of Dicaffeoylquinic Acids from Ilex Kudingcha on Intestinal Microecology in vitro – Minhao Xie – Journal of Agricultural Food Chemistry

*Review of the health effects of berries and their phytochemicals on the digestive and immune systems – Coen Govers – Nutrition Reviews

Probiotics / prebiotics

Single-species versus dual-species probiotic supplementation as an emerging therapeutic strategy for obesity – G.Karimi – Nutrition, Metabolism and Cardiovascular Diseases

Bioinformatics

ROCker: accurate detection and quantification of target genes in short-read metagenomic data sets by modeling sliding-window bitscores – Luis H. Orellana – Nucleic Acids Research

Phages and viruses

Review : Assessing Species Diversity Using Metavirome Data: Methods and Challenges – Damayanthi Herath – Computational and Structural Biotechnology Journal

Microbes in the news

Caves Host Gooey Biofilms Built by Methane-Eating Bacteria

3D Printed Artificial Small Intestine to Advance Research on Gut Bacteria

Enzymes from dangerous bacteria turn into important tools for protein chemistry

Microbes on the market

The University Medical Center Groningen and Novogene announce the start of the 10K Metagenome Project

Science, publishing, and career

Book Chapter : Leading Change in Undergraduate STEM Education – Adam K. Leibovich – Educational and Outreach Projects from the Cottrell Scholars Collaborative Undergraduate and Graduate Education Volume 1

Anitha’s non-microbiology picks

Congratulations Nancy Scherich! The winner of this year’s ‘Dance Your Ph.D.’ contest

ROSINA spectral measurements bring comet’s chemistry to life

Scary as they are, few vampires have a backbone

 

October 26, 2017

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In today’s digest we have some interesting discussion about lab/bioinformatics techniques, a few editorials on the microbiome job market, and even a little bit of philosophy learned from our tiny microbial friends.

Events and jobs

BioData World West 2018 – 13-14 March 2018 – San Francisco, CA

General microbiome

Cooperation and cheating as innovation: insights from cellular societies – Athena Aktipis – Philosophical Transactions of The Royal Society B

[Pre-Print] Metabolic Interactions Between Dynamic Bacterial Subpopulations – Adam Z Rosenthal – bioRxiv

Pregnancy and early life

Preterm Birth Affects the Risk of Developing Immune-Mediated Diseases – Sybelle Goedicke-Fritz – Frontiers in Immunology

Human oral microbiome

Metagenomic Analysis of Gingival Sulcus Microbiota and Pathogenesis of Periodontitis Associated with Type 2 Diabetes Mellitus – E. A. Babaev – Bulletin of Experimental Biology and Medicine

Human urinary tract microbiome

Re: Evaluation of the Urinary Microbiota of Women with Uncomplicated Stress Urinary Incontinence – Alan J. Wein – The Journal of Urology

Human gut microbiome

* The fecal microbiome of ALS patients – David Brenner – Neurobiology of Aging

Plant, root, and soil microbiome

Endosphere microbiome comparison between symptomatic and asymptomatic roots of Brassica napus infected with Plasmodiophora brassicae – Ying Zhao – PLOS ONE

Ureolytic microbial community is modulated by fertilization regimes and particle-size fractions in a Black soil of Northeastern China – Li Wang – Soil Biology and Biochemistry

Water and extremophile microbiome 

Metatranscriptomic and metagenomic description of the bacterial nitrogen metabolism in waste water wet oxidation effluents – Julien Crovadore – Heliyon

Genomic variation in microbial populations inhabiting the marine subseafloor at deep-sea hydrothermal vents – Rika E. Anderson – Nature

Food microbiology

Sequence Analysis of Changes in Microbial Composition in Different Milk Products During Fermentation and Storage – Barbora Zalewska – Current Microbiology

Probiotics / prebiotics

* Pharmabiotics as an Emerging Medication for Metabolic Syndrome and Its Related Diseases – Thi Thanh Binh Nguyen – Molecules

[Review] Recurrent urinary tract infections in women: How promising is the use of probiotics? – Varsha Gupta – Indian Journal of Medical Microbiology

Bioinformatics

Using convolutional neural networks to explore the microbiome – Derek Reiman – Engineering in Medicine and Biology Society (EMBC)

Techniques

‘Gracilibacillus phocaeensis’ sp. nov., ‘Sediminibacillus massiliensis’ sp. nov. and ‘Virgibacillus ndiopensis’ sp. nov., three halophilic species isolated from salty human stools by culturomics – B. Senghor – New Microbes and New Infections

Proteomic and metaproteomic approaches to understand host-microbe interactions – Amanda E. Starr – Analytical Chemistry

Impact of Method Variables on Microbiota Sample Disruption – Jaclyn Zecca and David Burden – OPS Diagnostics LLC

Microbes on the market 

Patenting the microbiome: trends, challenges and insights – Anthony D Sabatelli – Future Science

[Editorial] The aquaculture microbiome at the centre of business creation – Karen K. Dittmann – Microbial Biotechnology

Ed’s non-microbiology picks

I put quite a few on here today – enjoy 🙂

More than 75 percent decline over 27 years in total flying insect biomass in protected areas – Caspar A. Hallman – PLOS ONE

Cavitation-Induced Synthesis of Biogenic Molecules on Primordial Earth – Natan-Haim Kalson – ACS Central Science

Games people play: How video games improve probabilistic learning – Sabrina Schenk – Behavioural Brain Research

A process-oriented model linking adolescents’ sleep hygiene and psychological functioning: the moderating role of school start times -Jack S. Peltz – Sleep Health

Decreases in self-reported sleep duration among U.S. adolescents 2009-2015 and links to new media screen time – Jean M. Twenge – Sleep Medicine

Dogs’ recognition of human selfish and generous attitudes requires little but critical experience with people – Fabricio Carballo – PLOS ONE

October 25, 2017

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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

Bioinformatics

*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

 

October 22, 2017

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A wide range of interesting articles today on the mouth, respiratory and gut microbiomes: Airway microbiota and obstruction in asthma, the tongue microbiome and pneumonia in the elderly, gut microbiome interactions with host G-protein coupled receptors, the effects of prebiotics and milk oligosaccharides on the mouse gut metabolome and stressor induced immune alterations, the impact of social stress on the gut microbiome and the host gut transcriptome, the impact of a Bacteroides integrase in a mouse model of colitis, and evidence that oral bacteria can colonize the gut in genetically and dysbiotic susceptible mice, leading to increased gut inflammation. 

  • Events and jobs

Postdoctoral Researcher in Microbiome Bioinformatics – Karolinska Institutet

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  • Human respiratory microbiome

Different Functional Genes of Upper Airway Microbiome Associated with Natural Course of Childhood Asthma – Bong-Soo Kim – European Journal of Allergy and Clinical Immunology

*Atopic asthmatic immune phenotypes associated with airway microbiota and airway obstruction – Benjamin A. Turturice – PLOSone

  • Human oral microbiome

*Relationships of variations in the tongue microbiota and pneumonia mortality in nursing home residents – Shinya Kageyama – Journal of Gerontology

  • Human gut microbiome

Review: Host-Microbe Interactions: Aiming at GPCRs – Mirella Bucci – Nature Chemical Biology

Development of severe bronchopulmonary dysplasia is associated with alterations in fecal volatile organic compounds – Daniel J C Berkhout – Pediatric Research

Gut Fermentation of Dietary Fibres: Physico-Chemistry of Plant Cell Walls and Implications for Health – Barbara A. Williams – International Journal of Molecular Sciences

Review: Food allergy: The influence of breast-feeding and gut microbiota – S. Hazebrouck – Revue Française d’Allergologie

Review: Whole cereal grains and potential health effects: Involvement of the gut microbiota – Lingxiao Gong – Food Research International

Review: Probiotic strains and mechanistic insights for the treatment of type 2 diabetes – Christiane S. Hampe – Endocrine

Review: Early-Life Gut Dysbiosis: A Driver of Later-Life Fibrosis? – Karen J. Ho – Journal of Investigative Dermatology

Review: Nutritional programming by glucocorticoids in breast milk: targets, mechanisms and possible implications – Jonneke J. Hollanders – Best Practice & Research Clinical Endocrinology & Metabolism

Review: Less Invasive Screening for Colorectal Cancer by Microbiota Analysis: Is it a Reality or an Illusion? – Hisashi Onodera – EBioMedicine

  • Fecal Transplants

The taxonomic composition of the donor intestinal microbiota is a major factor influencing the efficacy of faecal microbiota transplantation in therapy refractory ulcerative colitis – P. Kump – Alimentary Pharamacology and Therapeutics

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  • Animal experiments

* Ectopic colonization of oral bacteria in the intestine drives TH1 cell induction and inflammation – Koji Atarashi – Science

*Stressor-induced immunomodulation is attenuated by prebiotics and milk oligosaccharides: Role of the colonic metabolome – M. Bailey – Brain, Behavior, and Immunity

*The colonic epithelial transcriptome and intestinal microbiome are significantly changed by social stressor exposure – A.R. Mackos – Brain, Behavior, and Immunity

*A Gut Microbial Mimic that Hijacks Diabetogenic Autoreactivity to Suppress Colitis – Roopa Hebbandi Nanjundappa – Cell

Metformin Alters Upper Small Intestinal Microbiota that Impact a Glucose-SGLT1-Sensing Glucoregulatory Pathway – Paige V. Bauer – Cell Metabolism

Distribution of species and antimicrobial resistance among enterococci isolated from the fecal microbiota – Andréa de Andrade Rangel de Freitas – Science of The Total Environment

Effect of Intestinal Flora on Protein Expression of Drug-Metabolizing Enzymes and Transporters in the Liver and Kidney of Germ-Free and Antibiotics-Treated Mice – Takuya Kuno – Molecular Pharmaceutics

Consequences of organ choice in describing bacterial pathogen assemblages in a rodent population – P. Villette – Epidemiology & Infection

High-Quality Whole-Genome Sequences of the Oligo-Mouse-Microbiota Bacterial Community – Debora Garzetti – Genome Announcements

  • Animal microbiome

Wild Mouse Gut Microbiota Promotes Host Fitness and Improves Disease Resistance – Stephan P. Rosshart – Cell

Impact of Low and High Doses of Marbofloxacin on the Selection of Resistant Enterobacteriaceae in the Commensal Gut Flora of Young Cattle: Discussion of Data from 2 Study Populations – Lhermie Guillaume – Foodborne Pathogens and Disease

  • Forensic Microbiome

Successive bacterial colonisation of pork and its implications for forensic investigations – Jessica Handke – Forensic Science International

Targeted sequencing of clade-specific markers from skin microbiomes for forensic human identification – Sarah E. Schmedes – Forensic Science International: Genetics

  • Plant, root, and soil microbiome

Characterization of fungal communities of developmental stages in table grape grown in the northern region of South Africa – P.C. Carmichael – Journal of Applied Microbiology

Mycorrhizae, invasions, and the temporal dynamics of mutualism disruption – Sara Grove – Journal of Ecology

Soil bacterial community mediates the effect of plant material on methanogenic decomposition of soil organic matter – Quan YuanSoil Biology and Biochemistry

Analysis of bacterial communities and characterization of antimicrobial strains from cave microbiota – Muhammad Yasir – Brazilian Journal of Microbiology

  • Waste and Pollution 

Bioaugmentation of thiabendazole-contaminated soils from a wastewater disposal site: Factors driving the efficacy of this strategy and the diversity of the indigenous soil bacterial community – Evangelia S. Papadopoulou – Environmental Pollution

  • Built environment

Human health risks for Legionella and Mycobacterium avium complex (MAC) from potable and non-potable uses of roof-harvested rainwater – Kerry A.Hamilton – Water Research

  • Techniques

Optimization of GC/TOF MS analysis conditions for assessing host-gut microbiota metabolic interactions: Chinese rhubarb alters fecal aromatic Amino acids and phenol metabolism – Shan Yin – Analytica Chimica Acta

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  • Microbes in the news

Stress may harm gut health as much as junk food – Honor Whiteman – Medical News Today

Different Microbial Communities Live Along Female Reproductive Tract – GenomeWeb

Gut Health May Begin in the Mouth – Lydialyle Gibson – Havard